Pipeline Report

Created by Bpipe, Wed Dec 10 16:22:55 GMT 2014

Result


Succeeded

Timeline


index_...
→
align
→
conver...
→
finali...
→
histo
→
draw_h...
→
count_...
draw_a...
1.565 s
3 minutes, 56.361 s
23.622 s
0.102 s
0.102 s
1.453 s
6.234 s
1.533 s

Pipeline Stages


Total Runtime = 7.278 seconds

  1. index_reference ✓

    Inputs
    • input/nanopore/Ecoli_R73_2D.fasta
    Commands
    Outputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.index_reference.lastindex
    Execution Time 2014-12-10 16:22:51 (0.104 seconds)

  2. align ✓

    Inputs
    • input/nanopore/Ecoli_R73_2D.fasta
    Commands
    Outputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.index_reference.align.maf
    Execution Time 2014-12-10 16:22:51 (0.044 seconds)

  3. convert ✓

    Inputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.index_reference.align.maf
    Commands
    Outputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.index_reference.align.convert.bam
    Tools
    • samtools : 1.1 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2014-12-10 16:22:51 (0.047 seconds)

  4. finalise_bam ✓

    Inputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.index_reference.align.convert.bam
    Commands
    Outputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.bam
    Execution Time 2014-12-10 16:22:51 (0.045 seconds)

  5. histo ✓

    Inputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.bam
    CommandsgenomeCoverageBed -ibam output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.bam | grep ^genome > output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.bam.cov.txt
    Outputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.bam
    Execution Time 2014-12-10 16:22:51 - 2014-12-10 16:22:54 (3.072 seconds)

  6. draw_histo ✓

    Inputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.bam
    Commands
    Outputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.draw_histo.png
    Execution Time 2014-12-10 16:22:54 (0.018 seconds)

  7. count_errors ✓

    Inputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.draw_histo.png
    Commands
    Outputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.count_errors.errors.txt
    Execution Time 2014-12-10 16:22:54 (0.023 seconds)

  8. draw_alignment_length_histogram ✓

    Inputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.count_errors.errors.txt
    Commands
    Outputs
    • output/alignment/nickloman-last-q2/Ecoli_R73_2D.final.count_errors.errors.draw_alignment_length_histogram.png
    Execution Time 2014-12-10 16:22:54 (0.018 seconds)