├── .dockerignore ├── .gitignore ├── Dockerfile ├── README.md ├── make-all.sh ├── manuscript ├── Figure1.png ├── Figure2.png ├── Figure3.png ├── Table1.docx ├── The impact of Docker containers on the performance of genomic pipelines.pdf ├── The impact of Docker containes on the performances of genomic pipelines (backup).docx ├── The impact of Docker containes on the performances of genomic pipelines (peer-review).pdf ├── The impact of Docker containes on the performances of genomic pipelines (v2).pdf ├── The impact of Docker containes on the performances of genomic pipelines.docx ├── fig-titles.txt └── ref.txt ├── nmdp-flow ├── Figures.R ├── Makefile ├── README.md ├── config │ ├── docker.config │ ├── native.config │ └── run.sh ├── delta.groovy ├── docker_1 │ ├── .nextflow.log │ ├── log_docker_11 │ ├── timeline.html │ └── trace.csv ├── docker_10 │ ├── .nextflow.log │ ├── log_docker_20 │ ├── timeline.html │ └── trace.csv ├── docker_2 │ ├── .nextflow.log │ ├── log_docker_12 │ ├── timeline.html │ └── trace.csv ├── docker_3 │ ├── .nextflow.log │ ├── log_docker_13 │ ├── timeline.html │ └── trace.csv ├── docker_4 │ ├── .nextflow.log │ ├── log_docker_14 │ ├── timeline.html │ └── trace.csv ├── docker_5 │ ├── .nextflow.log │ ├── log_docker_15 │ ├── timeline.html │ └── trace.csv ├── docker_6 │ ├── .nextflow.log │ ├── log_docker_16 │ ├── timeline.html │ └── trace.csv ├── docker_7 │ ├── .nextflow.log │ ├── log_docker_17 │ ├── timeline.html │ └── trace.csv ├── docker_8 │ ├── .nextflow.log │ ├── log_docker_18 │ ├── timeline.html │ └── trace.csv ├── docker_9 │ ├── .nextflow.log │ ├── log_docker_19 │ ├── timeline.html │ └── trace.csv ├── fig_correlation.png ├── file-formats.md ├── native_1 │ ├── .nextflow.log │ ├── log_native_11 │ ├── timeline.html │ └── trace.csv ├── native_10 │ ├── .nextflow.log │ ├── log_native_20 │ ├── timeline.html │ └── trace.csv ├── native_2 │ ├── .nextflow.log │ ├── log_native_12 │ ├── timeline.html │ └── trace.csv ├── native_3 │ ├── .nextflow.log │ ├── log_native_13 │ ├── timeline.html │ └── trace.csv ├── native_4 │ ├── .nextflow.log │ ├── log_native_14 │ ├── timeline.html │ └── trace.csv ├── native_5 │ ├── .nextflow.log │ ├── log_native_15 │ ├── timeline.html │ └── trace.csv ├── native_6 │ ├── .nextflow.log │ ├── log_native_16 │ ├── timeline.html │ └── trace.csv ├── native_7 │ ├── .nextflow.log │ ├── log_native_17 │ ├── timeline.html │ └── trace.csv ├── native_8 │ ├── .nextflow.log │ ├── log_native_18 │ ├── timeline.html │ └── trace.csv ├── native_9 │ ├── .nextflow.log │ ├── log_native_19 │ ├── timeline.html │ └── trace.csv ├── plot.csv ├── plot.sh ├── plot_docker.txt ├── plot_native.txt ├── stage.sh ├── stats_docker.txt ├── stats_native.txt ├── table.R ├── table.txt ├── time.sh ├── time_docker.txt ├── time_native.txt ├── trace_docker.txt └── trace_native.txt ├── piper-nf ├── Figures.R ├── Makefile ├── README.md ├── config │ ├── docker.config │ ├── native.config │ ├── run.sh │ ├── ver.nf │ ├── ver_docker.txt │ └── ver_native.txt ├── delta.groovy ├── docker_1 │ ├── .nextflow.log │ ├── log_docker_21 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── docker_10 │ ├── .nextflow.log │ ├── log_docker_30 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── docker_2 │ ├── .nextflow.log │ ├── log_docker_22 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── docker_3 │ ├── .nextflow.log │ ├── log_docker_23 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── docker_4 │ ├── .nextflow.log │ ├── log_docker_24 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── docker_5 │ ├── .nextflow.log │ ├── log_docker_25 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── docker_6 │ ├── .nextflow.log │ ├── log_docker_26 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── docker_7 │ ├── .nextflow.log │ ├── log_docker_27 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── docker_8 │ ├── .nextflow.log │ ├── log_docker_28 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── docker_9 │ ├── .nextflow.log │ ├── log_docker_29 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── fig_correlation.png ├── file-formats.md ├── native_1 │ ├── .nextflow.log │ ├── log_native_21 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── native_10 │ ├── .nextflow.log │ ├── log_native_30 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── native_2 │ ├── .nextflow.log │ ├── log_native_22 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── native_3 │ ├── .nextflow.log │ ├── log_native_23 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── native_4 │ ├── .nextflow.log │ ├── log_native_24 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── native_5 │ ├── .nextflow.log │ ├── log_native_25 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── native_6 │ ├── .nextflow.log │ ├── log_native_26 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── native_7 │ ├── .nextflow.log │ ├── log_native_27 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── native_8 │ ├── .nextflow.log │ ├── log_native_28 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── native_9 │ ├── .nextflow.log │ ├── log_native_29 │ ├── result │ │ ├── gen1.ex.gtf │ │ ├── gen2.ex.gtf │ │ ├── gen3.ex.gtf │ │ ├── gen4.ex.gtf │ │ ├── gen5.ex.gtf │ │ ├── gen6.ex.gtf │ │ ├── gen7.ex.gtf │ │ ├── gen8.ex.gtf │ │ ├── gen9.ex.gtf │ │ └── simMatrix.csv │ ├── timeline.html │ └── trace.csv ├── plot.csv ├── plot.sh ├── plot_docker.txt ├── plot_native.txt ├── stage.sh ├── stats_docker.txt ├── stats_native.txt ├── table.R ├── table.txt ├── time.sh ├── time_docker.txt ├── time_native.txt ├── trace_docker.txt └── trace_native.txt ├── rnaseq-toy ├── Figures.R ├── Makefile ├── README.md ├── config │ ├── docker.config │ └── native.config ├── delta.groovy ├── docker_1 │ ├── .nextflow.log │ ├── log_docker_1 │ ├── timeline.html │ └── trace.csv ├── docker_10 │ ├── .nextflow.log │ ├── log_docker_10 │ ├── timeline.html │ └── trace.csv ├── docker_2 │ ├── .nextflow.log │ ├── log_docker_2 │ ├── timeline.html │ └── trace.csv ├── docker_3 │ ├── .nextflow.log │ ├── log_docker_3 │ ├── timeline.html │ └── trace.csv ├── docker_4 │ ├── .nextflow.log │ ├── log_docker_4 │ ├── timeline.html │ └── trace.csv ├── docker_5 │ ├── .nextflow.log │ ├── log_docker_5 │ ├── timeline.html │ └── trace.csv ├── docker_6 │ ├── .nextflow.log │ ├── log_docker_6 │ ├── timeline.html │ └── trace.csv ├── docker_7 │ ├── .nextflow.log │ ├── log_docker_7 │ ├── timeline.html │ └── trace.csv ├── docker_8 │ ├── .nextflow.log │ ├── log_docker_8 │ ├── timeline.html │ └── trace.csv ├── docker_9 │ ├── .nextflow.log │ ├── log_docker_9 │ ├── timeline.html │ └── trace.csv ├── fig_correlation.png ├── file-formats.md ├── native_1 │ ├── .nextflow.log │ ├── log_native_1 │ ├── timeline.html │ └── trace.csv ├── native_10 │ ├── .nextflow.log │ ├── log_native_10 │ ├── timeline.html │ └── trace.csv ├── native_2 │ ├── .nextflow.log │ ├── log_native_2 │ ├── timeline.html │ └── trace.csv ├── native_3 │ ├── .nextflow.log │ ├── log_native_3 │ ├── timeline.html │ └── trace.csv ├── native_4 │ ├── .nextflow.log │ ├── log_native_4 │ ├── timeline.html │ └── trace.csv ├── native_5 │ ├── .nextflow.log │ ├── log_native_5 │ ├── timeline.html │ └── trace.csv ├── native_6 │ ├── .nextflow.log │ ├── log_native_6 │ ├── timeline.html │ └── trace.csv ├── native_7 │ ├── .nextflow.log │ ├── log_native_7 │ ├── timeline.html │ └── trace.csv ├── native_8 │ ├── .nextflow.log │ ├── log_native_8 │ ├── timeline.html │ └── trace.csv ├── native_9 │ ├── .nextflow.log │ ├── log_native_9 │ ├── timeline.html │ └── trace.csv ├── plot.csv ├── plot.sh ├── plot_docker.txt ├── plot_native.txt ├── rnatoy-local.zip ├── stage.sh ├── stats_docker.txt ├── stats_native.txt ├── table.R ├── table.txt ├── time.sh ├── time_docker.txt ├── time_native.txt ├── trace_docker.txt └── trace_native.txt ├── scripts ├── delta.groovy └── join.groovy └── supplementary.txt /.dockerignore: -------------------------------------------------------------------------------- 1 | .git* 2 | manuscript/* 3 | nmdp-flow/* 4 | piper-nf/* 5 | rnaseq-toy/* 6 | scripts/* 7 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | **/*.zip 2 | flow-all/ 3 | maria/ 4 | mta-* 5 | piper-debian/ 6 | rnatoy-aws-*/ 7 | rnatoy-crg-*/ -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | FROM rocker/r-base 2 | 3 | MAINTAINER Paolo Di Tommaso 4 | 5 | RUN wget -q http://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.4.zip && \ 6 | unzip apache-groovy-binary-2.4.4.zip && \ 7 | rm apache-groovy-binary-2.4.4.zip 8 | 9 | RUN apt-get update && apt-get install -y make datamash 10 | RUN apt-get install -y openjdk-7-jdk 11 | 12 | ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/groovy-2.4.4/bin/ 13 | 14 | RUN R -e 'install.packages("scales")' && \ 15 | R -e 'install.packages("reshape")' && \ 16 | R -e 'install.packages("ggplot2")' && \ 17 | R -e 'install.packages("grid")' 18 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | Docker benchmarks 2 | =================== 3 | 4 | This repository contains the benchmarks for these pipelines: 5 | 6 | * [Rnaseq-toy](https://github.com/nextflow-io/rnatoy/) 7 | * [Nmdp-flow](https://github.com/nextflow-io/nmdp-flow/) 8 | * [Piper-nf](https://github.com/cbcrg/piper-nf/) 9 | 10 | Quick start 11 | ------------ 12 | 13 | To reproduce the figures from raw data clone this repository: 14 | 15 | git clone https://github.com/cbcrg/docker-benchmarks.git && cd docker-benchmarks 16 | 17 | Then pull the required Docker image: 18 | 19 | docker pull cbcrg/make-peerj5515 20 | 21 | Finally launch the `make` script using the following command: 22 | 23 | docker run -v $PWD:$PWD -w $PWD cbcrg/make-peerj5515 bash make-all.sh 24 | 25 | (if you don't want or cannot use Docker, you will need to download and install 26 | the required dependencies: R, Datamash, Make and Groovy. See the included 27 | [Dockefile](https://raw.githubusercontent.com/cbcrg/docker-benchmarks/master/Dockerfile) for configuration details). 28 | 29 | 30 | 31 | Structure of the repository 32 | ---------------------------- 33 | 34 | Benchmarks scripts and data are organised in separate folders depending the pipeline executed: 35 | 36 | * [Rnaseq-toy](rnaseq-toy) 37 | * [nmdp-flow](nmdp-flow) 38 | * [piper-nf](piper-nf) 39 | 40 | Each of these folders contains a `Makefile` and other scripts used by it to generate the figures. 41 | Raw data of each executions are the files `docker_{1..10}/trace.csv` and `native_{1..10}/trace.csv` in the same folder. 42 | 43 | The main files produced by the `make` process are: 44 | 45 | * `table.txt`: the numbers included in the *Table 1* 46 | * `fig_correlation.png`: the figure in included in the manuscript. 47 | 48 | See the respective `Makefile`s for more details. 49 | 50 | 51 | Replicate benchmarks 52 | ---------------------- 53 | 54 | Pipeline executions can be replicated following the instructions 55 | in the respective repositories, listed below: 56 | 57 | * [nmdp-flow](https://github.com/nextflow-io/nmdp-flow/tree/peerj5515/) 58 | * [piper-nf](https://github.com/cbcrg/piper-nf/tree/peerj5515) 59 | * [rnaseq-toy](https://github.com/nextflow-io/rnatoy/tree/peerj5515) 60 | 61 | -------------------------------------------------------------------------------- /make-all.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -e 3 | set -o 4 | (cd nmdp-flow && make clean all) 5 | (cd piper-nf && make clean all) 6 | (cd rnaseq-toy && make clean all) 7 | 8 | echo 'DONE' 9 | echo '' 10 | echo "Table 1 data is provided by these files:" 11 | echo "- rnaseq-toy/table.txt" 12 | echo "- nmdp-flow/table.txt" 13 | echo "- piper-nf/table.txt" 14 | 15 | echo "" 16 | echo "Figures are the following files:" 17 | echo "- Fig 1: rnaseq-toy/fig_correlation.png" 18 | echo "- Fig 2: nmdp-flow/fig_correlation.png" 19 | echo "- Fig 3: piper-nf/fig_correlation.png" 20 | echo '' 21 | -------------------------------------------------------------------------------- /manuscript/Figure1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/manuscript/Figure1.png -------------------------------------------------------------------------------- /manuscript/Figure2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/manuscript/Figure2.png -------------------------------------------------------------------------------- /manuscript/Figure3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/manuscript/Figure3.png -------------------------------------------------------------------------------- /manuscript/Table1.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/manuscript/Table1.docx -------------------------------------------------------------------------------- /manuscript/The impact of Docker containers on the performance of genomic pipelines.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/manuscript/The impact of Docker containers on the performance of genomic pipelines.pdf -------------------------------------------------------------------------------- /manuscript/The impact of Docker containes on the performances of genomic pipelines (backup).docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/manuscript/The impact of Docker containes on the performances of genomic pipelines (backup).docx -------------------------------------------------------------------------------- /manuscript/The impact of Docker containes on the performances of genomic pipelines (peer-review).pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/manuscript/The impact of Docker containes on the performances of genomic pipelines (peer-review).pdf -------------------------------------------------------------------------------- /manuscript/The impact of Docker containes on the performances of genomic pipelines (v2).pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/manuscript/The impact of Docker containes on the performances of genomic pipelines (v2).pdf -------------------------------------------------------------------------------- /manuscript/The impact of Docker containes on the performances of genomic pipelines.docx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/manuscript/The impact of Docker containes on the performances of genomic pipelines.docx -------------------------------------------------------------------------------- /manuscript/fig-titles.txt: -------------------------------------------------------------------------------- 1 | Table 1 - Mean execution times for pipelines and tasks with and without Docker. Time is expressed in minutes. The mean and the standard deviation were estimated from 10 separate runs. Slowdown represents the ratio of the mean execution time with Docker to the mean execution time when Docker was not used. 2 | 3 | Figure 1 – RNA-Seq pipeline tasks, native vs. Docker mean execution times. Time elapsed (in minutes) to complete since the submission including the container instantiation. Each point represents the mean task time for the same type in one pipeline run. 4 | 5 | Figure 2 – Variant calling pipeline tasks, native vs. Docker mean execution times. Time elapsed (in minutes) to complete since the submission including the container instantiation. Each point represents the mean task time for the same type in one pipeline run. 6 | 7 | Figure 3 – Piper pipeline tasks, native vs. Docker mean execution times. Time elapsed (in minutes) to complete since the submission including the container instantiation. Each point represents the mean task time for the same type in one pipeline run. -------------------------------------------------------------------------------- /manuscript/ref.txt: -------------------------------------------------------------------------------- 1 | Altschul, SF, Gish W, Miller W, Myers EW & Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. (1990) Oct 5; 215:403-410. PMID: 2231712 2 | 3 | Boettiger C. 2015. An introduction to Docker for reproducible research. ACM SIGOPS Operating Systems Review, Special Issue on Repeatability and Sharing of Experimental Artifacts. 49(1), 71-79. doi:10.1145/2723872.2723882 4 | 5 | Di Tommaso P, et al. 2014. Nextflow: A novel tool for highly scalable computational pipelines. Available at http://dx.doi.org/10.6084/m9.figshare.1254958 6 | 7 | Felter W, Ferreira A, Rajamony R, Rubio J. 2014. An Updated Performance Comparison of Virtual Machines and Linux Contain. IBM Research. Available at http://ibm.co/V55Otq (accessed 1 Jun 2015) 8 | 9 | Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. 2013. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013 Apr 25;14(4):R36. doi: 10.1186/gb-2013-14-4-r36. 10 | 11 | Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Mar 4; 9(4): 357–359. doi: 10.1038/nmeth.1923 12 | 13 | Li H, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25 (16): 2078-2079. doi: 10.1093/bioinformatics/btp352 14 | 15 | Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics (2009) 25 (14): 1754-1760. doi: 10.1093/bioinformatics/btp324 16 | 17 | Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. (2000) Sep 8;302(1):205-17. doi:10.1006/jmbi.2000.4042 18 | 19 | Slater GSC, Birney E. 2005. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics (2005) 6:31 doi:10.1186/1471-2105-6-31 20 | 21 | Steven J. Mack, et al. 2015. Minimum Information for Reporting Next Generation Sequence Genotyping (MIRING): Guidelines for Reporting HLA and KIR Genotyping via Next Generation Sequencing. Available at http://biorxiv.org/content/early/2015/02/16/015230 (accessed 1 Jun 2015) 22 | 23 | Trapnell C, et al. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28, 511–515 doi:10.1038/nbt.1621 24 | 25 | Warren RL, Sutton GG, Jones SJM, Holt RA. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics (2007) 23 (4): 500-501. doi: 10.1093/bioinformatics/btl629 26 | -------------------------------------------------------------------------------- /nmdp-flow/Figures.R: -------------------------------------------------------------------------------- 1 | library(scales) 2 | library(reshape) 3 | library(ggplot2) 4 | library(grid) 5 | 6 | NF_stats<-read.csv("plot.csv",header=T) 7 | NF_stats = cbind(NF_stats, shape=rep("16",dim(NF_stats)[1])) 8 | 9 | nL = dim(read.table("stats_docker.txt", skip=1, header=F))[1] 10 | 11 | NF_median = data.frame(list( name = c("median"), realtime_docker = read.table("stats_docker.txt", skip=nL, header=F)[,2], realtime_native = read.table("stats_native.txt", skip=nL, header=F)[,2], shape = c("6"))) 12 | NF_mean = data.frame(list( name = c("mean"), realtime_docker = read.table("stats_docker.txt", skip=nL, header=F)[,3], realtime_native = read.table("stats_native.txt", skip=nL, header=F)[,3], shape = c("8"))) 13 | 14 | NF_stats$realtime_docker_log10 = log10((NF_stats$realtime_docker/1000)/60) 15 | NF_stats$realtime_native_log10 = log10((NF_stats$realtime_native/1000)/60) 16 | 17 | max_axis = max(c(NF_stats$realtime_docker_log10, NF_stats$realtime_native_log10)) * 1.08 18 | min_axis = min(c(NF_stats$realtime_docker_log10, NF_stats$realtime_native_log10)) * 1.01 19 | 20 | lbreaks = log10(c(1,10,100,1000)) 21 | llabels = c(1,10,100,1000) 22 | png(filename = "fig_correlation.png", width = 5, height = 4, units = 'in', res = 300) 23 | qplot(x=realtime_docker_log10, y=realtime_native_log10, data=NF_stats, main="", color=name, ylab="Native tasks avg. time (mins)", xlab="Docker tasks avg. time (mins)") + 24 | geom_point(size = 3, aes(shape = shape)) + 25 | geom_point( data = NF_median, aes(x=log10((realtime_docker/1000)/60), y=log10((realtime_native/1000)/60), shape = shape, color = NA), size = 3) + 26 | geom_point( data = NF_mean, aes(x=log10((realtime_docker/1000)/60), y=log10((realtime_native/1000)/60), shape = shape, color = NA), size = 3) + 27 | scale_shape_manual(values = c(16, 6, 8), breaks = c("6","8"), labels = c("median","mean")) + 28 | geom_abline(intercept = 0, size=.2) + 29 | scale_x_continuous(limits = c(min_axis,max_axis), breaks = lbreaks, labels = llabels) + 30 | scale_y_continuous(limits = c(min_axis,max_axis), breaks = lbreaks, labels = llabels) + 31 | labs(color = "Task", title='Variant calling', shape = "") + 32 | theme(axis.text.x=element_text(size=10), axis.text.y=element_text(size=10), axis.title.y=element_text(size=8), axis.title.x=element_text(size=8),legend.text=element_text(size=8),legend.title=element_text(size=8)) 33 | 34 | dev.off() 35 | 36 | 37 | -------------------------------------------------------------------------------- /nmdp-flow/README.md: -------------------------------------------------------------------------------- 1 | Flow stats 2 | ================ 3 | 4 | This folder contains the log files for the Flow pipeline executions. 