Pipeline Report

Created by Bpipe, Wed Dec 10 16:21:52 GMT 2014

Result


Succeeded

Timeline


index_...
→
align
→
conver...
→
finali...
→
histo
→
draw_h...
→
count_...
draw_a...
1.561 s
15 minutes, 5.575 s
54.014 s
0.676 s
0.676 s
1.399 s
14.876 s
2.166 s

Pipeline Stages


Total Runtime = 10.957 seconds

  1. index_reference ✓

    Inputs
    • input/nanopore/Ecoli_R7_2D.fasta
    Commands
    Outputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.index_reference.lastindex
    Execution Time 2014-12-10 16:21:44 (0.112 seconds)

  2. align ✓

    Inputs
    • input/nanopore/Ecoli_R7_2D.fasta
    Commands
    Outputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.index_reference.align.maf
    Execution Time 2014-12-10 16:21:44 (0.057 seconds)

  3. convert ✓

    Inputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.index_reference.align.maf
    Commands
    Outputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.index_reference.align.convert.bam
    Tools
    • samtools : - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
    Execution Time 2014-12-10 16:21:44 (0.045 seconds)

  4. finalise_bam ✓

    Inputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.index_reference.align.convert.bam
    Commands
    Outputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.bam
    Execution Time 2014-12-10 16:21:44 (0.043 seconds)

  5. histo ✓

    Inputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.bam
    CommandsgenomeCoverageBed -ibam output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.bam | grep ^genome > output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.bam.cov.txt
    Outputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.bam
    Execution Time 2014-12-10 16:21:44 - 2014-12-10 16:21:51 (6.683 seconds)

  6. draw_histo ✓

    Inputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.bam
    Commands
    Outputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.draw_histo.png
    Execution Time 2014-12-10 16:21:51 (0.018 seconds)

  7. count_errors ✓

    Inputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.draw_histo.png
    Commands
    Outputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.count_errors.errors.txt
    Execution Time 2014-12-10 16:21:51 (0.027 seconds)

  8. draw_alignment_length_histogram ✓

    Inputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.count_errors.errors.txt
    Commands
    Outputs
    • output/alignment/nickloman-last-q1/Ecoli_R7_2D.final.count_errors.errors.draw_alignment_length_histogram.png
    Execution Time 2014-12-10 16:21:51 (0.020 seconds)