Pipeline Report

Created by Bpipe, Wed Dec 10 16:23:21 GMT 2014

Result


Succeeded

Timeline


index_...
→
align
→
sort
→
finali...
→
histo
→
draw_h...
→
count_...
draw_a...
3.168 s
2 minutes, 3.122 s
8.942 s
0.103 s
0.103 s
1.273 s
4.337 s
1.622 s

Pipeline Stages


Total Runtime = 9.598 seconds

  1. index_reference ✓

    Inputs
    • input/nanopore/Ecoli_R73_2D.fasta
    Commandsbwa-0.7.10-r1017-dirty index input/refs/NC_000913.fna
    Outputs
    • input/nanopore/Ecoli_R73_2D.fasta
    Execution Time 2014-12-10 16:23:14 - 2014-12-10 16:23:18 (3.168 seconds)

  2. align ✓

    Inputs
    • input/nanopore/Ecoli_R73_2D.fasta
    Commands
    Outputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.align.sam
    Execution Time 2014-12-10 16:23:18 (0.050 seconds)

  3. sort ✓

    Inputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.align.sam
    Commands
    Outputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.align.sort.bam
    Tools
    • samtools : - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2014-12-10 16:23:18 (0.033 seconds)

  4. finalise_bam ✓

    Inputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.align.sort.bam
    Commands
    Outputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.bam
    Execution Time 2014-12-10 16:23:18 (0.039 seconds)

  5. histo ✓

    Inputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.bam
    CommandsgenomeCoverageBed -ibam output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.bam | grep ^genome > output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.bam.cov.txt
    Outputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.bam
    Execution Time 2014-12-10 16:23:18 - 2014-12-10 16:23:20 (2.519 seconds)

  6. draw_histo ✓

    Inputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.bam
    Commands
    Outputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.draw_histo.png
    Execution Time 2014-12-10 16:23:20 (0.016 seconds)

  7. count_errors ✓

    Inputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.draw_histo.png
    Commands
    Outputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.count_errors.errors.txt
    Execution Time 2014-12-10 16:23:20 (0.020 seconds)

  8. draw_alignment_length_histogram ✓

    Inputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.count_errors.errors.txt
    Commands
    Outputs
    • output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D.final.count_errors.errors.draw_alignment_length_histogram.png
    Execution Time 2014-12-10 16:23:20 (0.014 seconds)