5 | 6 | To generate the figures use the `make` command. It creates the following 7 | assets: 8 | 9 | * `time_native.txt`: Summary table of times for `native` executions 10 | * `time_docker.txt`: Summary table of times for `docker` executions 11 | * `fig_wall_time.png`: Box plot of pipeline wall-clock execution time 12 | * `fig_run_time.png`: Box plot of pipeline aggregate tasks run-time 13 | * `fig_correlation.png`: Correlation between docker and native tasks time execution 14 | -------------------------------------------------------------------------------- /nmdp-flow/config/docker.config: -------------------------------------------------------------------------------- 1 | params.experiment = "../data" 2 | params.reference = "../data/ref/chr6.fa" 3 | 4 | process.container = 'nextflow/flow' 5 | executor.queueSize = 10 6 | docker.enabled = true 7 | 8 | trace { 9 | enabled = true 10 | fields = 'task_id,hash,native_id,name,status,exit,submit,duration,realtime,%cpu,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,duration:num,realtime:num,rss:num,vmem:num,peak_rss:num,peak_vmem:num,rchar:num,wchar:num' 11 | } 12 | 13 | timeline { 14 | enabled = true 15 | } 16 | -------------------------------------------------------------------------------- /nmdp-flow/config/native.config: -------------------------------------------------------------------------------- 1 | params.experiment = "../data" 2 | params.reference = "../data/ref/chr6.fa" 3 | 4 | executor.queueSize = 10 5 | 6 | trace { 7 | enabled = true 8 | fields = 'task_id,hash,native_id,name,status,exit,submit,duration,realtime,%cpu,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,duration:num,realtime:num,rss:num,vmem:num,peak_rss:num,peak_vmem:num,rchar:num,wchar:num' 9 | } 10 | 11 | timeline { 12 | enabled = true 13 | } 14 | 15 | env { 16 | PATH="$HOME/linuxbrew/bin:/scratch/tmp/flow/ngs-tools-1.7/bin:$PATH" 17 | } 18 | 19 | -------------------------------------------------------------------------------- /nmdp-flow/config/run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -ue 2 | 3 | log() { 4 | echo "=== ${1}" >&2 5 | } 6 | 7 | unset NXF_WORK 8 | export NXF_VER=0.13.4 9 | nextflow info 10 | 11 | for i in {1..10}; do 12 | log "Submitting run ${i}..." 13 | for run in docker native; do 14 | (mkdir -p ${run}_${i} && cd ${run}_${i} && nextflow -c ../${run}.config run ../main.nf > log_${run}_${i}) 15 | sleep 10s 16 | done 17 | sleep 10s 18 | done 19 | -------------------------------------------------------------------------------- /nmdp-flow/delta.groovy: -------------------------------------------------------------------------------- 1 | ../scripts/delta.groovy -------------------------------------------------------------------------------- /nmdp-flow/fig_correlation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/nmdp-flow/fig_correlation.png -------------------------------------------------------------------------------- /nmdp-flow/plot.csv: -------------------------------------------------------------------------------- 1 | name,realtime_docker,realtime_native 2 | alignContigs,4191.625,348.625 3 | alignContigs,4062.625,1009.125 4 | alignContigs,4167,1009.375 5 | alignContigs,4029.25,363.125 6 | alignContigs,4145,994.75 7 | alignContigs,4157,359.375 8 | alignContigs,17054.375,366.125 9 | alignContigs,4069.25,993.875 10 | alignContigs,17099.5,997.75 11 | alignContigs,4545.25,383 12 | alignReads,28893.125,2993.625 13 | alignReads,30323.25,342.25 14 | alignReads,31181.125,981.375 15 | alignReads,31594.625,353.75 16 | alignReads,30582.875,2297.875 17 | alignReads,34686.625,1105.125 18 | alignReads,34903.5,1640.375 19 | alignReads,33797.75,385.75 20 | alignReads,36590.625,450.875 21 | alignReads,37149.875,1069.125 22 | fastqToSsake,35135.875,22613.25 23 | fastqToSsake,33665,22140.75 24 | fastqToSsake,34998.875,21558.5 25 | fastqToSsake,33383.125,22070.625 26 | fastqToSsake,37987,22062.375 27 | fastqToSsake,40766.5,22353.875 28 | fastqToSsake,43386.375,22772.875 29 | fastqToSsake,41679.125,22877.125 30 | fastqToSsake,43237.125,22804.75 31 | fastqToSsake,42784.25,22413.75 32 | interleave,43687.875,31590.625 33 | interleave,46776.25,32236.875 34 | interleave,47064.25,30523.25 35 | interleave,46313.125,31147.125 36 | interleave,49384.125,32432.25 37 | interleave,48421.5,31768.75 38 | interleave,50799.75,31842 39 | interleave,53252,32975.625 40 | interleave,52812.125,32058.25 41 | interleave,55459.125,32107.75 42 | reformat,36005.375,12063.375 43 | reformat,39766.375,12734.875 44 | reformat,37967.5,12751.25 45 | reformat,37490.125,12168.875 46 | reformat,39799.75,12724.5 47 | reformat,41132.75,12233 48 | reformat,42805.25,12217.375 49 | reformat,44938.75,12266 50 | reformat,42972.5,12229.5 51 | reformat,47090,12829.5 52 | ssake,9453389,9278939.25 53 | ssake,9459468.125,9350804 54 | ssake,9461669.125,9327518.125 55 | ssake,9464710.75,9310700.625 56 | ssake,9461462.5,9402224.5 57 | ssake,9448187.375,9324142.5 58 | ssake,9450485,9311689.125 59 | ssake,9487336.375,9342940.5 60 | ssake,9438973.625,9321528.875 61 | ssake,9473151.75,9392171.125 62 | -------------------------------------------------------------------------------- /nmdp-flow/plot.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | function stats() { 4 | STAGES=$(tail -n +2 $1 | cut -f 4 | cut -f 1 -d ' ' | sort | uniq) 5 | for x in $STAGES; do 6 | row=$(cat $1 | grep $x | sed 's/-/0/g' | datamash median 19 mean 19 median 20 mean 20 count 1) 7 | printf "$x\t$row\n" 8 | done 9 | } 10 | 11 | for file in ${1}_{1..10}/trace.csv;do 12 | stats $file 13 | done -------------------------------------------------------------------------------- /nmdp-flow/stage.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | function stats() { 4 | STAGES=$(cat trace_${1}.txt | cut -f 4 | cut -f 1 -d ' ' | uniq | sort) 5 | for x in $STAGES; do 6 | row=$(cat trace_${1}.txt | grep $x | sed 's/-/0/g' | datamash median 19 mean 19 median 20 mean 20 count 1) 7 | printf "$x\t$row\n" 8 | done 9 | 10 | row=$(cat trace_${1}.txt | sed 's/-/0/g' | datamash median 19 mean 19 median 20 mean 20 count 1) 11 | printf "ALL\t$row\n" 12 | 13 | } 14 | 15 | echo $1 | awk '{print toupper($0)}' 16 | stats $1 17 | -------------------------------------------------------------------------------- /nmdp-flow/stats_docker.txt: -------------------------------------------------------------------------------- 1 | DOCKER 2 | alignContigs 4131 6752.0875 39 279.5875 80 3 | alignReads 33085.5 32970.3375 19338 18208.4875 80 4 | fastqToSsake 30606.5 38702.325 18332.5 19303.0375 80 5 | interleave 46220 49397.0125 27963 28622.075 80 6 | reformat 40545.5 40996.8375 10576.5 11124.4125 80 7 | ssake 8708385 9459883.3625 8685748 9436560.8625 80 8 | ALL 39062 1604783.6604167 18332.5 1585683.0770833 480 9 | -------------------------------------------------------------------------------- /nmdp-flow/stats_native.txt: -------------------------------------------------------------------------------- 1 | NATIVE 2 | alignContigs 349.5 682.5125 278.5 296.45 80 3 | alignReads 369 1162.0125 275 409.675 80 4 | fastqToSsake 21714.5 22366.7875 19209.5 19426.9 80 5 | interleave 31901 31868.25 28335 29018.475 80 6 | reformat 11210.5 12421.825 10473.5 10756.3 80 7 | ssake 8572191.5 9336265.8625 8568660.5 9333899.45 80 8 | ALL 18402.5 1567461.2083333 14660.5 1565634.5416667 480 9 | -------------------------------------------------------------------------------- /nmdp-flow/table.R: -------------------------------------------------------------------------------- 1 | native <- read.delim("time_native.txt", header=TRUE) 2 | docker <- read.delim("time_docker.txt", header=TRUE) 3 | 4 | stderr <- function(x) sd(x)/sqrt(length(x)) 5 | 6 | native_mean_exec_time = mean(native$duration) / 1000 /60 7 | docker_mean_exec_time = mean(docker$duration) / 1000 /60 8 | 9 | native_err = stderr(native$duration) / 1000 /60 10 | docker_err = stderr(docker$duration) / 1000 /60 11 | 12 | native_stdev_exec_time = sd(native$duration) / 1000 /60 13 | docker_stddev_exec_time = sd(docker$duration) / 1000 /60 14 | 15 | # each instance executes 48 tasks 16 | native_mean_task_time = native_mean_exec_time / 48 17 | docker_mean_task_time = docker_mean_exec_time / 48 18 | 19 | cat(sprintf("VARIANT CALL. : native docker\n")) 20 | cat(sprintf("Task mean time : %.1f %.1f\n", native_mean_task_time, docker_mean_task_time)) 21 | cat(sprintf("Mean exec time : %.1f (±%.1f) %.1f (±%.1f) \n", native_mean_exec_time, native_err, docker_mean_exec_time, docker_err)) 22 | cat(sprintf("Stddev exec time: %.1f %.1f\n", native_stdev_exec_time, docker_stddev_exec_time)) 23 | cat(sprintf("Slow-down : %.3f\n" , docker_mean_exec_time/native_mean_exec_time)) 24 | -------------------------------------------------------------------------------- /nmdp-flow/table.txt: -------------------------------------------------------------------------------- 1 | VARIANT CALL. : native docker 2 | Task mean time : 26.1 26.7 3 | Mean exec time : 1254.0 (±1.6) 1283.8 (±0.8) 4 | Stddev exec time: 4.9 2.4 5 | Slow-down : 1.024 6 | -------------------------------------------------------------------------------- /nmdp-flow/time.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | function gettime { 4 | 5 | printf "begin\tend\telapsed\tdelta\tduration\trealtime\n" 6 | for x in ${1}_{1..10}; do 7 | duration=$(tail -n +2 $x/trace.csv | sed 's/-/0/g' | datamash sum 19) 8 | realtime=$(tail -n +2 $x/trace.csv | sed 's/-/0/g' | datamash sum 20) 9 | delta=$(groovy delta.groovy "$(cat $x/.nextflow.log | head -n 1 | cut -f 1,2 -d ' ')" "$(cat $x/.nextflow.log | tail -n 1 | cut -f 1,2 -d ' ')") 10 | printf "$delta\t$duration\t$realtime\n" 11 | done 12 | 13 | } 14 | 15 | gettime $1 16 | 17 | -------------------------------------------------------------------------------- /nmdp-flow/time_docker.txt: -------------------------------------------------------------------------------- 1 | begin end elapsed delta duration realtime 2 | May-11 16:28:05.582 May-11 20:12:10.478 3:44:4 13444896 77262087 76306417 3 | May-11 23:54:16.588 May-12 03:36:31.648 3:42:15 13335060 77015898 76204135 4 | May-12 07:15:47.421 May-12 10:56:43.085 3:40:55 13255664 76796379 75840419 5 | May-12 14:33:15.925 May-12 18:15:38.586 3:42:22 13342661 76958673 76079484 6 | May-12 21:53:03.479 May-13 01:35:30.391 3:42:26 13346912 77100797 76188340 7 | May-13 05:12:27.892 May-13 08:55:57.548 3:43:29 13409656 77244677 76177824 8 | May-13 12:38:29.533 May-13 16:21:23.206 3:42:53 13373673 77019597 76113267 9 | May-13 20:01:45.018 May-13 23:42:06.029 3:40:21 13221011 76915757 76069382 10 | May-14 03:23:09.229 May-14 07:07:37.456 3:44:28 13468227 77044841 76154932 11 | May-14 10:44:06.629 May-14 14:25:08.918 3:41:2 13262289 76937451 75993677 12 | -------------------------------------------------------------------------------- /nmdp-flow/time_native.txt: -------------------------------------------------------------------------------- 1 | begin end elapsed delta duration realtime 2 | May-11 12:50:29.690 May-11 16:27:52.180 3:37:22 13042490 75137679 75035811 3 | May-11 20:12:35.163 May-11 23:54:03.184 3:41:28 13288021 75759367 75685951 4 | May-12 03:36:55.512 May-12 07:15:34.439 3:38:38 13118927 75141504 75051162 5 | May-12 10:57:06.262 May-12 14:33:05.155 3:35:58 12958893 74785094 74685170 6 | May-12 18:15:59.390 May-12 21:52:52.699 3:36:53 13013309 75047474 74958988 7 | May-13 01:35:51.452 May-13 05:12:14.646 3:36:23 12983194 75037148 74955488 8 | May-13 08:56:18.372 May-13 12:38:18.747 3:42:0 13320375 75167031 75080411 9 | May-13 16:21:43.993 May-13 20:01:34.260 3:39:50 13190267 75679614 75594984 10 | May-13 23:42:26.810 May-14 03:22:54.983 3:40:28 13228173 75347764 75255480 11 | May-14 07:07:58.230 May-14 10:43:55.826 3:35:57 12957596 75278705 75201135 12 | -------------------------------------------------------------------------------- /piper-nf/Figures.R: -------------------------------------------------------------------------------- 1 | library(reshape) 2 | library(ggplot2) 3 | library(grid) 4 | NF_stats<-read.csv("plot.csv",header=T) 5 | NF_stats = cbind(NF_stats, shape=rep("16",dim(NF_stats)[1])) 6 | nL = dim(read.table("stats_docker.txt", skip=1, header=F))[1] 7 | NF_median = data.frame(list( name = c("median"), realtime_docker = read.table("stats_docker.txt", skip=nL, header=F)[,2], realtime_native = read.table("stats_native.txt", skip=nL, header=F)[,2], shape = c("6"))) 8 | NF_mean = data.frame(list( name = c("mean"), realtime_docker = read.table("stats_docker.txt", skip=nL, header=F)[,3], realtime_native = read.table("stats_native.txt", skip=nL, header=F)[,3], shape = c("8"))) 9 | 10 | max_axis = max(c(NF_stats[,2], NF_stats[,3]))/1000/60 * 1.09 11 | 12 | png(filename = "fig_correlation.png", width = 5, height = 4, units = 'in', res = 300) 13 | qplot(x=(realtime_docker/1000)/60, y=(realtime_native/1000)/60, data=NF_stats, main="", color=name, ylab="Native tasks avg. time (mins)", xlab="Docker tasks avg. time (mins)") + 14 | geom_point(size = 3, aes(shape = shape)) + 15 | geom_point( data = NF_median, aes(x=(realtime_docker/1000)/60, y=(realtime_native/1000)/60, shape = shape, color = NA), size = 3) + 16 | geom_point( data = NF_mean, aes(x=(realtime_docker/1000)/60, y=(realtime_native/1000)/60, shape = shape, color = NA), size = 3) + 17 | scale_shape_manual(values = c(16, 6, 8), breaks = c("6","8"), labels = c("median","mean")) + 18 | coord_cartesian(xlim=c(0,max_axis), ylim=c(0,max_axis)) + geom_abline(intercept = 0, size=.2) + theme(axis.text.x=element_text(size=10), axis.text.y=element_text(size=10), axis.title.y=element_text(size=8), axis.title.x=element_text(size=8),legend.text=element_text(size=8),legend.title=element_text(size=8)) + labs(color = "Task", title='PIPER', shape = "") 19 | 20 | dev.off() -------------------------------------------------------------------------------- /piper-nf/README.md: -------------------------------------------------------------------------------- 1 | Piper-nf stats 2 | ================ 3 | 4 | This folder contains the log files for the Piper-NF pipeline executions. 5 | 6 | To generate the figures use the `make` command. It creates the following 7 | assets: 8 | 9 | * `time_native.txt`: Summary table of times for `native` executions 10 | * `time_docker.txt`: Summary table of times for `docker` executions 11 | * `fig_wall_time.png`: Box plot of pipeline wall-clock execution time 12 | * `fig_run_time.png`: Box plot of pipeline aggregate tasks run-time 13 | * `fig_correlation.png`: Correlation between docker and native tasks time execution 14 | -------------------------------------------------------------------------------- /piper-nf/config/docker.config: -------------------------------------------------------------------------------- 1 | params { 2 | query = '../chicken/query100.fa' 3 | genomesFile = '../chicken/genomes.txt' 4 | genomesDb = 'db' 5 | } 6 | 7 | process { 8 | container = 'cbcrg/piper-nf:sl65' 9 | } 10 | 11 | executor.queueSize = 10 12 | docker.enabled = true 13 | docker.remove = false 14 | 15 | trace { 16 | enabled = true 17 | fields = 'task_id,hash,native_id,name,status,exit,submit,duration,realtime,%cpu,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,duration:num,realtime:num,rss:num,vmem:num,peak_rss:num,peak_vmem:num,rchar:num,wchar:num' 18 | } 19 | 20 | timeline { 21 | enabled = true 22 | } 23 | -------------------------------------------------------------------------------- /piper-nf/config/native.config: -------------------------------------------------------------------------------- 1 | params { 2 | query = '../chicken/query100.fa' 3 | genomesFile = '../chicken/genomes.txt' 4 | genomesDb = 'db' 5 | } 6 | 7 | executor.queueSize = 10 8 | 9 | trace { 10 | enabled = true 11 | fields = 'task_id,hash,native_id,name,status,exit,submit,duration,realtime,%cpu,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,duration:num,realtime:num,rss:num,vmem:num,peak_rss:num,peak_vmem:num,rchar:num,wchar:num' 12 | } 13 | 14 | timeline { 15 | enabled = true 16 | } 17 | 18 | env { 19 | DIR_4_TCOFFEE="/scratch/tmp/piper/tcoffee_10.00.r1613" 20 | LOCKDIR_4_TCOFFEE='/tmp/tc/lck/' 21 | TMP_4_TCOFFEE='/tmp/tc/tmp/' 22 | PATH="/scratch/tmp/piper/tcoffee_10.00.r1613/bin:/scratch/tmp/piper/ncbi-blast-2.2.29+/bin:$PATH" 23 | } 24 | 25 | -------------------------------------------------------------------------------- /piper-nf/config/run.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -ue 2 | 3 | log() { 4 | echo "=== ${1}" >&2 5 | } 6 | 7 | unset NXF_WORK 8 | export NXF_VER=0.14.0-SNAPSHOT 9 | export NXF_DEBUG=3 10 | nextflow info 11 | 12 | for i in {21..30}; do 13 | log "Submitting run ${i}..." 