Pipeline Report

Created by Bpipe, Wed Dec 10 16:23:07 GMT 2014

Result

Timeline

Pipeline Stages

Total Runtime = 7.410 seconds

1. index_reference ✓

   Inputs	input/nanopore/Ecoli_R73_2D.fasta
   Commands
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.index_reference.lastindex
   Execution Time	2014-12-10 16:23:3 (0.098 seconds)

2. align ✓

   Inputs	input/nanopore/Ecoli_R73_2D.fasta
   Commands
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.index_reference.align.maf
   Execution Time	2014-12-10 16:23:3 (0.043 seconds)

3. convert ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.index_reference.align.maf
   Commands
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_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 16:23:3 (0.045 seconds)

4. finalise_bam ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.index_reference.align.convert.bam
   Commands
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.bam
   Execution Time	2014-12-10 16:23:3 (0.045 seconds)

5. histo ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.bam
   Commands	genomeCoverageBed -ibam output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.bam | grep ^genome > output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.bam.cov.txt
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.bam
   Execution Time	2014-12-10 16:23:3 - 2014-12-10 16:23:6 (3.276 seconds)

6. draw_histo ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.bam
   Commands
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.draw_histo.png
   Execution Time	2014-12-10 16:23:6 (0.015 seconds)

7. count_errors ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.draw_histo.png
   Commands
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.count_errors.errors.txt
   Execution Time	2014-12-10 16:23:6 (0.019 seconds)

8. draw_alignment_length_histogram ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.count_errors.errors.txt
   Commands
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D.final.count_errors.errors.draw_alignment_length_histogram.png
   Execution Time	2014-12-10 16:23:6 (0.039 seconds)