PARCLIP Pipeline

Created by Bpipe, Tue Sep 26 18:02:29 EEST 2017

Result


Succeeded

Timeline


prepro...
→
align
→
PARpar...
→
PARaly...
→
sam2ba...
→
index
→
readAt...
→
annota...
→
read_b...
→
annota...
→
addInf...
→
visbed...
→
geneLv...
→
annota...
→
addInf...
→
geneLv...
→
statsT...
→
spatia...
spatia...
2 minutes, 39.092 s
16.753 s
0.135 s
0.040 s
2.053 s
0.014 s
2.220 s
1 minutes, 2.974 s
0.530 s
23.486 s
1.580 s
0.339 s
0.011 s
23.742 s
1.850 s
0.457 s
1.249 s
53.102 s
0.530 s

Pipeline Stages


Total Runtime = 1 minutes, 39.191 seconds

  1. preprocess ✓

    fastqToFASTA.pl v2.0 and collapseFA.pl v2.0

    Inputs
    • test.fastq
    Commands
    Outputs
    • test.fasta
    Execution Time 2017-9-26 18:0:50 (0.124 seconds)

  2. align ✓

    filterSAMMultiMapperTC.pl v2.0

    Inputs
    • test.fasta
    Commands
    Outputs
    • test.aligned.sam
    Tools
    • samtools : 0.1.19-44428cd - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    • bowtie : 0.12.9
    Execution Time 2017-9-26 18:0:50 (0.059 seconds)

  3. PARparams ✓

    editPARalyzerINIfile.pl v2.0

    Inputs
    • test.aligned.sam
    Commands
    Outputs
    • test.ini
    Execution Time 2017-9-26 18:0:50 (0.025 seconds)

  4. PARalyze ✓

    Inputs
    • test.ini
    Commands
    Outputs
    • test.clusters
    Execution Time 2017-9-26 18:0:50 (0.040 seconds)

  5. sam2bam ✓

    Inputs
    • test.clusters
    • test.groups
    • test.distribution
    • test.sam
    Commands
    Outputs
    • test.bam
    Tools
    • samtools : 0.1.19-44428cd - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2017-9-26 18:0:50 (0.011 seconds)

  6. index ✓

    Inputs
    • test.bam
    Commands
    Outputs
    • test.bam.bai
    Tools
    • samtools : 0.1.19-44428cd - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2017-9-26 18:0:50 (0.014 seconds)

  7. readAttributes ✓

    readAttributesTC.pl v2.0

    Inputs
    • test.sam
    Commands
    Outputs
    • test.attr
    Execution Time 2017-9-26 18:0:50 (0.020 seconds)

  8. annotateReads ✓

    Inputs
    • test.attr
    Commands
    Outputs
    • test.readcsv
    Execution Time 2017-9-26 18:0:50 (0.008 seconds)

  9. read_bed ✓

    reads2bed.pl v2.0

    Inputs
    • test.readcsv
    Commands
    Outputs
    • test.readbed
    Execution Time 2017-9-26 18:0:50 (0.009 seconds)

  10. annotateClusters ✓

    PARclusters2bed.py v2.0

    Inputs
    • test.clusters
    Commands
    Outputs
    • test.clusterbed
    Execution Time 2017-9-26 18:0:50 (0.017 seconds)

  11. addInfo ✓

    editClustersTC.pl v2.0

    Inputs
    • test.readbed
    • test.clusterbed
    Commands
    Outputs
    • test.clusters.csv
    Execution Time 2017-9-26 18:0:50 (0.019 seconds)

  12. visbed ✓

    visclusterbed.py v2.0

    Inputs
    • test.clusters.csv
    Commands
    Outputs
    • test.clusters.bed
    Execution Time 2017-9-26 18:0:50 (0.014 seconds)

  13. geneLvl ✓

    geneLevel.pl v1.0

    Inputs
    • test.clusters.csv
    Commands
    Outputs
    • test.gene_cl.csv
    Execution Time 2017-9-26 18:0:50 (0.011 seconds)

  14. annotateGroups ✓

    Inputs
    • test.groups
    Commands../scripts/annotate.pl -g ../files/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz -p ../scripts/annotationRank.txt -r ../files/hg19_rmsk.bed.gz -s ../files/hg19_rmsk_info -strict -oi test.groups | ../scripts/PARclusters2bed.py > test.groupbed
    Outputs
    • test.groupbed
    Execution Time 2017-9-26 18:0:50 - 2017-9-26 18:1:14 (23.930 seconds)

  15. addInfoGroups ✓

    editClustersTC.pl v2.0

    Inputs
    • test.readbed
    • test.groupbed
    CommandsintersectBed -a test.readbed -b test.groupbed -wao -s | awk -F " " 'BEGIN{OFS=",";} { print $5,$7,$8,$9,$11,$12}' | sed '/,\-1/d' | ../scripts/editClustersTC.pl > test.groups.csv
    Outputs
    • test.groups.csv
    Execution Time 2017-9-26 18:1:14 - 2017-9-26 18:1:16 (1.931 seconds)

  16. geneLvlGroups ✓

    geneLevel.pl v1.0

    Inputs
    • test.groups.csv
    Commandsperl ../scripts/geneLevel.pl test.groups.csv ../files/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz > test.gene_gr.csv
    Outputs
    • test.gene_gr.csv
    Execution Time 2017-9-26 18:1:16 (0.555 seconds)

  17. statsTable ✓

    Inputs
    • test.readbed
    Commands../scripts/extractDataTC.pl test > test.clusters.txt
    Outputs
    • test.clusters.txt
    Execution Time 2017-9-26 18:1:17 - 2017-9-26 18:1:18 (1.313 seconds)

  18. spatialPerl ✓

    Inputs
    • test.readbed
    Commandsperl ../scripts/Spatial.pl -g ../files/gencode.v19.chr_patch_hapl_scaff.annotation.gtf.gz -a test -strict -t ../files/isoforms.fpkm_tracking
    Outputs
    • tmp_test_spatial.csv
    Execution Time 2017-9-26 18:1:18 - 2017-9-26 18:2:11 (53.102 seconds)

  19. spatialR ✓

    Inputs
    • test.readbed
    Commandsunset TMP; unset TEMP; TEMPDIR="/tmp/47608273698326195-0" setsid Rscript - <<'!' yn<-'n' fn<-'test' resolution<-3 install.packages('../scripts/colorRamps_2.3.tar.gz', lib='../scripts/') install.packages('../scripts/schoolmath_0.4.tar.gz', lib='../scripts/') install.packages('../scripts/gtools_3.4.1.tar.gz', lib='../scripts/') install.packages('../scripts/ellipse_0.3-8.tar.gz', lib='../scripts/') install.packages('../scripts/RColorBrewer_1.1-2.tar.gz', lib='../scripts/') install.packages('../scripts/LSD_2.5.tar.gz', lib='../scripts/') library(colorRamps, lib.loc='../scripts/') library(schoolmath, lib.loc='../scripts/') library(gtools, lib.loc='../scripts/') library(ellipse, lib.loc='../scripts/') library(RColorBrewer, lib.loc='../scripts/') library(LSD, lib.loc='../scripts/') library(parallel) source('../scripts/Spatial.R') !
    Outputs
    • test.readbed
    Execution Time 2017-9-26 18:2:11 - 2017-9-26 18:2:28 (17.352 seconds)