14 | for run in docker native; do 15 | (mkdir -p ${run}_${i} && cd ${run}_${i} && nextflow -c ../${run}.config run ../piper-nf > log_${run}_${i}; rm -rf db work || true) 16 | sleep 10s 17 | done 18 | done 19 | -------------------------------------------------------------------------------- /piper-nf/config/ver.nf: -------------------------------------------------------------------------------- 1 | echo true 2 | 3 | process ver { 4 | ''' 5 | t_coffee -version; 6 | blastp -version; 7 | exonerate --version || true; 8 | echo $PATH; 9 | env | grep COFFEE 10 | ''' 11 | } 12 | -------------------------------------------------------------------------------- /piper-nf/config/ver_docker.txt: -------------------------------------------------------------------------------- 1 | DOCKER 2 | ======= 3 | 4 | $ nextflow -c docker.config run ver.nf 5 | N E X T F L O W ~ version 0.13.5 6 | Launching ver.nf 7 | [warm up] executor > local 8 | [7e/63dced] Submitted process > ver (1) 9 | PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:09 - Revision 1613 - Build 432) 10 | blastp: 2.2.29+ 11 | Package: blast 2.2.29, build Dec 10 2013 14:41:40 12 | exonerate from exonerate version 2.2.0 13 | Using glib version 2.4.7 14 | Built on Oct 17 2008 15 | Branch: unnamed branch 16 | /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/blast/bin:/opt/exonerate/bin:/opt/tcoffee/bin:/opt/wu-blast 17 | DIR_4_TCOFFEE=/opt/tcoffee 18 | CACHE_4_TCOFFEE=/tmp/cache/ 19 | EMAIL_4_TCOFFEE=tcoffee.msa@gmail.com 20 | LOCKDIR_4_TCOFFEE=/tmp/lck/ 21 | TMP_4_TCOFFEE=/tmp/tmp/ -------------------------------------------------------------------------------- /piper-nf/config/ver_native.txt: -------------------------------------------------------------------------------- 1 | NATIVE 2 | ======= 3 | 4 | $ nextflow -c native.config run ver.nf 5 | N E X T F L O W ~ version 0.13.5 6 | Launching ver.nf 7 | [warm up] executor > local 8 | [6f/996ca7] Submitted process > ver (1) 9 | PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:09 - Revision 1613 - Build 432) 10 | blastp: 2.2.29+ 11 | Package: blast 2.2.29, build Dec 10 2013 14:41:40 12 | exonerate from exonerate version 2.2.0 13 | Using glib version 2.4.7 14 | Built on Oct 17 2008 15 | Branch: unnamed branch 16 | /scratch/tmp/piper/tcoffee_10.00.r1613/bin:/scratch/tmp/piper/ncbi-blast-2.2.29+/bin:/software/as/el6.5/modules/Modules/3.2.10/bin/:/users/cn/ptommaso/cirrus/tools/bin:/users/cn/ptommaso/bin:/users/cn/ptommaso/tools/groovy/bin:/users/cn/ptommaso/jdk1.8.0_40/bin:/users/cn/ptommaso/tcoffee/Version_11.00.fb59e64/bin:/users/cn/ptommaso/tools/s3cmd:/usr/share/univage/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/lib64/openmpi/bin/:/usr/lib64/compat-openmpi/bin/:/software/cn/bin:/software/cn/FC12-x86_64/bin 17 | DIR_4_TCOFFEE=/scratch/tmp/piper/tcoffee_10.00.r1613 18 | CACHE_4_TCOFFEE=/nfs/users/cn/ptommaso/.t_coffee/cache/ 19 | EMAIL_4_TCOFFEE=paolo.ditommaso@gmail.com 20 | LOCKDIR_4_TCOFFEE=/tmp/tc/lck/ 21 | TMP_4_TCOFFEE=/tmp/tc/tmp/ -------------------------------------------------------------------------------- /piper-nf/delta.groovy: -------------------------------------------------------------------------------- 1 | ../scripts/delta.groovy -------------------------------------------------------------------------------- /piper-nf/docker_1/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/docker_1/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/docker_1/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/docker_1/result/gen4.ex.gtf: -------------------------------------------------------------------------------- 1 | JH603219.1 BLAST exon 3054083 3055022 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 2 | JH603219.1 BLAST exon 3055479 3056661 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 3 | JH603219.1 BLAST exon 3056701 3056837 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 4 | JH603219.1 BLAST exon 3057448 3057916 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 5 | JH603219.1 BLAST exon 3058115 3058526 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 6 | JH603219.1 BLAST exon 3059853 3060011 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 7 | JH603215.1 BLAST exon 6352355 6352920 . + . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 8 | JH603183.1 BLAST exon 3853078 3854281 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 9 | JH603183.1 BLAST exon 3854315 3855759 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 10 | JH603183.1 BLAST exon 3855840 3856104 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 11 | JH603183.1 BLAST exon 3857358 3857949 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 12 | JH603183.1 BLAST exon 3858329 3858807 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 13 | JH603183.1 BLAST exon 3859427 3859501 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 14 | JH603225.1 BLAST exon 4705067 4705152 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 15 | JH603225.1 BLAST exon 4703690 4704218 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 16 | JH603178.1 BLAST exon 15171586 15171630 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 17 | JH603178.1 BLAST exon 15170974 15171551 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 18 | -------------------------------------------------------------------------------- /piper-nf/docker_1/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/docker_1/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/docker_10/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/docker_10/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/docker_10/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/docker_10/result/gen4.ex.gtf: -------------------------------------------------------------------------------- 1 | JH603219.1 BLAST exon 3054083 3055022 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 2 | JH603219.1 BLAST exon 3055479 3056661 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 3 | JH603219.1 BLAST exon 3056701 3056837 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 4 | JH603219.1 BLAST exon 3057448 3057916 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 5 | JH603219.1 BLAST exon 3058115 3058526 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 6 | JH603219.1 BLAST exon 3059853 3060011 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 7 | JH603215.1 BLAST exon 6352355 6352920 . + . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 8 | JH603183.1 BLAST exon 3853078 3854281 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 9 | JH603183.1 BLAST exon 3854315 3855759 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 10 | JH603183.1 BLAST exon 3855840 3856104 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 11 | JH603183.1 BLAST exon 3857358 3857949 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 12 | JH603183.1 BLAST exon 3858329 3858807 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 13 | JH603183.1 BLAST exon 3859427 3859501 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 14 | JH603225.1 BLAST exon 4705067 4705152 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 15 | JH603225.1 BLAST exon 4703690 4704218 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 16 | JH603178.1 BLAST exon 15171586 15171630 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 17 | JH603178.1 BLAST exon 15170974 15171551 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 18 | -------------------------------------------------------------------------------- /piper-nf/docker_10/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/docker_10/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/docker_2/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/docker_2/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/docker_2/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/docker_2/result/gen4.ex.gtf: -------------------------------------------------------------------------------- 1 | JH603219.1 BLAST exon 3054083 3055022 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 2 | JH603219.1 BLAST exon 3055479 3056661 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 3 | JH603219.1 BLAST exon 3056701 3056837 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 4 | JH603219.1 BLAST exon 3057448 3057916 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 5 | JH603219.1 BLAST exon 3058115 3058526 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 6 | JH603219.1 BLAST exon 3059853 3060011 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 7 | JH603215.1 BLAST exon 6352355 6352920 . + . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 8 | JH603183.1 BLAST exon 3853078 3854281 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 9 | JH603183.1 BLAST exon 3854315 3855759 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 10 | JH603183.1 BLAST exon 3855840 3856104 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 11 | JH603183.1 BLAST exon 3857358 3857949 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 12 | JH603183.1 BLAST exon 3858329 3858807 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 13 | JH603183.1 BLAST exon 3859427 3859501 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 14 | JH603225.1 BLAST exon 4705067 4705152 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 15 | JH603225.1 BLAST exon 4703690 4704218 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 16 | JH603178.1 BLAST exon 15171586 15171630 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 17 | JH603178.1 BLAST exon 15170974 15171551 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 18 | -------------------------------------------------------------------------------- /piper-nf/docker_2/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/docker_2/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/docker_3/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/docker_3/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/docker_3/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/docker_3/result/gen4.ex.gtf: -------------------------------------------------------------------------------- 1 | JH603219.1 BLAST exon 3054083 3055022 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 2 | JH603219.1 BLAST exon 3055479 3056661 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 3 | JH603219.1 BLAST exon 3056701 3056837 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 4 | JH603219.1 BLAST exon 3057448 3057916 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 5 | JH603219.1 BLAST exon 3058115 3058526 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 6 | JH603219.1 BLAST exon 3059853 3060011 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 7 | JH603215.1 BLAST exon 6352355 6352920 . + . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 8 | JH603183.1 BLAST exon 3853078 3854281 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 9 | JH603183.1 BLAST exon 3854315 3855759 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 10 | JH603183.1 BLAST exon 3855840 3856104 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 11 | JH603183.1 BLAST exon 3857358 3857949 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 12 | JH603183.1 BLAST exon 3858329 3858807 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 13 | JH603183.1 BLAST exon 3859427 3859501 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 14 | JH603225.1 BLAST exon 4705067 4705152 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 15 | JH603225.1 BLAST exon 4703690 4704218 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 16 | JH603178.1 BLAST exon 15171586 15171630 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 17 | JH603178.1 BLAST exon 15170974 15171551 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 18 | -------------------------------------------------------------------------------- /piper-nf/docker_3/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/docker_3/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/docker_4/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/docker_4/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/docker_4/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/docker_4/result/gen4.ex.gtf: -------------------------------------------------------------------------------- 1 | JH603219.1 BLAST exon 3054083 3055022 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 2 | JH603219.1 BLAST exon 3055479 3056661 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 3 | JH603219.1 BLAST exon 3056701 3056837 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 4 | JH603219.1 BLAST exon 3057448 3057916 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 5 | JH603219.1 BLAST exon 3058115 3058526 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 6 | JH603219.1 BLAST exon 3059853 3060011 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 7 | JH603215.1 BLAST exon 6352355 6352920 . + . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 8 | JH603183.1 BLAST exon 3853078 3854281 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 9 | JH603183.1 BLAST exon 3854315 3855759 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 10 | JH603183.1 BLAST exon 3855840 3856104 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 11 | JH603183.1 BLAST exon 3857358 3857949 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 12 | JH603183.1 BLAST exon 3858329 3858807 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 13 | JH603183.1 BLAST exon 3859427 3859501 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 14 | JH603225.1 BLAST exon 4705067 4705152 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 15 | JH603225.1 BLAST exon 4703690 4704218 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 16 | JH603178.1 BLAST exon 15171586 15171630 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 17 | JH603178.1 BLAST exon 15170974 15171551 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 18 | -------------------------------------------------------------------------------- /piper-nf/docker_4/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/docker_4/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/docker_5/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/docker_5/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/docker_5/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/docker_5/result/gen4.ex.gtf: -------------------------------------------------------------------------------- 1 | JH603219.1 BLAST exon 3054083 3055022 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 2 | JH603219.1 BLAST exon 3055479 3056661 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 3 | JH603219.1 BLAST exon 3056701 3056837 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 4 | JH603219.1 BLAST exon 3057448 3057916 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 5 | JH603219.1 BLAST exon 3058115 3058526 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 6 | JH603219.1 BLAST exon 3059853 3060011 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 7 | JH603215.1 BLAST exon 6352355 6352920 . + . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 8 | JH603183.1 BLAST exon 3853078 3854281 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 9 | JH603183.1 BLAST exon 3854315 3855759 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 10 | JH603183.1 BLAST exon 3855840 3856104 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 11 | JH603183.1 BLAST exon 3857358 3857949 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 12 | JH603183.1 BLAST exon 3858329 3858807 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 13 | JH603183.1 BLAST exon 3859427 3859501 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 14 | JH603225.1 BLAST exon 4705067 4705152 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 15 | JH603225.1 BLAST exon 4703690 4704218 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 16 | JH603178.1 BLAST exon 15171586 15171630 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 17 | JH603178.1 BLAST exon 15170974 15171551 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 18 | -------------------------------------------------------------------------------- /piper-nf/docker_5/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/docker_5/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/docker_6/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/docker_6/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/docker_6/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/docker_6/result/gen4.ex.gtf: -------------------------------------------------------------------------------- 1 | JH603219.1 BLAST exon 3054083 3055022 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 2 | JH603219.1 BLAST exon 3055479 3056661 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 3 | JH603219.1 BLAST exon 3056701 3056837 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 4 | JH603219.1 BLAST exon 3057448 3057916 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 5 | JH603219.1 BLAST exon 3058115 3058526 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 6 | JH603219.1 BLAST exon 3059853 3060011 . + . query_id "CUFF.115238.2"; hitName "CUFF.115238.2_hit1"; gene_id "FAKE__CUFF.115238.2"; transcript_id "CUFF.115238.2"; 7 | JH603215.1 BLAST exon 6352355 6352920 . + . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 8 | JH603183.1 BLAST exon 3853078 3854281 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 9 | JH603183.1 BLAST exon 3854315 3855759 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 10 | JH603183.1 BLAST exon 3855840 3856104 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 11 | JH603183.1 BLAST exon 3857358 3857949 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 12 | JH603183.1 BLAST exon 3858329 3858807 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 13 | JH603183.1 BLAST exon 3859427 3859501 . + . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 14 | JH603225.1 BLAST exon 4705067 4705152 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 15 | JH603225.1 BLAST exon 4703690 4704218 . - . query_id "CUFF.71472.2"; hitName "CUFF.71472.2_hit1"; gene_id "FAKE__CUFF.71472.2"; transcript_id "CUFF.71472.2"; 16 | JH603178.1 BLAST exon 15171586 15171630 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 17 | JH603178.1 BLAST exon 15170974 15171551 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 18 | -------------------------------------------------------------------------------- /piper-nf/docker_6/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/docker_6/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/docker_7/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/docker_7/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/docker_7/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/docker_7/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/docker_7/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/docker_8/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/docker_8/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/docker_8/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/docker_8/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/docker_8/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/docker_9/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/docker_9/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/docker_9/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/docker_9/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/docker_9/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/fig_correlation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/fig_correlation.png -------------------------------------------------------------------------------- /piper-nf/native_1/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/native_1/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/native_1/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/native_1/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/native_1/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/native_10/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/native_10/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/native_10/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/native_10/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/native_10/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/native_2/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/native_2/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/native_2/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/native_2/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/native_2/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/native_3/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/native_3/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/native_3/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/native_3/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/native_3/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/native_4/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/native_4/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/native_4/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/native_4/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/native_4/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/native_5/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/native_5/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/native_5/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/native_5/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/native_5/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/native_6/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/native_6/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/native_6/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/native_6/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/native_6/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/native_7/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/native_7/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/native_7/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/native_7/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/native_7/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/native_8/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/native_8/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/native_8/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/native_8/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/native_8/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/native_9/result/gen2.ex.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/piper-nf/native_9/result/gen2.ex.gtf -------------------------------------------------------------------------------- /piper-nf/native_9/result/gen3.ex.gtf: -------------------------------------------------------------------------------- 1 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 26805 28710 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25871 26740 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | scaffold:ChrPicBel3.0.1:JH584413.1:1:3366583:1 BLAST exon 25571 25818 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 4 | -------------------------------------------------------------------------------- /piper-nf/native_9/result/gen8.ex.gtf: -------------------------------------------------------------------------------- 1 | JH208510.1 BLAST exon 1147359 1149269 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 2 | JH208510.1 BLAST exon 1146203 1147327 . - . query_id "CUFF.42845.2"; hitName "CUFF.42845.2_hit1"; gene_id "FAKE__CUFF.42845.2"; transcript_id "CUFF.42845.2"; 3 | JH208064.1 BLAST exon 638021 638519 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 4 | JH208064.1 BLAST exon 620428 620462 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 5 | -------------------------------------------------------------------------------- /piper-nf/native_9/result/gen9.ex.gtf: -------------------------------------------------------------------------------- 1 | 1 BLAST exon 107237250 107237597 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 2 | 1 BLAST exon 107223051 107223453 . - . query_id "CUFF.13755.2"; hitName "CUFF.13755.2_hit1"; gene_id "FAKE__CUFF.13755.2"; transcript_id "CUFF.13755.2"; 3 | 3 BLAST exon 18611962 18613160 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 4 | 3 BLAST exon 18610503 18611925 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 5 | 3 BLAST exon 18610160 18610413 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 6 | 3 BLAST exon 18608025 18609157 . - . query_id "CUFF.77894.3"; hitName "CUFF.77894.3_hit1"; gene_id "FAKE__CUFF.77894.3"; transcript_id "CUFF.77894.3"; 7 | Un BLAST exon 86679235 86679435 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 8 | Un BLAST exon 86678445 86678573 . - . query_id "CUFF.132887.3"; hitName "CUFF.132887.3_hit1"; gene_id "FAKE__CUFF.132887.3"; transcript_id "CUFF.132887.3"; 9 | 6 BLAST exon 32760104 32760592 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 10 | 6 BLAST exon 32752325 32752415 . - . query_id "CUFF.115782.2"; hitName "CUFF.115782.2_hit1"; gene_id "FAKE__CUFF.115782.2"; transcript_id "CUFF.115782.2"; 11 | 9 BLAST exon 22734950 22735576 . - . query_id "CUFF.128925.1"; hitName "CUFF.128925.1_hit1"; gene_id "FAKE__CUFF.128925.1"; transcript_id "CUFF.128925.1"; 12 | -------------------------------------------------------------------------------- /piper-nf/plot.csv: -------------------------------------------------------------------------------- 1 | name,realtime_docker,realtime_native 2 | blast,31146.666666667,6301.4444444444 3 | blast,29505.111111111,6864.2222222222 4 | blast,40868.222222222,6491 5 | blast,24392.555555556,6516 6 | blast,44983.666666667,6505.7777777778 7 | blast,49012.111111111,6489.8888888889 8 | blast,44739.222222222,6434.6666666667 9 | blast,7261.1111111111,6467.3333333333 10 | blast,31045.111111111,7154.4444444444 11 | blast,31068.111111111,6739.4444444444 12 | exonerate,121584.91666667,122149.08333333 13 | exonerate,120918.83333333,124430.91666667 14 | exonerate,112629.66666667,123610.75 15 | exonerate,114895,120650.75 16 | exonerate,122405.83333333,112832.16666667 17 | exonerate,144380.91666667,124799.33333333 18 | exonerate,116671.91666667,127432.91666667 19 | exonerate,131335.08333333,120905.5 20 | exonerate,151931.66666667,121869.91666667 21 | exonerate,142371.08333333,120041.08333333 22 | formatBlast,104239.33333333,51481.666666667 23 | formatBlast,121674.11111111,50359.555555556 24 | formatBlast,113656.44444444,50584.111111111 25 | formatBlast,121415,52903.111111111 26 | formatBlast,146624.88888889,53131 27 | formatBlast,98414.333333333,52462.111111111 28 | formatBlast,128060.44444444,52475.555555556 29 | formatBlast,106843.22222222,52118.666666667 30 | formatBlast,112685.22222222,53684.444444444 31 | formatBlast,114934,54919.444444444 32 | formatChr,268906.33333333,154991.77777778 33 | formatChr,248231.77777778,152795.22222222 34 | formatChr,260874.33333333,154333.22222222 35 | formatChr,262093.66666667,152819.33333333 36 | formatChr,245606.66666667,157574.55555556 37 | formatChr,261269.88888889,161422.33333333 38 | formatChr,245731.77777778,157442.77777778 39 | formatChr,270959.66666667,155567.33333333 40 | formatChr,273030.77777778,153337.22222222 41 | formatChr,268424.88888889,151686.44444444 42 | similarity,11663.434782609,2522.4130434783 43 | similarity,11342.673913043,2420.1086956522 44 | similarity,11892.956521739,2631.2173913043 45 | similarity,12191.282608696,2516.3043478261 46 | similarity,11688.065217391,2415.8913043478 47 | similarity,12592.847826087,2424.7173913043 48 | similarity,12282.086956522,2425.2391304348 49 | similarity,12350.608695652,2530.3695652174 50 | similarity,12633.086956522,2641.9347826087 51 | similarity,12695.369565217,3338.152173913 52 | -------------------------------------------------------------------------------- /piper-nf/plot.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | function stats() { 4 | STAGES=$(tail -n +2 $1 | cut -f 4 | cut -f 1 -d ' ' | sort | uniq) 5 | for x in $STAGES; do 6 | row=$(cat $1 | grep $x | sed 's/-/0/g' | datamash median 19 mean 19 median 20 mean 20 count 1) 7 | printf "$x\t$row\n" 8 | done 9 | } 10 | 11 | for file in ${1}_{1..10}/trace.csv;do 12 | stats $file 13 | done 14 | -------------------------------------------------------------------------------- /piper-nf/stage.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | function stats() { 4 | STAGES=$(cat trace_${1}.txt | cut -f 4 | cut -f 1 -d ' ' | uniq | sort) 5 | for x in $STAGES; do 6 | row=$(cat trace_${1}.txt | grep $x | sed 's/-/0/g' | datamash median 19 mean 19 median 20 mean 20 count 1) 7 | printf "$x\t$row\n" 8 | done 9 | 10 | row=$(cat trace_${1}.txt | sed 's/-/0/g' | datamash median 19 mean 19 median 20 mean 20 count 1) 11 | printf "ALL\t$row\n" 12 | } 13 | 14 | echo $1 | awk '{print toupper($0)}' 15 | stats $1 16 | -------------------------------------------------------------------------------- /piper-nf/stats_docker.txt: -------------------------------------------------------------------------------- 1 | DOCKER 2 | blast 16585 33402.188888889 5259.5 6258.5666666667 90 3 | exonerate 55761 127912.49166667 46882 118422.49166667 120 4 | formatBlast 99899 116854.7 55382 67711.277777778 90 5 | formatChr 200097 260512.97777778 168780.5 219768.33333333 90 6 | matrix 1450 1546.2 37.5 37.6 10 7 | normExonerate 4 9.7916666666667 1 2.9583333333333 120 8 | similarity 12153 12133.241304348 717.5 1192.8086956522 460 9 | ALL 12978.5 59098.68877551 1346 42037.304081633 980 10 | -------------------------------------------------------------------------------- /piper-nf/stats_native.txt: -------------------------------------------------------------------------------- 1 | NATIVE 2 | blast 5805.5 6596.4222222222 3729 4105.9888888889 90 3 | exonerate 45061 121872.24166667 44562.5 119269.69166667 120 4 | formatBlast 41769.5 52411.966666667 39449 49817.444444444 90 5 | formatChr 102461 155197.02222222 101346 152771.58888889 90 6 | matrix 208.5 207.4 167.5 166.2 10 7 | normExonerate 4 9.85 1 0.68333333333333 120 8 | similarity 493 2586.6347826087 390 898.21086956522 460 9 | ALL 5515.5 35812.514285714 962 34010.036734694 980 10 | -------------------------------------------------------------------------------- /piper-nf/table.R: -------------------------------------------------------------------------------- 1 | native <- read.delim("time_native.txt", header=TRUE) 2 | docker <- read.delim("time_docker.txt", header=TRUE) 3 | 4 | stderr <- function(x) sd(x)/sqrt(length(x)) 5 | 6 | native_mean_exec_time = mean(native$duration) / 1000 /60 7 | docker_mean_exec_time = mean(docker$duration) / 1000 /60 8 | 9 | native_err = stderr(native$duration) / 1000 /60 10 | docker_err = stderr(docker$duration) / 1000 /60 11 | 12 | native_stdev_exec_time = sd(native$duration) / 1000 /60 13 | docker_stddev_exec_time = sd(docker$duration) / 1000 /60 14 | 15 | # each instance executes 98 instances 16 | native_mean_task_time = native_mean_exec_time / 98 17 | docker_mean_task_time = docker_mean_exec_time / 98 18 | 19 | cat(sprintf("PIPER : native docker\n")) 20 | cat(sprintf("Task mean time : %.1f %.1f\n", native_mean_task_time, docker_mean_task_time)) 21 | cat(sprintf("Mean exec time : %.1f (±%.1f) %.1f (±%.1f) \n", native_mean_exec_time, native_err, docker_mean_exec_time, docker_err)) 22 | cat(sprintf("Stddev exec time: %.1f %.1f\n", native_stdev_exec_time, docker_stddev_exec_time)) 23 | cat(sprintf("Slow-down : %.3f\n" , docker_mean_exec_time/native_mean_exec_time)) 24 | -------------------------------------------------------------------------------- /piper-nf/table.txt: -------------------------------------------------------------------------------- 1 | PIPER : native docker 2 | Task mean time : 0.6 1.0 3 | Mean exec time : 58.5 (±0.2) 96.5 (±0.8) 4 | Stddev exec time: 0.6 2.6 5 | Slow-down : 1.650 6 | -------------------------------------------------------------------------------- /piper-nf/time.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | function gettime { 4 | 5 | printf "begin\tend\telapsed\tdelta\tduration\trealtime\n" 6 | for x in ${1}_{1..10}; do 7 | duration=$(tail -n +2 $x/trace.csv | sed 's/-/0/g' | datamash sum 19) 8 | realtime=$(tail -n +2 $x/trace.csv | sed 's/-/0/g' | datamash sum 20) 9 | delta=$(groovy delta.groovy "$(cat $x/.nextflow.log | head -n 1 | cut -f 1,2 -d ' ')" "$(cat $x/.nextflow.log | tail -n 1 | cut -f 1,2 -d ' ')") 10 | printf "$delta\t$duration\t$realtime\n" 11 | done 12 | 13 | } 14 | 15 | gettime $1 16 | 17 | -------------------------------------------------------------------------------- /piper-nf/time_docker.txt: -------------------------------------------------------------------------------- 1 | begin end elapsed delta duration realtime 2 | May-10 09:14:33.517 May-10 09:27:00.775 0:12:27 747258 5653040 4104952 3 | May-10 09:36:52.812 May-10 09:49:32.283 0:12:39 759471 5819617 4161389 4 | May-10 09:59:11.977 May-10 10:14:00.767 0:14:48 888790 5865334 4243833 5 | May-10 10:24:47.769 May-10 10:39:10.191 0:14:22 862422 5828507 4158720 6 | May-10 10:50:21.181 May-10 11:05:16.049 0:14:54 894868 5980631 4169272 7 | May-10 11:16:29.647 May-10 11:30:24.258 0:13:54 834611 5980202 4306470 8 | May-10 11:40:38.589 May-10 11:54:42.048 0:14:3 843459 5917244 4063902 9 | May-10 12:05:19.078 May-10 12:19:24.738 0:14:5 845660 5732180 4123930 10 | May-10 12:29:25.994 May-10 12:42:34.787 0:13:8 788793 5515195 3940912 11 | May-10 12:53:35.517 May-10 13:05:50.692 0:12:15 735175 5624765 3923178 12 | -------------------------------------------------------------------------------- /piper-nf/time_native.txt: -------------------------------------------------------------------------------- 1 | begin end elapsed delta duration realtime 2 | May-10 09:27:19.810 May-10 09:36:34.612 0:9:14 554802 3516791 3317701 3 | May-10 09:49:50.899 May-10 09:58:53.228 0:9:2 542329 3544082 3355773 4 | May-10 10:14:19.455 May-10 10:24:29.719 0:10:10 610264 3563241 3392197 5 | May-10 10:39:28.463 May-10 10:50:02.465 0:10:34 634002 3496067 3329339 6 | May-10 11:05:38.291 May-10 11:16:11.360 0:10:33 633069 3503797 3329395 7 | May-10 11:30:43.017 May-10 11:40:19.337 0:9:36 576320 3449072 3271328 8 | May-10 11:55:00.972 May-10 12:05:00.868 0:9:59 599896 3547148 3382713 9 | May-10 12:19:45.090 May-10 12:29:07.822 0:9:22 562732 3475863 3298704 10 | May-10 12:42:53.304 May-10 12:53:15.393 0:10:22 622089 3534570 3359150 11 | May-10 13:06:09.276 May-10 13:15:54.695 0:9:45 585419 3465633 3293536 12 | -------------------------------------------------------------------------------- /rnaseq-toy/Figures.R: -------------------------------------------------------------------------------- 1 | library(reshape) 2 | library(ggplot2) 3 | library(grid) 4 | NF_stats<-read.csv("plot.csv",header=T) 5 | NF_stats = cbind(NF_stats, shape=rep("16",dim(NF_stats)[1])) 6 | 7 | nL = dim(read.table("stats_docker.txt", skip=1, header=F))[1] 8 | 9 | NF_median = data.frame(list( name = c("median"), realtime_docker = read.table("stats_docker.txt", skip=nL, header=F)[,2], realtime_native = read.table("stats_native.txt", skip=nL, header=F)[,2], shape = c("6"))) 10 | NF_mean = data.frame(list( name = c("mean"), realtime_docker = read.table("stats_docker.txt", skip=nL, header=F)[,3], realtime_native = read.table("stats_native.txt", skip=nL, header=F)[,3], shape = c("8"))) 11 | 12 | png(filename = "fig_correlation.png", width = 5, height = 4, units = 'in', res = 300) 13 | max_axis = max(c(NF_stats[,2], NF_stats[,3]))/1000/60 * 1.08 14 | qplot(x=(realtime_docker/1000)/60, y=(realtime_native/1000)/60, data=NF_stats, main="", color=name, ylab="Native tasks avg. time (mins)", xlab="Docker tasks avg. time (mins)") + 15 | geom_point(size = 3, aes(shape = shape)) + 16 | geom_point( data = NF_median, aes(x=(realtime_docker/1000)/60, y=(realtime_native/1000)/60, shape = shape, color = NA), size = 3) + 17 | geom_point( data = NF_mean, aes(x=(realtime_docker/1000)/60, y=(realtime_native/1000)/60, shape = shape, color = NA), size = 3) + 18 | coord_cartesian(xlim=c(0,max_axis), ylim=c(0,max_axis)) + 19 | scale_shape_manual(values = c(16, 6, 8), breaks = c("6","8"), labels = c("median","mean")) + 20 | geom_abline(intercept = 0, size=.2)+ 21 | theme(axis.text.x=element_text(size=10), axis.text.y=element_text(size=10), axis.title.y=element_text(size=8), axis.title.x=element_text(size=8),legend.text=element_text(size=8),legend.title=element_text(size=8)) + 22 | labs(color = "Task", title='RNA-Seq', shape = "") 23 | dev.off() 24 | -------------------------------------------------------------------------------- /rnaseq-toy/README.md: -------------------------------------------------------------------------------- 1 | RNAToy stats 2 | ================ 3 | 4 | This folder contains the log files for the RNAToy pipeline executions. 5 | 6 | To generate the figures use the `make` command. It creates the following 7 | assets: 8 | 9 | * `time_native.txt`: Summary table of times for `native` executions 10 | * `time_docker.txt`: Summary table of times for `docker` executions 11 | * `fig_wall_time.png`: Box plot of pipeline wall-clock execution time 12 | * `fig_run_time.png`: Box plot of pipeline aggregate tasks run-time 13 | * `fig_correlation.png`: Correlation between docker and native tasks time execution 14 | -------------------------------------------------------------------------------- /rnaseq-toy/config/docker.config: -------------------------------------------------------------------------------- 1 | params.pair1 = '../data/*_sub_1.fastq.gz' 2 | params.pair2 = '../data/*_sub_2.fastq.gz' 3 | params.annot = '../data/mm65.long.ok.gtf' 4 | params.genome = '../data/mouse_genome_mm9.fa' 5 | 6 | process.container = 'nextflow/rnatoy:sl65' 7 | process.time = '8h' 8 | 9 | process.$mapping.cpus = 8 10 | process.$makeTranscript.cpus = 8 11 | 12 | docker.enabled = true 13 | 14 | trace { 15 | enabled=true 16 | fields = 'task_id,hash,native_id,name,status,exit,submit,duration,realtime,%cpu,rss,vmem,peak_rss,peak_vmem,rchar,wchar,duration:num,realtime:num,rss:num,vmem:num,peak_rss:num,peak_vmem:num,rchar:num,wchar:num,syscr,syscw,read_bytes:num,write_bytes:num' 17 | } 18 | 19 | -------------------------------------------------------------------------------- /rnaseq-toy/config/native.config: -------------------------------------------------------------------------------- 1 | params.pair1 = '../data/*_sub_1.fastq.gz' 2 | params.pair2 = '../data/*_sub_2.fastq.gz' 3 | params.annot = '../data/mm65.long.ok.gtf' 4 | params.genome = '../data/mouse_genome_mm9.fa' 5 | 6 | process.memory = '8G' 7 | process.time = '8h' 8 | 9 | process.$mapping.cpus = 8 10 | process.$makeTranscript.cpus = 8 11 | 12 | trace { 13 | enabled=true 14 | fields = 'task_id,hash,native_id,name,status,exit,submit,duration,realtime,%cpu,rss,vmem,peak_rss,peak_vmem,rchar,wchar,duration:num,realtime:num,rss:num,vmem:num,peak_rss:num,peak_vmem:num,rchar:num,wchar:num,syscr,syscw,read_bytes:num,write_bytes:num' 15 | } 16 | 17 | env { 18 | PATH="/scratch/tmp/rnatoy-mouse/bowtie2-2.2.3:/scratch/tmp/rnatoy-mouse/cufflinks-2.2.1.Linux_x86_64:/scratch/tmp/rnatoy-mouse/tophat-2.0.12.Linux_x86_64:$PATH" 19 | } 20 | -------------------------------------------------------------------------------- /rnaseq-toy/delta.groovy: -------------------------------------------------------------------------------- 1 | ../scripts/delta.groovy -------------------------------------------------------------------------------- /rnaseq-toy/docker_1/log_docker_1: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [ab/7a2bf4] Submitted process > buildIndex (1) 11 | [b3/06c896] Submitted process > mapping (3) 12 | [7f/e3f762] Submitted process > mapping (4) 13 | [c9/efef6b] Submitted process > mapping (2) 14 | [31/cd8dd5] Submitted process > mapping (1) 15 | [a6/1c1227] Submitted process > makeTranscript (1) 16 | [b7/477d3a] Submitted process > makeTranscript (2) 17 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [35/2b10a5] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [06/9dd480] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_1/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 ab/7a2bf4 15568 buildIndex (1) COMPLETED 0 2015-05-04 21:30:06.357 1h 36m 57s 1h 36m 56s 99.8% 4.5 GB 4.6 GB 4.6 GB 4.6 GB 10.1 GB 3.4 GB 5817432 5815728 4829069312 4979990528 4936048640 4980813824 10832504233 3623229245 41493 374436 5165056 3623497728 3 | 2 31/cd8dd5 2706 mapping (1) COMPLETED 0 2015-05-04 23:07:03.866 4h 5m 43s 4h 5m 37s 359.3% 5.7 GB 7 GB 5.8 GB 7.1 GB 132.2 GB 54.9 GB 14743480 14737426 6173208576 7531311104 6264094720 7622979584 141938712489 58977320388 67426992 96209723 20267008 11808358400 4 | 4 b3/06c896 2708 mapping (3) COMPLETED 0 2015-05-04 23:07:03.866 4h 12m 30s 4h 12m 24s 779.9% 5.2 GB 6.2 GB 5.2 GB 6.2 GB 135.7 GB 57.8 GB 15149666 15144295 5600018432 6630617088 5604589568 6698242048 145700100323 62033527023 70720744 96861226 20267008 12509634560 5 | 6 a6/1c1227 15040 makeTranscript (1) COMPLETED 0 2015-05-05 03:12:49.541 7m 19s 6m 37s 281.0% 812.2 MB 1.4 GB 1 GB 1.8 GB 3.1 GB 182 MB 438766 396600 851668992 1453428736 1107685376 1979838464 3343415504 190812351 456124 264405 2990080 190943232 6 | 7 b7/477d3a 30865 makeTranscript (2) COMPLETED 0 2015-05-05 03:19:33.542 5m 17s 4m 36s 436.0% 667 MB 1.2 GB 1 GB 1.6 GB 3.3 GB 182.2 MB 316756 275913 699441152 1319964672 1126207488 1733132288 3516271059 191074686 468220 264791 2990080 191139840 7 | 3 c9/efef6b 2714 mapping (2) COMPLETED 0 2015-05-04 23:07:03.866 4h 19m 34s 4h 19m 28s 651.5% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 157.4 GB 74.9 GB 15573718 15568102 6826414080 8176680960 6830743552 8181149696 169054130844 80470225050 64574009 114994292 20267008 18273177600 8 | 8 35/2b10a5 8691 makeTranscript (3) COMPLETED 0 2015-05-05 03:26:37.596 5m 40s 5m 36s 400.0% 832.7 MB 1.4 GB 1 GB 1.7 GB 4.6 GB 181.8 MB 340358 335551 873132032 1471242240 1100906496 1789517824 4936996092 190598655 557904 263726 2990080 190685184 9 | 5 7f/e3f762 2710 mapping (4) COMPLETED 0 2015-05-04 23:07:03.866 4h 36m 50s 4h 36m 46s 807.7% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 166.9 GB 84.7 GB 16610240 16605552 6852366336 8202592256 6862811136 8213819392 179246816856 90895237540 53925013 148351045 20267008 18073571328 10 | 9 06/9dd480 24069 makeTranscript (4) COMPLETED 0 2015-05-05 03:43:54.118 5m 30s 5m 24s 430.0% 667.7 MB 1.2 GB 1 GB 1.6 GB 4.1 GB 184.8 MB 329569 323689 700170240 1328721920 1096142848 1731391488 4427960718 193790728 560495 269105 2990080 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_10/log_docker_10: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [95/6ff967] Submitted process > buildIndex (1) 11 | [c3/36bc07] Submitted process > mapping (4) 12 | [9f/dacfb4] Submitted process > mapping (1) 13 | [d7/ce353e] Submitted process > mapping (2) 14 | [ab/e433a7] Submitted process > mapping (3) 15 | [de/a96cc9] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [7b/8a35f2] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [3d/d11cce] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [89/f4062d] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_10/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 95/6ff967 8458 buildIndex (1) COMPLETED 0 2015-05-07 06:33:11.347 1h 38m 5s 1h 38m 3s 99.8% 4.5 GB 4.6 GB 4.6 GB 4.6 GB 10.1 GB 3.4 GB 5885340 5883181 4831162368 4979990528 4936044544 4980813824 10832504233 3611965245 41493 373061 5165056 3612241920 3 | 2 9f/dacfb4 28269 mapping (1) COMPLETED 0 2015-05-07 08:11:16.768 4h 3m 59s 4h 3m 52s 783.6% 5.8 GB 7.1 GB 5.9 GB 7.1 GB 132.2 GB 54.9 GB 14639369 14632338 6243389440 7600246784 6370324480 7622979584 141939731529 58984115669 74943940 96205269 316104704 11858104320 4 | 6 de/a96cc9 27380 makeTranscript (1) COMPLETED 0 2015-05-07 12:15:18.417 5m 30s 5m 21s 361.0% 952.3 MB 1.7 GB 1.1 GB 1.9 GB 3.1 GB 185 MB 329580 320541 998551552 1789308928 1228939264 2040995840 3364872495 194006049 458644 269562 3121152 194260992 5 | 5 c3/36bc07 28268 mapping (4) COMPLETED 0 2015-05-07 08:11:16.767 4h 17m 4s 4h 16m 56s 574.8% 5.2 GB 6.2 GB 5.2 GB 6.2 GB 135.7 GB 57.8 GB 15423933 15416126 5584515072 6630449152 5591019520 6696325120 145683167547 62035357925 73500786 96845458 376291328 12564590592 6 | 7 7b/8a35f2 30489 makeTranscript (2) COMPLETED 0 2015-05-07 12:28:20.709 4m 59s 4m 53s 413.0% 760.9 MB 1.2 GB 1 GB 1.8 GB 3.3 GB 181.5 MB 299314 292870 797904896 1340690432 1096282112 1976168448 3513329188 190338357 467890 263566 3121152 190410752 7 | 4 ab/e433a7 28275 mapping (3) COMPLETED 0 2015-05-07 08:11:16.768 4h 25m 3s 4h 24m 56s 682.5% 6.3 GB 7.6 GB 6.4 GB 7.6 GB 157.5 GB 75 GB 15903252 15895832 6817566720 8176680960 6822076416 8181149696 169146583847 80487080078 60628315 115051189 887922688 18336751616 8 | 8 3d/d11cce 8826 makeTranscript (3) COMPLETED 0 2015-05-07 12:36:20.030 5m 55s 5m 48s 387.0% 768.6 MB 1.3 GB 1 GB 1.9 GB 4.6 GB 181.8 MB 354907 347959 805974016 1437175808 1102614528 1990848512 4937471393 190635468 557950 263797 3121152 190730240 9 | 3 d7/ce353e 28271 mapping (2) COMPLETED 0 2015-05-07 08:11:16.768 4h 40m 45s 4h 40m 39s 803.2% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 166.9 GB 84.6 GB 16844849 16838981 6849699840 8202592256 6860644352 8213819392 179256615992 90891492106 75415323 148361514 786587648 18077913088 10 | 9 89/f4062d 23409 makeTranscript (4) COMPLETED 0 2015-05-07 12:52:01.628 5m 23s 5m 19s 433.0% 819 MB 1.4 GB 1 GB 1.6 GB 4.1 GB 184.8 MB 323448 319349 858820608 1460113408 1103843328 1762119680 4427960718 193790728 560495 269105 3121152 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_2/log_docker_2: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [ab/fbf032] Submitted process > buildIndex (1) 11 | [e4/1b810b] Submitted process > mapping (3) 12 | [78/d1191d] Submitted process > mapping (4) 13 | [cb/a851fc] Submitted process > mapping (1) 14 | [db/8b97d0] Submitted process > mapping (2) 15 | [57/1894a2] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [22/0e835a] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [45/d1525a] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [45/7e87b7] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_2/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 ab/fbf032 18433 buildIndex (1) COMPLETED 0 2015-05-05 09:55:48.242 1h 38m 36s 1h 38m 34s 99.8% 4.5 GB 4.6 GB 4.6 GB 4.6 GB 10.1 GB 3.4 GB 5916036 5914190 4829057024 4979990528 4936036352 4980813824 10832504233 3610515261 41493 372884 5165056 3610791936 3 | 3 db/8b97d0 5519 mapping (2) COMPLETED 0 2015-05-05 11:34:24.369 4h 22s 4h 16s 774.0% 5.8 GB 7 GB 5.8 GB 7.1 GB 132.2 GB 54.9 GB 14422004 14415570 6177128448 7531343872 6268010496 7623012352 141919757289 58976763343 74875997 96193797 20824064 11808501760 4 | 6 57/1894a2 24225 makeTranscript (1) COMPLETED 0 2015-05-05 15:34:47.359 5m 49s 5m 39s 338.0% 773.1 MB 1.4 GB 1 GB 1.9 GB 3.1 GB 182.2 MB 348712 339298 810672128 1455517696 1094295552 2030174208 3345283096 191039028 456332 264893 2990080 191139840 5 | 4 e4/1b810b 5513 mapping (3) COMPLETED 0 2015-05-05 11:34:24.364 4h 13m 10s 4h 13m 3s 616.4% 5.2 GB 6.2 GB 5.2 GB 6.2 GB 135.7 GB 57.8 GB 15190104 15182733 5587791872 6630588416 5592797184 6700752896 145690807091 62050484454 72777447 96841983 21172224 12528361472 6 | 7 22/0e835a 28491 makeTranscript (2) COMPLETED 0 2015-05-05 15:47:34.476 4m 59s 4m 54s 410.0% 873.5 MB 1.5 GB 1 GB 1.7 GB 3.3 GB 183.6 MB 299296 293906 915918848 1569820672 1096531968 1825173504 3527209229 192509359 469460 267258 2990080 192577536 7 | 2 cb/a851fc 5517 mapping (1) COMPLETED 0 2015-05-05 11:34:24.369 4h 22m 4h 21m 53s 528.6% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 157.5 GB 75 GB 15719547 15713289 6826360832 8176680960 6830690304 8181149696 169123821226 80480653471 64024409 115037938 21299200 18287804416 8 | 8 45/d1525a 8502 makeTranscript (3) COMPLETED 0 2015-05-05 15:56:23.927 5m 57s 5m 52s 387.0% 722.9 MB 1.5 GB 1 GB 1.9 GB 4.6 GB 182.6 MB 357017 351765 758030336 1598656512 1103511552 2041184256 4947249644 191503378 558898 265440 2990080 191594496 9 | 5 78/d1191d 5514 mapping (4) COMPLETED 0 2015-05-05 11:34:24.364 4h 37m 48s 4h 37m 41s 829.4% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 166.9 GB 84.6 GB 16668382 16660630 6850265088 8202625024 6860709888 8213852160 179235427414 90883803967 56181398 148374995 20762624 18062082048 10 | 9 45/7e87b7 22233 makeTranscript (4) COMPLETED 0 2015-05-05 16:12:12.760 5m 22s 5m 19s 433.0% 897.4 MB 1.4 GB 1 GB 1.6 GB 4.1 GB 184.8 MB 322321 318624 940957696 1506385920 1097560064 1758064640 4427960718 193790728 560495 269105 2990080 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_3/log_docker_3: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [e7/a5d1dd] Submitted process > buildIndex (1) 11 | [5b/8eb1e7] Submitted process > mapping (1) 12 | [1d/e2be26] Submitted process > mapping (2) 13 | [d4/8ce70e] Submitted process > mapping (4) 14 | [18/af15ae] Submitted process > mapping (3) 15 | [a5/cc3703] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [c4/b4589e] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [45/ae2776] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [43/dbd866] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_3/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 e7/a5d1dd 25470 buildIndex (1) COMPLETED 0 2015-05-05 22:36:39.323 1h 40m 28s 1h 40m 26s 99.8% 4.5 GB 4.6 GB 4.6 GB 4.6 GB 10.1 GB 3.4 GB 6027755 6025572 4829069312 4979990528 4936048640 4980813824 10832504233 3625596733 41493 374725 5165056 3625877504 3 | 2 5b/8eb1e7 14066 mapping (1) COMPLETED 0 2015-05-06 00:17:07.178 4h 3m 33s 4h 3m 26s 753.9% 5.7 GB 7 GB 5.8 GB 7.1 GB 132.2 GB 54.9 GB 14612522 14605675 6165749760 7531278336 6257143808 7622946816 141950184570 58965724650 74917241 96228009 207441920 11826098176 4 | 6 a5/cc3703 13367 makeTranscript (1) COMPLETED 0 2015-05-06 04:20:40.580 6m 22s 6m 16s 301.0% 886.5 MB 1.5 GB 1.1 GB 1.9 GB 3.1 GB 184.2 MB 382146 375574 929579008 1597173760 1226715136 2039701504 3361173717 193134806 458192 268411 2990080 193351680 5 | 4 18/af15ae 14073 mapping (3) COMPLETED 0 2015-05-06 00:17:07.181 4h 13m 43s 4h 13m 37s 513.7% 5.2 GB 6.2 GB 5.2 GB 6.2 GB 135.7 GB 57.8 GB 15223088 15216736 5577601024 6630440960 5592449024 6700605440 145665765211 62052602082 73217257 96830650 316715008 12545744896 6 | 7 c4/b4589e 9980 makeTranscript (2) COMPLETED 0 2015-05-06 04:30:50.276 5m 3s 4m 52s 406.0% 910.4 MB 1.5 GB 1 GB 1.9 GB 3.3 GB 180.4 MB 302755 291533 954626048 1587384320 1096777728 2026504192 3501807409 189143468 466532 261605 2990080 189210624 7 | 3 1d/e2be26 14068 mapping (2) COMPLETED 0 2015-05-06 00:17:07.180 4h 21m 32s 4h 21m 26s 770.5% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 157.5 GB 74.9 GB 15692379 15685535 6823342080 8176680960 6828032000 8181149696 169073387717 80476250262 62294318 115004296 783003648 18337312768 8 | 8 45/ae2776 20295 makeTranscript (3) COMPLETED 0 2015-05-06 04:38:39.573 5m 39s 5m 35s 403.0% 818.7 MB 1.3 GB 1 GB 1.6 GB 4.6 GB 183 MB 338607 334966 858460160 1420398592 1106046976 1722408960 4953002541 191893748 559491 266126 2990080 191971328 9 | 5 d4/8ce70e 14071 mapping (4) COMPLETED 0 2015-05-06 00:17:07.180 4h 38m 28s 4h 38m 21s 885.0% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 166.9 GB 84.6 GB 16707736 16700728 6841114624 8202592256 6851940352 8213819392 179236811006 90885135164 59583018 148379115 759910400 18063593472 10 | 9 43/dbd866 3289 makeTranscript (4) COMPLETED 0 2015-05-06 04:55:34.929 5m 25s 5m 21s 430.0% 735.5 MB 1.2 GB 1 GB 1.6 GB 4.1 GB 184.8 MB 324765 320759 771215360 1309106176 1096273920 1762119680 4427960718 193790728 560495 269105 2990080 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_4/log_docker_4: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [e2/5b684d] Submitted process > buildIndex (1) 11 | [60/e5cc51] Submitted process > mapping (2) 12 | [e4/168216] Submitted process > mapping (1) 13 | [df/d5d136] Submitted process > mapping (4) 14 | [e5/6752fc] Submitted process > mapping (3) 15 | [ce/de2a5c] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [61/fecf67] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [14/f68104] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [fe/ee0a62] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_4/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 e2/5b684d 16067 buildIndex (1) COMPLETED 0 2015-05-06 11:14:43.445 1h 31m 26s 1h 31m 24s 99.8% 4.5 GB 4.6 GB 4.6 GB 4.6 GB 10.1 GB 3.4 GB 5485727 5483505 4831154176 4979990528 4936036352 4980813824 10832504233 3628275517 41493 375052 5165056 3628511232 3 | 3 60/e5cc51 1057 mapping (2) COMPLETED 0 2015-05-06 12:46:09.258 4h 2m 27s 4h 2m 20s 789.2% 5.7 GB 7 GB 5.8 GB 7.1 GB 132.2 GB 54.9 GB 14547208 14540394 6156996608 7531311104 6252015616 7622979584 141971427959 58984583088 74968977 96232773 119009280 11830792192 4 | 6 ce/de2a5c 27525 makeTranscript (1) COMPLETED 0 2015-05-06 16:48:37.164 5m 49s 5m 41s 337.0% 846 MB 1.5 GB 1 GB 1.8 GB 3.1 GB 181.4 MB 348637 340516 887128064 1577160704 1094864896 1912725504 3339450759 190192708 455672 263391 2990080 190296064 5 | 4 e5/6752fc 1062 mapping (3) COMPLETED 0 2015-05-06 12:46:09.259 4h 15m 13s 4h 15m 8s 493.1% 5.2 GB 6.2 GB 5.2 GB 6.2 GB 135.7 GB 57.8 GB 15313129 15307539 5582299136 6630617088 5588852736 6700625920 145704984669 62051864803 71542246 96851645 458354688 12576194560 6 | 7 61/fecf67 29906 makeTranscript (2) COMPLETED 0 2015-05-06 17:01:22.398 4m 54s 4m 48s 416.0% 680.1 MB 1.3 GB 1 GB 1.6 GB 3.3 GB 181.8 MB 293770 288116 713121792 1372160000 1093836800 1707728896 3512430330 190628287 467782 263886 2990080 190693376 7 | 2 e4/168216 1058 mapping (1) COMPLETED 0 2015-05-06 12:46:09.259 4h 22m 52s 4h 22m 45s 600.2% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 157.5 GB 75 GB 15771843 15764832 6821744640 8176648192 6826307584 8181116928 169152819694 80477651086 70332948 115061247 934666240 18368290816 8 | 8 14/f68104 7487 makeTranscript (3) COMPLETED 0 2015-05-06 17:09:01.114 5m 48s 5m 44s 393.0% 869.7 MB 1.5 GB 1 GB 1.7 GB 4.6 GB 185.1 MB 347870 343732 911925248 1588174848 1109164032 1839853568 4973000629 194109410 561472 269480 2990080 194199552 9 | 5 df/d5d136 1060 mapping (4) COMPLETED 0 2015-05-06 12:46:09.259 4h 38m 43s 4h 38m 37s 885.2% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 166.9 GB 84.7 GB 16722878 16716526 6847565824 8202592256 6858072064 8213819392 179246808695 90895151544 67073852 148350885 759595008 18073567232 10 | 9 fe/ee0a62 21184 makeTranscript (4) COMPLETED 0 2015-05-06 17:24:52.149 5m 26s 5m 21s 430.0% 736.2 MB 1.2 GB 1 GB 1.7 GB 4.1 GB 185.2 MB 325850 321282 771956736 1328721920 1104048128 1781735424 4427960718 194155911 560495 269574 2990080 194236416 11 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_5/log_docker_5: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [de/9db2d4] Submitted process > buildIndex (1) 11 | [e4/ae8aa0] Submitted process > mapping (1) 12 | [b0/7383f2] Submitted process > mapping (4) 13 | [72/a0da2e] Submitted process > mapping (2) 14 | [aa/b13b5e] Submitted process > mapping (3) 15 | [d5/747a5b] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [89/443cc9] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [eb/e2f444] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [9f/5d7ad9] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_5/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 de/9db2d4 2772 buildIndex (1) COMPLETED 0 2015-05-06 23:48:39.145 1h 30m 39s 1h 30m 37s 99.8% 4.5 GB 4.6 GB 4.6 GB 4.6 GB 10.1 GB 3.4 GB 5439374 5437160 4829057024 4979994624 4936036352 4980817920 10832504233 3607230269 41493 372483 5165056 3607449600 3 | 2 e4/ae8aa0 18698 mapping (1) COMPLETED 0 2015-05-07 01:19:18.598 4h 3m 14s 4h 3m 8s 774.5% 5.7 GB 7 GB 5.8 GB 7.1 GB 132.2 GB 54.9 GB 14593920 14587810 6162989056 7531343872 6254522368 7623012352 141927246156 58984390570 74887737 96194501 143941632 11823370240 4 | 6 d5/747a5b 21089 makeTranscript (1) COMPLETED 0 2015-05-07 05:22:33.427 5m 58s 5m 48s 336.0% 866.1 MB 1.4 GB 1 GB 1.8 GB 3.1 GB 183.6 MB 358364 348465 908148736 1502711808 1112756224 1932746752 3356974043 192491668 457706 267389 2990080 192692224 5 | 4 aa/b13b5e 18704 mapping (3) COMPLETED 0 2015-05-07 01:19:18.600 4h 15m 34s 4h 15m 28s 475.0% 5.2 GB 6.2 GB 5.2 GB 6.2 GB 135.7 GB 57.8 GB 15334149 15327996 5583790080 6630449152 5589626880 6700613632 145694145977 62040834276 71948106 96850279 290537472 12563034112 6 | 7 89/443cc9 22509 makeTranscript (2) COMPLETED 0 2015-05-07 05:34:52.764 4m 55s 4m 50s 414.0% 545.9 MB 1.2 GB 1 GB 1.6 GB 3.3 GB 183.3 MB 294942 290052 572440576 1305051136 1093693440 1741889536 3525548827 192167453 469294 266700 2990080 192233472 7 | 3 72/a0da2e 18702 mapping (2) COMPLETED 0 2015-05-07 01:19:18.599 4h 23m 17s 4h 23m 10s 610.9% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 157.4 GB 75 GB 15796764 15790398 6828232704 8176680960 6832832512 8181149696 169044456601 80487711504 70089837 114976106 613875712 18324156416 8 | 8 eb/e2f444 815 makeTranscript (3) COMPLETED 0 2015-05-07 05:42:35.379 5m 48s 5m 44s 393.0% 768.7 MB 1.5 GB 1 GB 1.7 GB 4.6 GB 185 MB 348244 344142 806051840 1628016640 1112064000 1789517824 4973000629 194033477 561472 269380 2990080 194129920 9 | 5 b0/7383f2 18700 mapping (4) COMPLETED 0 2015-05-07 01:19:18.599 4h 39m 3s 4h 38m 57s 783.8% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 166.9 GB 84.6 GB 16743070 16736791 6854258688 8202559488 6864777216 8213786624 179242585273 90890935111 75224734 148350246 471044096 18072481792 10 | 9 9f/5d7ad9 15574 makeTranscript (4) COMPLETED 0 2015-05-07 05:58:21.682 5m 24s 5m 20s 432.0% 687.4 MB 1.2 GB 1 GB 1.6 GB 4.1 GB 184.8 MB 323613 319661 720760832 1309409280 1097310208 1762422784 4427960718 193790728 560495 269105 2990080 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_6/log_docker_6: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [c8/112d42] Submitted process > buildIndex (1) 11 | [53/173117] Submitted process > mapping (1) 12 | [61/814457] Submitted process > mapping (3) 13 | [84/071bd1] Submitted process > mapping (2) 14 | [db/850f3f] Submitted process > mapping (4) 15 | [e3/9dc564] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [67/b0cf88] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [6b/83b319] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [6a/095c91] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_6/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 c8/112d42 2947 buildIndex (1) COMPLETED 0 2015-05-05 03:43:40.671 1h 31m 46s 1h 31m 44s 99.9% 4.5 GB 4.6 GB 4.6 GB 4.6 GB 10.1 GB 3.4 GB 5506150 5503790 4831166464 4979990528 4936048640 4980813824 10832504233 3627685693 41493 374980 5165056 3627921408 3 | 2 53/173117 19889 mapping (1) COMPLETED 0 2015-05-05 05:15:27.481 4h 37s 4h 27s 794.1% 5.8 GB 7.1 GB 5.8 GB 7.1 GB 132.2 GB 54.9 GB 14436782 14426868 6217990144 7573344256 6267506688 7622979584 141938850600 58963844571 74963283 96220153 20258816 11794812928 4 | 6 e3/9dc564 7628 makeTranscript (1) COMPLETED 0 2015-05-05 09:16:04.593 5m 51s 5m 46s 332.0% 650.9 MB 1.3 GB 1.1 GB 1.7 GB 3.1 GB 183.9 MB 351228 346491 682471424 1375830016 1191157760 1828843520 3359141118 192831464 457966 267946 3121152 192925696 5 | 3 84/071bd1 19892 mapping (2) COMPLETED 0 2015-05-05 05:15:27.481 4h 13m 56s 4h 13m 46s 427.5% 5.2 GB 6.2 GB 5.2 GB 6.2 GB 135.7 GB 57.8 GB 15236019 15226144 5589327872 6630617088 5595013120 6700781568 145705733943 62045794533 69557832 96856391 20258816 12521955328 6 | 7 67/b0cf88 12166 makeTranscript (2) COMPLETED 0 2015-05-05 09:29:23.517 4m 55s 4m 51s 413.0% 683.9 MB 1.3 GB 1 GB 1.9 GB 3.3 GB 182.8 MB 294864 291288 717123584 1372160000 1097441280 2026504192 3521454234 191681944 468834 265829 3121152 191762432 7 | 5 db/850f3f 19894 mapping (4) COMPLETED 0 2015-05-05 05:15:27.482 4h 21m 31s 4h 21m 22s 600.4% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 157.5 GB 75 GB 15691376 15682162 6828609536 8176615424 6832939008 8181084160 169104498692 80476971163 62929290 115050061 20258816 18279845888 8 | 8 6b/83b319 22242 makeTranscript (3) COMPLETED 0 2015-05-05 09:36:58.867 5m 50s 5m 45s 392.0% 729.1 MB 1.3 GB 1 GB 1.9 GB 4.6 GB 183.8 MB 349843 345211 764563456 1386840064 1109430272 1990848512 4961212215 192706665 560286 267449 3121152 192806912 9 | 4 61/814457 19890 mapping (3) COMPLETED 0 2015-05-05 05:15:27.481 4h 37m 19s 4h 37m 10s 858.3% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 166.9 GB 84.7 GB 16638605 16629685 6857334784 8202592256 6867820544 8213819392 179246820940 90895298994 64138080 148350093 20258816 18073530368 10 | 9 6a/095c91 4701 makeTranscript (4) COMPLETED 0 2015-05-05 09:52:46.098 5m 23s 5m 19s 432.0% 902.2 MB 1.4 GB 1 GB 1.7 GB 4.1 GB 184.8 MB 322667 318879 946003968 1530056704 1095290880 1781735424 4427960718 193790728 560495 269105 3121152 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_7/log_docker_7: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [19/161a25] Submitted process > buildIndex (1) 11 | [6d/b78c81] Submitted process > mapping (2) 12 | [b5/3a6a16] Submitted process > mapping (1) 13 | [59/ff059a] Submitted process > mapping (3) 14 | [b1/15ed26] Submitted process > mapping (4) 15 | [b9/8b60ae] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [2b/a4caee] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [d3/e13d33] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [82/03dbff] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_7/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 19/161a25 19478 buildIndex (1) COMPLETED 0 2015-05-05 16:18:09.905 1h 37m 5s 1h 37m 4s 99.9% 4.5 GB 4.6 GB 4.6 GB 4.6 GB 10.1 GB 3.4 GB 5825456 5823537 4829073408 4979994624 4936052736 4980817920 10832504233 3613226813 41493 373215 5165056 3613503488 3 | 2 b5/3a6a16 6534 mapping (1) COMPLETED 0 2015-05-05 17:55:15.473 4h 1m 46s 4h 1m 41s 693.4% 5.7 GB 7 GB 5.8 GB 7.1 GB 132.2 GB 54.9 GB 14505726 14500894 6167670784 7531376640 6260563968 7623045120 141918120705 58975190501 75036647 96195537 31350784 11823611904 4 | 6 b9/8b60ae 30223 makeTranscript (1) COMPLETED 0 2015-05-05 21:57:01.498 6m 10s 6m 5s 316.0% 903.9 MB 1.5 GB 1 GB 1.7 GB 3.1 GB 182 MB 369601 364830 947773440 1586692096 1109684224 1848860672 3343500464 190843310 456134 264462 3121152 191119360 5 | 4 59/ff059a 6537 mapping (3) COMPLETED 0 2015-05-05 17:55:15.473 4h 15m 33s 4h 15m 27s 523.9% 5.2 GB 6.2 GB 5.2 GB 6.2 GB 135.7 GB 57.8 GB 15332588 15326629 5588140032 6630449152 5593665536 6700441600 145711621571 62051647737 69463629 96861349 382746624 12556537856 6 | 7 2b/a4caee 4148 makeTranscript (2) COMPLETED 0 2015-05-05 22:10:48.070 4m 45s 4m 39s 435.0% 834.9 MB 1.4 GB 1 GB 1.6 GB 3.3 GB 184.6 MB 284982 278721 875495424 1506385920 1092575232 1758064640 3534267079 193516057 470249 268764 3121152 193585152 7 | 5 b1/15ed26 6540 mapping (4) COMPLETED 0 2015-05-05 17:55:15.473 4h 23m 42s 4h 23m 37s 569.5% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 157.4 GB 75 GB 15821793 15816635 6826450944 8176648192 6831132672 8181116928 169044464788 80487908106 62188724 114975648 787128320 18346307584 8 | 8 d3/e13d33 15569 makeTranscript (3) COMPLETED 0 2015-05-05 22:18:57.281 5m 51s 5m 47s 390.0% 855.8 MB 1.4 GB 1 GB 1.8 GB 4.6 GB 182.6 MB 351184 346984 897380352 1510567936 1103900672 1934229504 4946897227 191449642 558861 265382 3121152 191524864 9 | 3 6d/b78c81 6532 mapping (2) COMPLETED 0 2015-05-05 17:55:15.472 4h 39m 31s 4h 39m 25s 842.1% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 166.9 GB 84.7 GB 16771052 16764633 6851178496 8202592256 6861979648 8213819392 179246816959 90895311312 50829697 148351416 653090816 18076909568 10 | 9 82/03dbff 29147 makeTranscript (4) COMPLETED 0 2015-05-05 22:34:46.536 5m 28s 5m 24s 433.0% 837.1 MB 1.4 GB 1 GB 1.6 GB 4.1 GB 184.8 MB 328106 324208 877711360 1478578176 1098534912 1711394816 4427960718 193790728 560495 269105 3121152 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_8/log_docker_8: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [01/9ee93e] Submitted process > buildIndex (1) 11 | [43/379afd] Submitted process > mapping (2) 12 | [53/6e57a7] Submitted process > mapping (3) 13 | [3e/8657fa] Submitted process > mapping (1) 14 | [9d/09a454] Submitted process > mapping (4) 15 | [0f/44f337] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [00/246d56] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [bd/4cb64b] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [ec/2a071b] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_8/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 01/9ee93e 1024 buildIndex (1) COMPLETED 0 2015-05-06 05:04:52.372 1h 33m 20s 1h 33m 18s 99.8% 4.5 GB 4.6 GB 4.6 GB 4.6 GB 10.1 GB 3.4 GB 5600248 5597917 4831170560 4979994624 4936052736 4980817920 10832504233 3618461501 41493 373854 5160960 3618697216 3 | 2 3e/8657fa 17776 mapping (1) COMPLETED 0 2015-05-06 06:38:12.833 4h 6m 26s 4h 6m 20s 759.3% 5.8 GB 7 GB 5.8 GB 7.1 GB 132.2 GB 54.9 GB 14785665 14780324 6204813312 7559712768 6268329984 7622979584 141978250811 58984718237 74958531 96238377 199995392 11833249792 4 | 6 0f/44f337 28359 makeTranscript (1) COMPLETED 0 2015-05-06 10:44:39.245 6m 30s 6m 25s 297.0% 822.2 MB 1.4 GB 1 GB 1.7 GB 3.1 GB 184.3 MB 390048 384860 862146560 1543606272 1102086144 1850155008 3361944888 193301922 458276 268612 3121152 193761280 5 | 4 53/6e57a7 17773 mapping (3) COMPLETED 0 2015-05-06 06:38:12.832 4h 17m 2s 4h 16m 56s 477.8% 5.2 GB 6.2 GB 5.2 GB 6.2 GB 135.6 GB 57.8 GB 15421830 15416318 5588774912 6630449152 5592678400 6700613632 145646534865 62048612587 70635906 96803917 470155264 12551254016 6 | 7 00/246d56 26745 makeTranscript (2) COMPLETED 0 2015-05-06 10:55:14.670 5m 2s 4m 52s 413.0% 761.1 MB 1.3 GB 1 GB 1.7 GB 3.3 GB 181.8 MB 302016 291802 798101504 1385705472 1114431488 1838718976 3515903195 190681712 468182 264251 3121152 190767104 7 | 5 9d/09a454 17779 mapping (4) COMPLETED 0 2015-05-06 06:38:12.833 4h 24m 43s 4h 24m 35s 769.9% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 157.5 GB 75 GB 15882531 15875073 6818791424 8176648192 6823133184 8181116928 169115293866 80484540573 55326087 115029552 877105152 18355802112 8 | 8 bd/4cb64b 4125 makeTranscript (3) COMPLETED 0 2015-05-06 11:02:55.378 5m 40s 5m 35s 403.0% 922.8 MB 1.5 GB 1 GB 1.7 GB 4.6 GB 182.3 MB 339593 335420 967659520 1655275520 1110953984 1789517824 4943354188 191165934 558510 264824 3121152 191242240 9 | 3 43/379afd 17771 mapping (2) COMPLETED 0 2015-05-06 06:38:12.829 4h 41m 42s 4h 41m 35s 795.6% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 166.9 GB 84.6 GB 16902014 16894609 6855196672 8202559488 6865715200 8213786624 179232338211 90880641851 62323278 148348678 865845248 18058915840 10 | 9 ec/2a071b 18332 makeTranscript (4) COMPLETED 0 2015-05-06 11:19:54.855 5m 25s 5m 20s 435.0% 857.7 MB 1.5 GB 1 GB 1.6 GB 4.1 GB 184.8 MB 324872 320322 899330048 1580388352 1092173824 1731391488 4427960718 193790728 560495 269105 3121152 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_9/log_docker_9: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [15/26af4c] Submitted process > buildIndex (1) 11 | [aa/993cc7] Submitted process > mapping (1) 12 | [b6/2ac237] Submitted process > mapping (4) 13 | [50/bbe044] Submitted process > mapping (3) 14 | [d1/1d5a6d] Submitted process > mapping (2) 15 | [df/c4b182] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [9f/561099] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [39/456bda] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [78/8ab96d] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/docker_9/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 15/26af4c 26478 buildIndex (1) COMPLETED 0 2015-05-06 17:44:01.393 1h 33m 46s 1h 33m 44s 99.8% 4.5 GB 4.6 GB 4.6 GB 4.6 GB 10.1 GB 3.4 GB 5626161 5623614 4829065216 4979990528 4936044544 4980813824 10832504233 3626284861 41493 374809 5160960 3626512384 3 | 2 aa/993cc7 11945 mapping (1) COMPLETED 0 2015-05-06 19:17:47.637 4h 7m 49s 4h 7m 42s 489.7% 5.7 GB 7 GB 5.8 GB 7.1 GB 132.2 GB 54.9 GB 14868796 14861919 6156918784 7532912640 6248148992 7623045120 141927242093 58984374196 70383562 96193775 468946944 11828379648 4 | 6 df/c4b182 27844 makeTranscript (1) COMPLETED 0 2015-05-06 23:25:37.314 6m 31s 6m 23s 299.0% 977 MB 1.7 GB 1 GB 1.9 GB 3.1 GB 184.6 MB 391136 383396 1024458752 1838354432 1096830976 2039701504 3363070560 193614118 458406 268990 3121152 193744896 5 | 4 50/bbe044 11948 mapping (3) COMPLETED 0 2015-05-06 19:17:47.637 4h 16m 30s 4h 16m 23s 727.3% 5.2 GB 6.2 GB 5.2 GB 6.2 GB 135.7 GB 57.8 GB 15389616 15383323 5576081408 6630440960 5581815808 6699765760 145675601455 62021841117 68944043 96848681 351379456 12577665024 6 | 7 9f/561099 17232 makeTranscript (2) COMPLETED 0 2015-05-06 23:34:17.267 5m 26s 5m 19s 373.0% 836.8 MB 1.4 GB 1 GB 1.7 GB 3.3 GB 184.8 MB 325709 319231 877490176 1523167232 1095065600 1774837760 3536047297 193777202 470470 269140 3121152 193855488 7 | 5 b6/2ac237 11947 mapping (4) COMPLETED 0 2015-05-06 19:17:47.637 4h 25m 18s 4h 25m 11s 789.4% 6.3 GB 7.6 GB 6.4 GB 7.6 GB 157.5 GB 75 GB 15917909 15910815 6817959936 8176680960 6822342656 8181149696 169071269944 80487895804 57282075 115043681 758403072 18339074048 8 | 8 39/456bda 31150 makeTranscript (3) COMPLETED 0 2015-05-06 23:43:05.558 5m 58s 5m 53s 384.0% 715.8 MB 1.2 GB 1 GB 1.7 GB 4.6 GB 182.9 MB 357539 353053 750563328 1319731200 1102991360 1789509632 4950091550 191755461 559198 265799 3121152 191848448 9 | 3 d1/1d5a6d 11952 mapping (2) COMPLETED 0 2015-05-06 19:17:47.638 4h 40m 2s 4h 39m 56s 808.0% 6.4 GB 7.6 GB 6.4 GB 7.6 GB 166.9 GB 84.6 GB 16802499 16796440 6849245184 8202592256 6859931648 8213819392 179234208368 90882521903 60634289 148349271 631500800 18061369344 10 | 9 78/8ab96d 12073 makeTranscript (4) COMPLETED 0 2015-05-06 23:57:50.150 5m 26s 5m 22s 432.0% 761.1 MB 1.3 GB 1 GB 1.8 GB 4.1 GB 184.8 MB 326175 321936 798048256 1376518144 1100419072 1963753472 4427960718 193790728 560495 269105 3121152 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/fig_correlation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/rnaseq-toy/fig_correlation.png -------------------------------------------------------------------------------- /rnaseq-toy/native_1/log_native_1: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [0f/e4f9d7] Submitted process > buildIndex (1) 11 | [8e/7da28b] Submitted process > mapping (3) 12 | [0e/1a415a] Submitted process > mapping (2) 13 | [88/1e51e6] Submitted process > mapping (4) 14 | [35/922ae9] Submitted process > mapping (1) 15 | [96/1ec650] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [c4/7639de] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [6b/e5cd78] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [8e/b209fa] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/native_1/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 0f/e4f9d7 20540 buildIndex (1) COMPLETED 0 2015-05-05 03:49:50.500 1h 26m 29s 1h 26m 29s 99.8% 4.5 GB 4.7 GB 4.6 GB 4.7 GB 10.1 GB 3.4 GB 5189182 5188542 4829020160 5077082112 4935999488 5077889024 10832499787 3626137405 41503 374791 0 3626356736 3 | 3 0e/1a415a 30440 mapping (2) COMPLETED 0 2015-05-05 05:16:20.554 4h 53s 4h 52s 753.9% 5.7 GB 7.9 GB 5.8 GB 8 GB 132.3 GB 54.9 GB 14453435 14451708 6173802496 8519045120 6264713216 8610488320 142009705898 58972876652 68953898 96274855 0 11803680768 4 | 6 96/1ec650 7040 makeTranscript (1) COMPLETED 0 2015-05-05 09:17:14.929 6m 27s 6m 25s 293.0% 851.3 MB 1.5 GB 1 GB 1.9 GB 3.1 GB 183.6 MB 386523 384871 892657664 1623920640 1103413248 2009792512 3357700608 192569097 457788 267512 0 192675840 5 | 4 8e/7da28b 30438 mapping (3) COMPLETED 0 2015-05-05 05:16:20.553 4h 10m 52s 4h 10m 51s 520.7% 5.2 GB 7.1 GB 5.2 GB 7.1 GB 135.7 GB 57.8 GB 15051778 15051332 5597044736 7572627456 5600423936 7642542080 145708554439 62034461817 72019749 96867040 0 12510666752 6 | 7 c4/7639de 31892 makeTranscript (2) COMPLETED 0 2015-05-05 09:27:12.341 5m 4s 4m 59s 397.0% 653.6 MB 1.3 GB 1 GB 1.7 GB 3.3 GB 184.8 MB 303664 299202 685400064 1402134528 1094938624 1804795904 3536342873 193812914 470497 269205 0 193892352 7 | 2 35/922ae9 30449 mapping (1) COMPLETED 0 2015-05-05 05:16:20.556 4h 18m 36s 4h 18m 31s 780.7% 6.4 GB 8.5 GB 6.4 GB 8.5 GB 157.5 GB 75 GB 15515557 15510740 6828945408 9164251136 6833278976 9168777216 169113900639 80487975318 61902094 115025532 0 18291077120 8 | 8 6b/e5cd78 9894 makeTranscript (3) COMPLETED 0 2015-05-05 09:34:56.128 5m 46s 5m 44s 387.0% 839 MB 1.6 GB 1 GB 1.8 GB 4.6 GB 182.9 MB 346111 344089 879771648 1685250048 1105010688 1886584832 4951580719 191803980 559352 265933 0 191897600 9 | 5 88/1e51e6 30442 mapping (4) COMPLETED 0 2015-05-05 05:16:20.539 4h 33m 47s 4h 33m 45s 813.7% 6.4 GB 8.6 GB 6.4 GB 8.6 GB 166.9 GB 84.6 GB 16426698 16425113 6851731456 9190162432 6862176256 9201356800 179250658272 90885311698 69541247 148359177 0 18063593472 10 | 9 8e/b209fa 23083 makeTranscript (4) COMPLETED 0 2015-05-05 09:50:07.263 5m 15s 5m 14s 430.0% 719.3 MB 1.3 GB 1 GB 1.7 GB 4.1 GB 184.8 MB 314677 314253 754290688 1402134528 1096830976 1855131648 4427956085 193790728 560491 269105 0 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/native_10/log_native_10: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [af/df7d33] Submitted process > buildIndex (1) 11 | [2a/f536b2] Submitted process > mapping (4) 12 | [a7/499306] Submitted process > mapping (2) 13 | [b0/b41e83] Submitted process > mapping (3) 14 | [28/43f63f] Submitted process > mapping (1) 15 | [b4/3cec62] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [1b/a49ac4] Submitted process > makeTranscript (2) 18 | [ac/1265e0] Submitted process > makeTranscript (3) 19 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [3c/3e4066] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/native_10/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 af/df7d33 7654 buildIndex (1) COMPLETED 0 2015-05-07 00:03:42.145 1h 43m 59s 1h 43m 54s 99.8% 4.5 GB 4.7 GB 4.6 GB 4.7 GB 10.1 GB 3.4 GB 6238597 6234163 4828950528 5077082112 4935929856 5077889024 10832499787 3626686269 41503 374858 0 3626979328 3 | 2 28/43f63f 29027 mapping (1) COMPLETED 0 2015-05-07 01:47:40.814 4h 12m 32s 4h 12m 30s 555.0% 5.7 GB 7.9 GB 5.8 GB 8 GB 132.2 GB 54.9 GB 15152461 15149894 6170976256 8518979584 6261886976 8610422784 141968830063 58961833838 71310703 96247757 28028928 11820367872 4 | 6 b4/3cec62 13443 makeTranscript (1) COMPLETED 0 2015-05-07 06:00:14.167 5m 54s 5m 50s 328.0% 834.3 MB 1.5 GB 1 GB 1.9 GB 3.1 GB 183.2 MB 353556 350434 874786816 1607135232 1117872128 2060132352 3353685439 192116501 457333 266704 0 192200704 5 | 3 a7/499306 29021 mapping (2) COMPLETED 0 2015-05-07 01:47:40.812 4h 20m 59s 4h 20m 58s 667.7% 5.2 GB 7 GB 5.2 GB 7.1 GB 135.7 GB 57.8 GB 15658982 15658113 5596405760 7502913536 5604732928 7642542080 145705676902 62038893713 75018554 96861357 31744000 12553326592 6 | 5 2a/f536b2 29019 mapping (4) COMPLETED 0 2015-05-07 01:47:40.812 4h 23m 23s 4h 23m 21s 778.2% 6.4 GB 8.5 GB 6.4 GB 8.5 GB 157.5 GB 75 GB 15802536 15800635 6825418752 9164251136 6829748224 9168777216 169140306558 80482203375 69343341 115047468 39866368 18350002176 7 | 7 1b/a49ac4 487 makeTranscript (2) COMPLETED 0 2015-05-07 06:08:39.804 4m 57s 4m 55s 402.0% 744.3 MB 1.4 GB 1 GB 1.9 GB 3.3 GB 182.4 MB 297197 294912 780496896 1536352256 1089175552 2056462336 3521640814 191296643 468852 265410 0 191377408 8 | 8 ac/1265e0 13260 makeTranscript (3) COMPLETED 0 2015-05-07 06:11:03.363 6m 4s 6m 3s 373.0% 861.7 MB 1.5 GB 1 GB 1.9 GB 4.6 GB 182.8 MB 363761 362598 903544832 1618149376 1109659648 2071142400 4948625894 191681720 559037 265723 0 191758336 9 | 4 b0/b41e83 29024 mapping (3) COMPLETED 0 2015-05-07 01:47:40.813 4h 39m 49s 4h 39m 47s 785.3% 6.4 GB 8.6 GB 6.4 GB 8.6 GB 167 GB 84.6 GB 16788764 16786639 6853890048 9190162432 6864334848 9201356800 179269776665 90889817328 71701879 148373380 440451072 18080120832 10 | 9 3c/3e4066 13072 makeTranscript (4) COMPLETED 0 2015-05-07 06:27:29.601 5m 25s 5m 20s 430.0% 837 MB 1.5 GB 1 GB 1.7 GB 4.1 GB 185.2 MB 325184 320179 877613056 1616642048 1098629120 1804795904 4427956085 194155911 560491 269574 0 194236416 11 | -------------------------------------------------------------------------------- /rnaseq-toy/native_2/log_native_2: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [e0/0fa573] Submitted process > buildIndex (1) 11 | [7f/09a425] Submitted process > mapping (3) 12 | [8f/77f9a2] Submitted process > mapping (2) 13 | [d3/7caa2c] Submitted process > mapping (4) 14 | [3a/d264d0] Submitted process > mapping (1) 15 | [74/9c6220] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [a2/c9b1c1] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [b8/3565b1] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [ac/675f67] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/native_2/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 e0/0fa573 17736 buildIndex (1) COMPLETED 0 2015-05-05 16:17:52.547 1h 37m 18s 1h 37m 13s 99.8% 4.5 GB 4.7 GB 4.6 GB 4.7 GB 10.1 GB 3.4 GB 5838189 5833224 4831031296 5077078016 4935913472 5077884928 10832499787 3628193597 41503 375042 0 3628462080 3 | 2 3a/d264d0 4368 mapping (1) COMPLETED 0 2015-05-05 17:55:11.007 4h 1m 1s 4h 57s 780.1% 5.8 GB 7.9 GB 5.8 GB 8 GB 132.3 GB 54.9 GB 14460951 14457228 6176006144 8519045120 6266916864 8610488320 142011715707 58984677219 75349483 96266185 315392 11838038016 4 | 6 74/9c6220 10028 makeTranscript (1) COMPLETED 0 2015-05-05 21:56:12.685 6m 10s 6m 5s 309.0% 768.6 MB 1.5 GB 1 GB 1.9 GB 3.1 GB 185 MB 370308 365294 805933056 1586155520 1095802880 2076905472 3364867862 194006049 458640 269562 94208 194113536 5 | 4 7f/09a425 4362 mapping (3) COMPLETED 0 2015-05-05 17:55:11.006 4h 12m 15s 4h 12m 12s 521.0% 5.2 GB 7 GB 5.2 GB 7.1 GB 135.7 GB 57.8 GB 15135439 15132336 5569015808 7538073600 5573853184 7584964608 145723737973 62050026641 69849278 96868200 65536 12587331584 6 | 7 a2/c9b1c1 6579 makeTranscript (2) COMPLETED 0 2015-05-05 22:07:26.459 4m 52s 4m 49s 413.0% 651.3 MB 1.4 GB 1 GB 1.7 GB 3.3 GB 183.4 MB 292060 289321 682926080 1469243392 1093713920 1871900672 3525955443 192338436 469332 266905 0 192405504 7 | 3 8f/77f9a2 4365 mapping (2) COMPLETED 0 2015-05-05 17:55:11.006 4h 20m 24s 4h 20m 23s 759.5% 6.4 GB 8.5 GB 6.4 GB 8.5 GB 157.5 GB 74.9 GB 15624105 15623104 6825955328 9164283904 6830284800 9168809984 169085164883 80473745130 72577790 115013123 4812800 18335838208 8 | 8 b8/3565b1 17361 makeTranscript (3) COMPLETED 0 2015-05-05 22:15:35.131 5m 46s 5m 44s 388.0% 693.7 MB 1.3 GB 1 GB 1.7 GB 4.6 GB 182.9 MB 346116 344152 727404544 1444593664 1110212608 1869811712 4950622678 191774552 559251 265855 0 191852544 9 | 5 d3/7caa2c 4367 mapping (4) COMPLETED 0 2015-05-05 17:55:11.007 4h 35m 41s 4h 35m 41s 788.3% 6.4 GB 8.6 GB 6.4 GB 8.6 GB 166.9 GB 84.6 GB 16541244 16540988 6853894144 9190195200 6864334848 9201389568 179241382679 90874678418 51401727 148359823 5996544 18053132288 10 | 9 ac/675f67 30113 makeTranscript (4) COMPLETED 0 2015-05-05 22:30:52.263 5m 19s 5m 16s 429.0% 885.6 MB 1.5 GB 1 GB 1.7 GB 4.1 GB 184.8 MB 319488 316448 928591872 1627140096 1097011200 1828458496 4427956085 193790728 560491 269105 0 193884160 11 | -------------------------------------------------------------------------------- /rnaseq-toy/native_3/log_native_3: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [1e/8cb23a] Submitted process > buildIndex (1) 11 | [bb/365bf9] Submitted process > mapping (1) 12 | [e0/d54784] Submitted process > mapping (3) 13 | [84/1d0aa8] Submitted process > mapping (4) 14 | [99/3d2cca] Submitted process > mapping (2) 15 | [bc/e8d31f] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [8a/9652e7] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [c6/498113] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [3b/07d86e] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/native_3/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 1e/8cb23a 31189 buildIndex (1) COMPLETED 0 2015-05-06 05:01:16.113 1h 32m 33s 1h 32m 30s 99.8% 4.5 GB 4.7 GB 4.6 GB 4.7 GB 10.1 GB 3.4 GB 5552819 5550238 4860100608 5077078016 4935929856 5077884928 10832499787 3617421117 41503 373727 237568 3617656832 3 | 3 99/3d2cca 14956 mapping (2) COMPLETED 0 2015-05-06 06:33:49.316 4h 3m 37s 4h 3m 37s 808.6% 5.8 GB 7.9 GB 5.8 GB 8 GB 132.2 GB 54.9 GB 14617044 14616683 6176808960 8519077888 6267715584 8610521088 141956361804 58971783018 75393742 96228685 79953920 11871666176 4 | 6 bc/e8d31f 32076 makeTranscript (1) COMPLETED 0 2015-05-06 10:37:27.314 6m 12s 6m 9s 309.0% 845.5 MB 1.6 GB 1 GB 1.9 GB 3.1 GB 184.2 MB 372139 368850 886587392 1666904064 1101246464 2076905472 3361169084 193100649 458188 268378 126976 193212416 5 | 5 84/1d0aa8 14951 mapping (4) COMPLETED 0 2015-05-06 06:33:49.315 4h 15m 56s 4h 15m 53s 713.8% 5.2 GB 7 GB 5.2 GB 7.1 GB 135.7 GB 57.8 GB 15356447 15352880 5590581248 7499362304 5600362496 7569965056 145694236208 62019744908 75868698 96865687 156913664 12594044928 6 | 7 8a/9652e7 30587 makeTranscript (2) COMPLETED 0 2015-05-06 10:49:45.800 5m 34s 5m 33s 354.0% 747 MB 1.4 GB 1 GB 1.7 GB 3.3 GB 182.1 MB 334111 333490 783278080 1483055104 1113821184 1818607616 3518647107 190950114 468481 264844 0 191033344 7 | 2 bb/365bf9 14948 mapping (1) COMPLETED 0 2015-05-06 06:33:49.313 4h 27m 15s 4h 27m 13s 575.1% 6.4 GB 8.5 GB 6.4 GB 8.5 GB 157.6 GB 75 GB 16035491 16033038 6830125056 9164283904 6834454528 9168809984 169177348551 80484308739 69769763 115073806 86392832 18299830272 8 | 8 c6/498113 16168 makeTranscript (3) COMPLETED 0 2015-05-06 11:01:04.821 5m 26s 5m 23s 415.0% 832.2 MB 1.5 GB 1 GB 1.7 GB 4.6 GB 183.4 MB 326266 323472 872677376 1618141184 1105629184 1869811712 4956801215 192316863 559855 266766 0 192393216 9 | 4 e0/d54784 14953 mapping (3) COMPLETED 0 2015-05-06 06:33:49.314 4h 35m 8s 4h 35m 6s 785.5% 6.4 GB 8.6 GB 6.4 GB 8.6 GB 166.9 GB 84.6 GB 16508483 16506301 6852005888 9190195200 6862446592 9201389568 179255572939 90890247376 66686475 148360286 84340736 18073387008 10 | 9 3b/07d86e 20701 makeTranscript (4) COMPLETED 0 2015-05-06 11:08:57.809 5m 20s 5m 18s 429.0% 837.1 MB 1.5 GB 1 GB 1.7 GB 4.1 GB 184.8 MB 319686 317940 877752320 1616642048 1097109504 1828458496 4427956085 193790728 560491 269105 0 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/native_4/log_native_4: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [a0/5aefc4] Submitted process > buildIndex (1) 11 | [cb/f21bde] Submitted process > mapping (3) 12 | [54/1a3988] Submitted process > mapping (2) 13 | [21/4bd4a8] Submitted process > mapping (4) 14 | [36/eb670a] Submitted process > mapping (1) 15 | [6b/9987e9] Submitted process > makeTranscript (1) 16 | [98/f91ece] Submitted process > makeTranscript (2) 17 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [fe/c8e9b7] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [86/3fba02] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/native_4/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 a0/5aefc4 16952 buildIndex (1) COMPLETED 0 2015-05-06 17:30:35.164 1h 36m 58s 1h 36m 58s 99.8% 4.5 GB 4.7 GB 4.6 GB 4.7 GB 10.1 GB 3.4 GB 5818487 5817976 4828938240 5077082112 4935917568 5077889024 10832499787 3613169469 41503 373208 233472 3613450240 3 | 2 36/eb670a 3316 mapping (1) COMPLETED 0 2015-05-06 19:07:33.745 4h 9m 19s 4h 9m 15s 629.7% 5.8 GB 7.9 GB 5.8 GB 8 GB 132.2 GB 54.9 GB 14958585 14955241 6174765056 8519077888 6265671680 8610521088 141968694060 58954575700 57211008 96252172 4464640 11829702656 4 | 4 cb/f21bde 3308 mapping (3) COMPLETED 0 2015-05-06 19:07:33.743 4h 11m 40s 4h 11m 40s 790.2% 5.2 GB 7 GB 5.2 GB 7 GB 135.7 GB 57.8 GB 15100169 15100021 5605076992 7496732672 5613670400 7567200256 145697889536 62037386390 75917496 96856233 9195520 12549455872 5 | 6 6b/9987e9 5630 makeTranscript (1) COMPLETED 0 2015-05-06 23:16:53.480 5m 33s 5m 29s 368.0% 659.1 MB 1.4 GB 1 GB 1.9 GB 3.1 GB 184.4 MB 332511 328989 691163136 1472913408 1095327744 2076905472 3362213071 193371869 458302 268684 475197440 193449984 6 | 7 98/f91ece 15555 makeTranscript (2) COMPLETED 0 2015-05-06 23:19:13.929 6m 30s 6m 29s 306.0% 798.6 MB 1.5 GB 1 GB 1.8 GB 3.3 GB 182.9 MB 390173 388645 837402624 1569910784 1095143424 1922240512 3522601334 191782939 468964 266048 0 191889408 7 | 3 54/1a3988 3310 mapping (2) COMPLETED 0 2015-05-06 19:07:33.744 4h 28m 39s 4h 28m 37s 783.8% 6.4 GB 8.5 GB 6.4 GB 8.5 GB 157.5 GB 75 GB 16119315 16117150 6825123840 9164251136 6829453312 9168777216 169159212179 80483800827 72221263 115061277 371232768 18337476608 8 | 8 fe/c8e9b7 3927 makeTranscript (3) COMPLETED 0 2015-05-06 23:36:13.074 5m 26s 5m 21s 419.0% 733.7 MB 1.4 GB 1 GB 1.9 GB 4.6 GB 185.2 MB 325705 321108 769359872 1499131904 1107857408 2020806656 4972995991 194180671 561467 269563 0 194256896 9 | 5 21/4bd4a8 3313 mapping (4) COMPLETED 0 2015-05-06 19:07:33.744 4h 35m 15s 4h 35m 14s 793.2% 6.4 GB 8.6 GB 6.4 GB 8.6 GB 166.9 GB 84.6 GB 16514880 16514308 6849921024 9190227968 6860365824 9201422336 179247935636 90881391802 80288083 148359461 284049408 18128764928 10 | 9 86/3fba02 6516 makeTranscript (4) COMPLETED 0 2015-05-06 23:42:48.635 5m 24s 5m 20s 430.0% 816.1 MB 1.5 GB 1 GB 1.7 GB 4.1 GB 185.2 MB 324398 319743 855793664 1607819264 1104064512 1869979648 4427956085 194155866 560491 269573 0 194236416 11 | -------------------------------------------------------------------------------- /rnaseq-toy/native_5/log_native_5: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [ed/6437ac] Submitted process > buildIndex (1) 11 | [e9/2ed94b] Submitted process > mapping (1) 12 | [e3/84bcfd] Submitted process > mapping (4) 13 | [44/17195e] Submitted process > mapping (3) 14 | [a7/84b7cb] Submitted process > mapping (2) 15 | [9a/f9e9bb] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [90/ddad8a] Submitted process > makeTranscript (2) 18 | [f4/d0ba3f] Submitted process > makeTranscript (3) 19 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [24/0abd1b] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/native_5/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 ed/6437ac 11111 buildIndex (1) COMPLETED 0 2015-05-07 06:04:01.445 1h 31m 5s 1h 31m 1s 99.8% 4.5 GB 4.7 GB 4.6 GB 4.7 GB 10.1 GB 3.4 GB 5464851 5460610 4828950528 5077078016 4935929856 5077884928 10832499787 3626014525 41503 374776 0 3626233856 3 | 2 e9/2ed94b 26653 mapping (1) COMPLETED 0 2015-05-07 07:35:06.392 4h 7m 46s 4h 7m 44s 506.9% 5.8 GB 7.9 GB 5.8 GB 8 GB 132.2 GB 54.9 GB 14866044 14864132 6188417024 8534470656 6264229888 8610455552 142001945735 58975743839 75313430 96264935 1413120 11819991040 4 | 6 9a/f9e9bb 19288 makeTranscript (1) COMPLETED 0 2015-05-07 11:42:53.411 7m 21s 7m 16s 259.0% 757.4 MB 1.6 GB 1 GB 2.1 GB 3.1 GB 185 MB 440795 436278 794173440 1741348864 1104146432 2271948800 3364867862 193978533 458640 269527 0 277557248 5 | 4 44/17195e 26661 mapping (3) COMPLETED 0 2015-05-07 07:35:06.394 4h 18m 21s 4h 18m 21s 661.2% 5.2 GB 7.1 GB 5.2 GB 7.1 GB 135.7 GB 57.8 GB 15501418 15500989 5574828032 7572590592 5581205504 7642505216 145716637488 62035518600 75895843 96873732 307200 12609867776 6 | 3 a7/84b7cb 26659 mapping (2) COMPLETED 0 2015-05-07 07:35:06.393 4h 21m 15s 4h 21m 14s 789.4% 6.4 GB 8.5 GB 6.4 GB 8.5 GB 157.5 GB 75 GB 15674685 15673668 6826274816 9164218368 6830608384 9168744448 169153600169 80478238472 83658882 115060012 581632 18396909568 7 | 7 90/ddad8a 16161 makeTranscript (2) COMPLETED 0 2015-05-07 11:53:27.822 4m 51s 4m 50s 412.0% 775 MB 1.3 GB 1 GB 1.8 GB 3.3 GB 182 MB 290616 289696 812650496 1402134528 1090506752 1922240512 3514208851 190827227 467992 264279 0 190889984 8 | 8 f4/d0ba3f 399 makeTranscript (3) COMPLETED 0 2015-05-07 11:56:21.095 6m 8s 6m 7s 367.0% 864.3 MB 1.6 GB 1 GB 1.8 GB 4.6 GB 182.8 MB 367976 366906 906301440 1685250048 1111138304 1936920576 4948625899 191681720 559038 265723 0 191758336 9 | 5 e3/84bcfd 26654 mapping (4) COMPLETED 0 2015-05-07 07:35:06.393 4h 41m 38s 4h 41m 37s 817.6% 6.4 GB 8.6 GB 6.4 GB 8.6 GB 167 GB 84.6 GB 16898223 16897129 6853267456 9190162432 6863921152 9201356800 179265020941 90885029099 44760896 148372966 84287488 18087780352 10 | 9 24/0abd1b 523 makeTranscript (4) COMPLETED 0 2015-05-07 12:16:44.629 5m 20s 5m 18s 426.0% 699.1 MB 1.5 GB 1 GB 1.7 GB 4.1 GB 184.8 MB 319612 318379 733097984 1599791104 1091854336 1804795904 4427956085 193790728 560491 269105 0 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/native_6/log_native_6: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [3b/915013] Submitted process > buildIndex (1) 11 | [14/213773] Submitted process > mapping (1) 12 | [5c/215d1c] Submitted process > mapping (2) 13 | [40/4c008a] Submitted process > mapping (3) 14 | [e8/152abf] Submitted process > mapping (4) 15 | [90/8cc2fb] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [c4/2b5a57] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [83/127e9d] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [df/ea7021] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/native_6/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 3b/915013 9858 buildIndex (1) COMPLETED 0 2015-05-04 21:28:59.610 1h 34m 21s 1h 34m 19s 99.7% 4.5 GB 4.7 GB 4.6 GB 4.7 GB 10.1 GB 3.4 GB 5661132 5659020 4828934144 5077078016 4935913472 5077884928 10832499787 3614914365 41503 373421 0 3615166464 3 | 2 14/213773 27379 mapping (1) COMPLETED 0 2015-05-04 23:03:20.821 4h 1m 29s 4h 1m 25s 642.9% 5.8 GB 7.9 GB 5.8 GB 8 GB 132.3 GB 54.9 GB 14488778 14485443 6174720000 8519045120 6265630720 8610488320 142028941996 58982502233 67521591 96284052 0 11813167104 4 | 6 90/8cc2fb 23250 makeTranscript (1) COMPLETED 0 2015-05-05 03:04:51.042 6m 38s 6m 34s 286.0% 1 GB 1.7 GB 1.1 GB 2 GB 3.1 GB 184.8 MB 397833 393654 1087586304 1808465920 1198333952 2127241216 3364794180 193763281 458624 269252 0 193884160 5 | 5 e8/152abf 27386 mapping (4) COMPLETED 0 2015-05-04 23:03:20.822 4h 11m 5s 4h 11m 5s 528.5% 5.2 GB 7 GB 5.2 GB 7.1 GB 135.7 GB 57.8 GB 15064744 15064671 5600141312 7535366144 5605507072 7605964800 145712734596 62031475841 66828486 96873453 0 12507619328 6 | 7 c4/2b5a57 14510 makeTranscript (2) COMPLETED 0 2015-05-05 03:14:25.579 5m 5s 5m 1s 397.0% 839.4 MB 1.5 GB 1 GB 1.8 GB 3.3 GB 185.1 MB 305327 300751 880144384 1620250624 1099288576 1932730368 3536560774 194054185 470536 269525 0 194134016 7 | 4 40/4c008a 27383 mapping (3) COMPLETED 0 2015-05-04 23:03:20.821 4h 18m 49s 4h 18m 44s 777.8% 6.4 GB 8.5 GB 6.4 GB 8.5 GB 157.5 GB 75 GB 15528609 15524398 6828212224 9164218368 6832545792 9168744448 169100218465 80487897496 64335711 115015685 0 18291052544 8 | 8 83/127e9d 27855 makeTranscript (3) COMPLETED 0 2015-05-05 03:22:09.440 5m 48s 5m 47s 386.0% 670.1 MB 1.5 GB 1 GB 1.7 GB 4.6 GB 182.2 MB 348263 347174 702689280 1618141184 1101611008 1819475968 4942535291 191079766 558425 264670 0 191168512 9 | 3 5c/215d1c 27377 mapping (2) COMPLETED 0 2015-05-04 23:03:20.821 4h 34m 4s 4h 34m 2s 837.2% 6.4 GB 8.6 GB 6.4 GB 8.6 GB 167 GB 84.6 GB 16443506 16442174 6851088384 9190195200 6861533184 9201389568 179262468352 90882477242 66255725 148371473 0 18060689408 10 | 9 df/ea7021 7383 makeTranscript (4) COMPLETED 0 2015-05-05 03:37:24.358 5m 23s 5m 19s 428.0% 849.3 MB 1.5 GB 1 GB 1.7 GB 4.1 GB 184.8 MB 322531 318594 890535936 1599791104 1096282112 1851461632 4427956085 193790728 560491 269105 0 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/native_7/log_native_7: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [81/19f8bb] Submitted process > buildIndex (1) 11 | [d4/f21ebd] Submitted process > mapping (4) 12 | [ac/18eea2] Submitted process > mapping (3) 13 | [53/bab4f0] Submitted process > mapping (1) 14 | [18/0cf59b] Submitted process > mapping (2) 15 | [d9/7aaa9d] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [e8/bba909] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [d7/f408b8] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [34/baceb3] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/native_7/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 81/19f8bb 32525 buildIndex (1) COMPLETED 0 2015-05-05 09:58:31.118 1h 36m 52s 1h 36m 51s 99.8% 4.5 GB 4.7 GB 4.6 GB 4.7 GB 10.1 GB 3.4 GB 5811525 5810911 4828950528 5077082112 4935929856 5077889024 10832499787 3607811901 41503 372554 0 3608072192 3 | 2 53/bab4f0 17801 mapping (1) COMPLETED 0 2015-05-05 11:35:22.928 4h 4m 32s 4h 4m 31s 637.4% 5.7 GB 7.9 GB 5.8 GB 8 GB 132.2 GB 54.9 GB 14672326 14670914 6172512256 8519045120 6263422976 8610488320 141976398520 58979364709 72452541 96240448 0 11811082240 4 | 6 d9/7aaa9d 8119 makeTranscript (1) COMPLETED 0 2015-05-05 15:39:57.129 6m 21s 6m 17s 299.0% 663.9 MB 1.4 GB 1 GB 1.8 GB 3.1 GB 184.3 MB 380931 377015 696139776 1472913408 1098432512 1925910528 3361650072 193282732 458240 268571 0 193400832 5 | 3 18/0cf59b 17805 mapping (2) COMPLETED 0 2015-05-05 11:35:22.929 4h 14m 56s 4h 14m 53s 523.3% 5.2 GB 7 GB 5.2 GB 7 GB 135.7 GB 57.8 GB 15295882 15292992 5595111424 7497564160 5608378368 7568297984 145708274219 62048085119 72951886 96856903 0 12525391872 6 | 7 e8/bba909 1597 makeTranscript (2) COMPLETED 0 2015-05-05 15:50:18.834 5m 9s 5m 9s 380.0% 791 MB 1.5 GB 1 GB 1.7 GB 3.3 GB 179.7 MB 309152 309081 829452288 1592971264 1087492096 1871904768 3497435544 188393111 466054 260373 0 188469248 7 | 5 d4/f21ebd 17795 mapping (4) COMPLETED 0 2015-05-05 11:35:22.927 4h 23m 10s 4h 23m 10s 784.6% 6.4 GB 8.5 GB 6.4 GB 8.5 GB 157.5 GB 74.9 GB 15790208 15790144 6825926656 9164283904 6830256128 9168809984 169114781830 80465893122 74392710 115040561 0 18269274112 8 | 8 d7/f408b8 12926 makeTranscript (3) COMPLETED 0 2015-05-05 15:58:33.192 6m 10s 6m 7s 359.0% 757.5 MB 1.4 GB 1 GB 1.9 GB 4.6 GB 183.8 MB 370063 367194 794320896 1530052608 1105231872 2087915520 4961207582 192723678 560282 267472 0 192823296 9 | 4 ac/18eea2 17797 mapping (3) COMPLETED 0 2015-05-05 11:35:22.927 4h 37m 9s 4h 37m 4s 790.8% 6.4 GB 8.6 GB 6.4 GB 8.6 GB 166.9 GB 84.7 GB 16628582 16623653 6851473408 9190162432 6861918208 9201356800 179260505376 90895217497 72572543 148361222 4096 18073518080 10 | 9 34/baceb3 24116 makeTranscript (4) COMPLETED 0 2015-05-05 16:12:31.525 5m 26s 5m 22s 428.0% 707.5 MB 1.5 GB 1 GB 1.7 GB 4.1 GB 184.8 MB 325608 322380 741912576 1616642048 1098469376 1878802432 4427956085 193790728 560491 269105 0 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/native_8/log_native_8: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [38/895959] Submitted process > buildIndex (1) 11 | [8f/ad5594] Submitted process > mapping (2) 12 | [08/e06d04] Submitted process > mapping (1) 13 | [2e/05b40a] Submitted process > mapping (3) 14 | [f2/bdb7d3] Submitted process > mapping (4) 15 | [a7/bf10a5] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [5c/f7ce45] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [42/2b7223] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [d9/4e71ca] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/native_8/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 38/895959 24707 buildIndex (1) COMPLETED 0 2015-05-05 22:40:41.001 1h 41m 12s 1h 41m 7s 99.8% 4.5 GB 4.7 GB 4.6 GB 4.7 GB 10.1 GB 3.4 GB 6071702 6067368 4831092736 5077082112 4935974912 5077889024 10832499787 3626243901 41503 374804 167936 3626520576 3 | 2 08/e06d04 12629 mapping (1) COMPLETED 0 2015-05-06 00:21:52.792 4h 28s 4h 25s 619.5% 5.8 GB 8 GB 5.8 GB 8 GB 132.2 GB 54.9 GB 14427703 14425089 6200557568 8547487744 6263103488 8610488320 141995970095 58979417948 75335861 96256856 2400256 11829215232 4 | 6 a7/bf10a5 12666 makeTranscript (1) COMPLETED 0 2015-05-06 04:22:20.843 5m 44s 5m 39s 342.0% 653.2 MB 1.3 GB 1 GB 2 GB 3.1 GB 185 MB 343846 338736 684912640 1405804544 1102381056 2128093184 3364867862 194006049 458640 269562 417792 194088960 5 | 5 f2/bdb7d3 12632 mapping (4) COMPLETED 0 2015-05-06 00:21:52.792 4h 10m 49s 4h 10m 49s 537.7% 5.2 GB 7.1 GB 5.2 GB 7.1 GB 135.7 GB 57.8 GB 15049049 15048856 5588541440 7572590592 5594992640 7642505216 145686730719 62032934026 75851313 96849471 13549568 12641218560 6 | 7 5c/f7ce45 7563 makeTranscript (2) COMPLETED 0 2015-05-06 04:32:41.856 5m 59s 5m 55s 327.0% 713.1 MB 1.5 GB 993.8 MB 1.7 GB 3.3 GB 184.6 MB 358910 354975 747757568 1603461120 1042051072 1804795904 3534321405 193555006 470251 268813 0 193646592 7 | 4 2e/05b40a 12636 mapping (3) COMPLETED 0 2015-05-06 00:21:52.792 4h 23m 4s 4h 23m 3s 671.5% 6.4 GB 8.5 GB 6.4 GB 8.5 GB 157.5 GB 74.9 GB 15784019 15783422 6828609536 9164251136 6832939008 9168777216 169100442320 80470537989 75604089 115027224 458051584 18298445824 8 | 8 42/2b7223 26107 makeTranscript (3) COMPLETED 0 2015-05-06 04:44:56.823 6m 3s 6m 1s 371.0% 799.3 MB 1.4 GB 1 GB 1.7 GB 4.6 GB 183.5 MB 362987 360848 838144000 1496502272 1110728704 1843130368 4957376286 192414161 559905 266907 0 192507904 9 | 3 8f/ad5594 12626 mapping (2) COMPLETED 0 2015-05-06 00:21:52.791 4h 37m 23s 4h 37m 21s 802.7% 6.4 GB 8.6 GB 6.4 GB 8.6 GB 166.9 GB 84.6 GB 16642978 16640657 6849974272 9190195200 6860414976 9201389568 179255987034 90890562786 61691406 148362116 335679488 18075324416 10 | 9 d9/4e71ca 5752 makeTranscript (4) COMPLETED 0 2015-05-06 04:59:15.781 5m 20s 5m 16s 430.0% 808.7 MB 1.4 GB 1 GB 1.7 GB 4.1 GB 184.8 MB 319934 316489 848023552 1502801920 1095532544 1804795904 4427956085 193790728 560491 269105 0 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/native_9/log_native_9: -------------------------------------------------------------------------------- 1 | N E X T F L O W ~ version 0.13.4 2 | Launching 'nextflow-io/rnatoy' - revision: fdbbe257c2 [master] 3 | R N A T O Y P I P E L I N E 4 | ================================= 5 | genome : ../data/mouse_genome_mm9.fa 6 | annotat : ../data/mm65.long.ok.gtf 7 | pair1 : ../data/*_sub_1.fastq.gz 8 | pair2 : ../data/*_sub_2.fastq.gz 9 | [warm up] executor > local 10 | [b7/3b2803] Submitted process > buildIndex (1) 11 | [7f/270d90] Submitted process > mapping (1) 12 | [4c/a78e19] Submitted process > mapping (2) 13 | [64/b72d42] Submitted process > mapping (3) 14 | [88/cc4deb] Submitted process > mapping (4) 15 | [6d/86bf19] Submitted process > makeTranscript (1) 16 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep1.gtf 17 | [7c/a84131] Submitted process > makeTranscript (2) 18 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep1.gtf 19 | [b7/0f70f6] Submitted process > makeTranscript (3) 20 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE18Rep2.gtf 21 | [30/61f4fe] Submitted process > makeTranscript (4) 22 | Saving: transcript_wgEncodeCshlLongRnaSeqCnsE14Rep2.gtf 23 | -------------------------------------------------------------------------------- /rnaseq-toy/native_9/trace.csv: -------------------------------------------------------------------------------- 1 | task_id hash native_id name status exit submit duration realtime %cpu rss vmem peak_rss peak_vmem rchar wchar duration realtime rss vmem peak_rss peak_vmem rchar wchar syscr syscw read_bytes write_bytes 2 | 1 b7/3b2803 13839 buildIndex (1) COMPLETED 0 2015-05-06 11:25:44.585 1h 34m 24s 1h 34m 22s 99.8% 4.5 GB 4.7 GB 4.6 GB 4.7 GB 10.1 GB 3.4 GB 5664315 5662482 4829016064 5077082112 4935995392 5077889024 10832499787 3613693757 41503 373272 307200 3613945856 3 | 2 7f/270d90 31471 mapping (1) COMPLETED 0 2015-05-06 13:00:08.966 4h 4m 43s 4h 4m 40s 546.0% 5.7 GB 7.9 GB 5.8 GB 8 GB 132.3 GB 54.9 GB 14683314 14680312 6172336128 8518979584 6263246848 8610422784 142010782244 58984644458 72821580 96266463 11595776 11848613888 4 | 6 6d/86bf19 15087 makeTranscript (1) COMPLETED 0 2015-05-06 17:04:53.282 6m 17s 6m 14s 304.0% 777.4 MB 1.4 GB 1.2 GB 2 GB 3.1 GB 184.1 MB 377250 374114 815136768 1456140288 1285505024 2149777408 3360892458 193062517 458158 268316 126976 193167360 5 | 4 64/b72d42 31475 mapping (3) COMPLETED 0 2015-05-06 13:00:08.966 4h 12m 41s 4h 12m 37s 801.7% 5.2 GB 7 GB 5.2 GB 7 GB 135.7 GB 57.8 GB 15160798 15156995 5598957568 7497015296 5603401728 7567478784 145719438362 62053008547 75942946 96862155 15732736 12561571840 6 | 7 7c/a84131 1154 makeTranscript (2) COMPLETED 0 2015-05-06 17:12:49.774 5m 53s 5m 52s 334.0% 683.2 MB 1.3 GB 1 GB 1.8 GB 3.3 GB 181.7 MB 352914 352265 716431360 1415946240 1109704704 1936052224 3514625492 190515241 468038 263891 0 190611456 7 | 5 88/cc4deb 31484 mapping (4) COMPLETED 0 2015-05-06 13:00:08.967 4h 26m 24s 4h 26m 23s 678.4% 6.4 GB 8.5 GB 6.4 GB 8.5 GB 157.5 GB 74.9 GB 15983567 15983403 6826528768 9164283904 6830862336 9168809984 169114924510 80468444949 60514005 115039204 361213952 18361409536 8 | 8 b7/0f70f6 22015 makeTranscript (3) COMPLETED 0 2015-05-06 17:26:32.553 6m 22s 6m 20s 347.0% 879.7 MB 1.5 GB 1 GB 1.8 GB 4.6 GB 183.1 MB 382015 379567 922398720 1645924352 1095507968 1897979904 4953765015 192025095 559558 266313 0 192118784 9 | 3 4c/a78e19 31473 mapping (2) COMPLETED 0 2015-05-06 13:00:08.966 4h 38m 15s 4h 38m 12s 806.7% 6.4 GB 8.6 GB 6.4 GB 8.6 GB 166.9 GB 84.7 GB 16694643 16692350 6851928064 9190195200 6862372864 9201389568 179244244403 90892405964 66123664 148350818 147755008 18086739968 10 | 9 30/61f4fe 30939 makeTranscript (4) COMPLETED 0 2015-05-06 17:38:23.630 5m 20s 5m 18s 430.0% 875.7 MB 1.5 GB 1 GB 1.7 GB 4.1 GB 184.8 MB 319929 318030 918224896 1607823360 1103007744 1809154048 4427956085 193790728 560491 269105 0 193867776 11 | -------------------------------------------------------------------------------- /rnaseq-toy/plot.csv: -------------------------------------------------------------------------------- 1 | name,realtime_docker,realtime_native 2 | buildIndex,5439374,5189182 3 | buildIndex,5485727,5464851 4 | buildIndex,5506150,5552819 5 | buildIndex,5600248,5661132 6 | buildIndex,5626161,5664315 7 | buildIndex,5817432,5811525 8 | buildIndex,5825456,5818487 9 | buildIndex,5885340,5838189 10 | buildIndex,5916036,6071702 11 | buildIndex,6027755,6238597 12 | makeTranscript,326812.25,343196.75 13 | makeTranscript,337068.25,338050.5 14 | makeTranscript,339132.25,337743.75 15 | makeTranscript,356362.25,331993 16 | makeTranscript,331836.5,343488.5 17 | makeTranscript,331290.75,334924.5 18 | makeTranscript,329650.5,354749.75 19 | makeTranscript,329031.75,346438.5 20 | makeTranscript,333468.25,346419.25 21 | makeTranscript,350139.75,358027 22 | mapping,15519276,15361867 23 | mapping,15500009.25,15381409.25 24 | mapping,15558931.25,15440434.75 25 | mapping,15500695.5,15475937.25 26 | mapping,15588764.5,15596749.5 27 | mapping,15616975.75,15630580.5 28 | mapping,15607789.75,15735092.5 29 | mapping,15748010,15673237.25 30 | mapping,15744705,15629366.25 31 | mapping,15702850.75,15850685.75 32 | -------------------------------------------------------------------------------- /rnaseq-toy/plot.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | function stats() { 4 | STAGES=$(tail -n +2 $1 | cut -f 4 | cut -f 1 -d ' ' | sort | uniq) 5 | for x in $STAGES; do 6 | row=$(cat $1 | grep $x | sed 's/-/0/g' | datamash median 17 mean 17 median 18 mean 18 count 1) 7 | printf "$x\t$row\n" 8 | done 9 | } 10 | 11 | for file in ${1}_{1..10}/trace.csv;do 12 | stats $file 13 | done 14 | -------------------------------------------------------------------------------- /rnaseq-toy/plot_docker.txt: -------------------------------------------------------------------------------- 1 | buildIndex 5439374 5439374 5437160 5437160 1 2 | buildIndex 5485727 5485727 5483505 5483505 1 3 | buildIndex 5506150 5506150 5503790 5503790 1 4 | buildIndex 5600248 5600248 5597917 5597917 1 5 | buildIndex 5626161 5626161 5623614 5623614 1 6 | buildIndex 5817432 5817432 5815728 5815728 1 7 | buildIndex 5825456 5825456 5823537 5823537 1 8 | buildIndex 5885340 5885340 5883181 5883181 1 9 | buildIndex 5916036 5916036 5914190 5914190 1 10 | buildIndex 6027755 6027755 6025572 6025572 1 11 | makeTranscript 326514 326812.25 319945 320179.75 4 12 | makeTranscript 331686 337068.25 327862.5 330708 4 13 | makeTranscript 332232.5 339132.25 327871 333101 4 14 | makeTranscript 334963.5 356362.25 329620 332938.25 4 15 | makeTranscript 335516.5 331836.5 328961 325898.25 4 16 | makeTranscript 335928.5 331290.75 331901.5 325580 4 17 | makeTranscript 336255 329650.5 332045 325467.25 4 18 | makeTranscript 336860 329031.75 330899 323411.5 4 19 | makeTranscript 339645 333468.25 335596 328685.75 4 20 | makeTranscript 341857 350139.75 337494.5 344404 4 21 | mapping 15361692 15519276 15356198.5 15513843.75 4 22 | mapping 15454825.5 15500009.25 15448011 15493055.5 4 23 | mapping 15457733.5 15558931.25 15451135.5 15552168.5 4 24 | mapping 15463697.5 15500695.5 15454153 15491214.75 4 25 | mapping 15542486 15588764.5 15536185.5 15582322.75 4 26 | mapping 15565456.5 15616975.75 15559197 15610748.75 4 27 | mapping 15577190.5 15607789.75 15571632 15602197.75 4 28 | mapping 15652180.5 15748010 15645695.5 15741581 4 29 | mapping 15653762.5 15744705 15647069 15738124.25 4 30 | mapping 15663592.5 15702850.75 15655979 15695819.25 4 31 | -------------------------------------------------------------------------------- /rnaseq-toy/plot_native.txt: -------------------------------------------------------------------------------- 1 | buildIndex 5189182 5189182 5188542 5188542 1 2 | buildIndex 5464851 5464851 5460610 5460610 1 3 | buildIndex 5552819 5552819 5550238 5550238 1 4 | buildIndex 5661132 5661132 5659020 5659020 1 5 | buildIndex 5664315 5664315 5662482 5662482 1 6 | buildIndex 5811525 5811525 5810911 5810911 1 7 | buildIndex 5818487 5818487 5817976 5817976 1 8 | buildIndex 5838189 5838189 5833224 5833224 1 9 | buildIndex 6071702 6071702 6067368 6067368 1 10 | buildIndex 6238597 6238597 6234163 6234163 1 11 | makeTranscript 329108 343196.75 325048.5 339621.25 4 12 | makeTranscript 330188.5 338050.5 328481 335938 4 13 | makeTranscript 330394 337743.75 329171 335603.75 4 14 | makeTranscript 332802 331993 330300 328803.75 4 15 | makeTranscript 335397 343488.5 332884 340043.25 4 16 | makeTranscript 339370 334924.5 335306.5 332030.75 4 17 | makeTranscript 343794 354749.75 342642.5 352814.75 4 18 | makeTranscript 347835.5 346438.5 344787 343917.5 4 19 | makeTranscript 351378 346419.25 346855.5 342762 4 20 | makeTranscript 365082 358027 363189.5 355994 4 21 | mapping 15283667.5 15361867 15281036 15359723.25 4 22 | mapping 15296676.5 15381409.25 15294534.5 15379171.5 4 23 | mapping 15379772 15440434.75 15377720 15438414 4 24 | mapping 15416534 15475937.25 15416139 15474506 4 25 | mapping 15543045 15596749.5 15541568 15594425.75 4 26 | mapping 15572182.5 15630580.5 15570199 15628265 4 27 | mapping 15588051.5 15735092.5 15587328.5 15733979.5 4 28 | mapping 15609742 15673237.25 15608585.5 15671680 4 29 | mapping 15695969 15629366.25 15692959 15627225.5 4 30 | mapping 15730759 15850685.75 15729374 15848820.25 4 31 | -------------------------------------------------------------------------------- /rnaseq-toy/rnatoy-local.zip: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cbcrg/docker-benchmarks/0e78a3fb9c2ef8e6384e801ed3aabf9b0692a644/rnaseq-toy/rnatoy-local.zip -------------------------------------------------------------------------------- /rnaseq-toy/stage.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | function stats() { 4 | STAGES=$(cat trace_${1}.txt | cut -f 4 | cut -f 1 -d ' ' | uniq | sort) 5 | for x in $STAGES; do 6 | row=$(cat trace_${1}.txt | grep $x | sed 's/-/0/g' | datamash median 17 mean 17 median 18 mean 18 count 1) 7 | printf "$x\t$row\n" 8 | done 9 | 10 | row=$(cat trace_${1}.txt | sed 's/-/0/g' | datamash median 17 mean 17 median 18 mean 18 count 1) 11 | printf "ALL\t$row\n" 12 | } 13 | 14 | echo $1 | awk '{print toupper($0)}' 15 | stats $1 16 | -------------------------------------------------------------------------------- /rnaseq-toy/stats_docker.txt: -------------------------------------------------------------------------------- 1 | DOCKER 2 | buildIndex 5721796.5 5712967.9 5719671 5710819.4 10 3 | makeTranscript 329574.5 336479.25 323948.5 329037.375 40 4 | mapping 15498825.5 15608800.775 15492210 15602107.625 40 5 | ALL 5721796.5 7721565.3333333 5719671 7715044.3777778 90 6 | -------------------------------------------------------------------------------- /rnaseq-toy/stats_native.txt: -------------------------------------------------------------------------------- 1 | NATIVE 2 | buildIndex 5737920 5731079.9 5736696.5 5728453.4 10 3 | makeTranscript 338978.5 343503.15 336113 340752.9 40 4 | mapping 15522083 15577536 15517569 15575621.075 40 5 | ALL 5737920 7712804.0555556 5736696.5 7710438.8111111 90 6 | -------------------------------------------------------------------------------- /rnaseq-toy/table.R: -------------------------------------------------------------------------------- 1 | native <- read.delim("time_native.txt", header=TRUE) 2 | docker <- read.delim("time_docker.txt", header=TRUE) 3 | 4 | stderr <- function(x) sd(x)/sqrt(length(x)) 5 | 6 | native_mean_exec_time = mean(native$duration) / 1000 /60 7 | docker_mean_exec_time = mean(docker$duration) / 1000 /60 8 | 9 | native_err = stderr(native$duration) / 1000 /60 10 | docker_err = stderr(docker$duration) / 1000 /60 11 | 12 | native_stdev_exec_time = sd(native$duration) / 1000 /60 13 | docker_stddev_exec_time = sd(docker$duration) / 1000 /60 14 | 15 | # each instance executes 9 tasks 16 | native_mean_task_time = native_mean_exec_time / 9 17 | docker_mean_task_time = docker_mean_exec_time / 9 18 | 19 | cat(sprintf("RNA-SEQ : native docker\n")) 20 | cat(sprintf("Task mean time : %.1f %.1f\n", native_mean_task_time, docker_mean_task_time)) 21 | cat(sprintf("Mean exec time : %.1f (±%.1f) %.1f (±%.1f) \n", native_mean_exec_time, native_err, docker_mean_exec_time, docker_err)) 22 | cat(sprintf("Stddev exec time: %.1f %.1f\n", native_stdev_exec_time, docker_stddev_exec_time)) 23 | cat(sprintf("Slow-down : %.3f\n" , docker_mean_exec_time/native_mean_exec_time)) 24 | -------------------------------------------------------------------------------- /rnaseq-toy/table.txt: -------------------------------------------------------------------------------- 1 | RNA-SEQ : native docker 2 | Task mean time : 128.5 128.7 3 | Mean exec time : 1156.9 (±4.3) 1158.2 (±2.1) 4 | Stddev exec time: 13.5 6.7 5 | Slow-down : 1.001 6 | -------------------------------------------------------------------------------- /rnaseq-toy/time.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | function gettime { 4 | 5 | printf "begin\tend\telapsed\tdelta\tduration\trealtime\n" 6 | for x in ${1}_{1..10}; do 7 | duration=$(tail -n +2 $x/trace.csv | sed 's/-/0/g' | datamash sum 17) 8 | realtime=$(tail -n +2 $x/trace.csv | sed 's/-/0/g' | datamash sum 18) 9 | delta=$(groovy delta.groovy "$(cat $x/.nextflow.log | head -n 1 | cut -f 1,2 -d ' ')" "$(cat $x/.nextflow.log | tail -n 1 | cut -f 1,2 -d ' ')") 10 | printf "$delta\t$duration\t$realtime\n" 11 | done 12 | 13 | } 14 | 15 | gettime $1 16 | 17 | -------------------------------------------------------------------------------- /rnaseq-toy/time_docker.txt: -------------------------------------------------------------------------------- 1 | begin end elapsed delta duration realtime 2 | May-04 21:30:05.195 May-05 03:49:24.779 6:19:19 22759584 69319985 69202856 3 | May-05 09:55:46.273 May-05 16:17:35.404 6:21:49 22909131 69243419 69190005 4 | May-05 22:36:36.954 May-06 05:00:59.889 6:24:22 23062935 69611753 69557078 5 | May-06 11:14:41.505 May-06 17:30:18.202 6:15:36 22536697 69156912 69106442 6 | May-06 23:48:37.187 May-07 06:03:45.504 6:15:8 22508317 69232440 69182475 7 | May-05 03:43:34.004 May-05 09:58:08.944 6:14:34 22474940 68827534 68770518 8 | May-05 16:18:08.612 May-05 22:40:14.838 6:22:6 22926226 69590488 69547071 9 | May-06 05:04:50.219 May-06 11:25:19.913 6:20:29 22829694 69948817 69896645 10 | May-06 17:43:59.354 May-07 00:03:16.515 6:19:17 22757161 70005540 69953727 11 | May-07 06:33:09.182 May-07 12:57:25.311 6:24:16 23056129 70003992 69947177 12 | -------------------------------------------------------------------------------- /rnaseq-toy/time_native.txt: -------------------------------------------------------------------------------- 1 | begin end elapsed delta duration realtime 2 | May-05 03:49:45.848 May-05 09:55:22.140 6:5:36 21936292 67987625 67969850 3 | May-05 16:17:49.720 May-05 22:36:12.038 6:18:22 22702318 68927900 68902095 4 | May-06 05:01:14.033 May-06 11:14:17.672 6:13:3 22383639 69422486 69402892 5 | May-06 17:30:33.091 May-06 23:48:13.259 6:17:40 22660168 69884223 69863181 6 | May-07 06:03:59.447 May-07 12:22:04.444 6:18:4 22684997 69824220 69807787 7 | May-04 21:28:56.931 May-05 03:42:47.810 6:13:50 22430879 68560723 68535879 8 | May-05 09:58:29.927 May-05 16:17:57.545 6:19:27 22767618 69584277 69564284 9 | May-05 22:40:39.006 May-06 05:04:36.003 6:23:56 23036997 69361128 69336440 10 | May-06 11:25:42.772 May-06 17:43:44.025 6:18:1 22681253 69618745 69599518 11 | May-07 00:03:39.995 May-07 06:32:55.053 6:29:15 23355058 70981038 70957567 12 | -------------------------------------------------------------------------------- /scripts/delta.groovy: -------------------------------------------------------------------------------- 1 | def d1 = '15-' + args[0] 2 | def d2 = '15-' + args[1] 3 | def beginning = Date.parse('yy-MMM-dd HH:mm:ss.S', d1).time as BigInteger 4 | def ending = Date.parse('yy-MMM-dd HH:mm:ss.S', d2).time as BigInteger 5 | 6 | def delta = ending - beginning 7 | 8 | def period( delta ) { 9 | def hours = 0 10 | def mins = 0 11 | def (secs,millis) = delta.divideAndRemainder(1000) 12 | 13 | if( secs >= 60 ) { 14 | (mins,secs) = secs.divideAndRemainder(60) 15 | 16 | if( mins >= 60 ) { 17 | (hours,mins) = mins.divideAndRemainder(60) 18 | } 19 | } 20 | 21 | "$hours:$mins:$secs" 22 | } 23 | 24 | print "${args[0]}\t${args[1]}\t${period(delta)}\t${delta}" 25 | -------------------------------------------------------------------------------- /scripts/join.groovy: -------------------------------------------------------------------------------- 1 | /* 2 | * Read "plot_native.txt" and "plot_docker.txt" tab-separated files. 3 | * Each rows contain the following fields 4 | * 5 | * 1. Task type 6 | * 2. Median task duration time 7 | * 3. Mean task duration time 8 | * 4. Median task real execution time 9 | * 5. Mean task duration time 10 | * 6. Number of tasks executed 11 | * 12 | */ 13 | 14 | def file1 = new File('plot_native.txt') 15 | def file2 = new File('plot_docker.txt') 16 | 17 | def all = [] 18 | def index = 0 19 | 20 | file1.readLines().each { line -> 21 | def cols = line.tokenize('\t') 22 | def key = cols[0] // note: index is zero based 23 | def time = cols[2] // third column: Mean task duration time 24 | 25 | def name = key.tokenize()[0] 26 | if( name == 'normExonerate' || name == 'matrix' ) return 27 | 28 | all[index++] = [ name: name, native: time ] 29 | } 30 | 31 | index = 0 32 | 33 | file2.readLines().each { line -> 34 | def cols = line.tokenize('\t') 35 | def key = cols[0] 36 | def time = cols[2] // third column: Mean task duration time 37 | 38 | def name = key.tokenize()[0] 39 | if( name == 'normExonerate' || name == 'matrix' ) return 40 | 41 | assert name == all[index].name 42 | all[index].docker = time 43 | index ++ 44 | } 45 | 46 | println "name,realtime_docker,realtime_native" 47 | 48 | all.each { record -> println "${record.name},${record.docker},${record.native}" } 49 | -------------------------------------------------------------------------------- /supplementary.txt: -------------------------------------------------------------------------------- 1 | Nmpd-flow - varcall pipeline 2 | ------------------------ 3 | 4 | Image nextflow/nmdp-flow:peerj5515 [6583ce78ca29] 5 | https://registry.hub.docker.com/u/nextflow/nmdp-flow 6 | 7 | Github repo 8 | https://github.com/nextflow-io/nmdp-flow/tree/docker-benchmark 9 | 10 | Data 11 | s3://cbcrg-eu/nmdpflow-data/ 12 | 13 | Piper 14 | ------ 15 | 16 | Image cbcrg/piper-nf:peerj5515 [dc982a05a3da] 17 | https://registry.hub.docker.com/u/cbcrg/piper-nf 18 | 19 | Github repo [cirrus] 20 | https://github.com/cbcrg/piper-nf/tree/docker-benchmark 21 | 22 | Data 23 | s3://cbcrg-eu/piper-chicken/ 24 | 25 | 26 | RnaSeq 27 | ------- 28 | 29 | Image nextflow/rnatoy:peerj5515 [fa576fc1203a] 30 | 31 | Github repo 32 | https://github.com/nextflow-io/rnatoy/tree/docker-benchmark 33 | 34 | Data 35 | s3://cbcrg-eu/rnatoy-mouse/ 36 | 37 | --------------------------------------------------------------------------------