Pipeline Report

Created by Bpipe, Wed Dec 10 16:44:23 GMT 2014

Result

Timeline

Pipeline Stages

Total Runtime = 1 minutes, 41.073 seconds

1. index_reference ✓

   Inputs	input/nanopore/Ecoli_R73_2D_wf19.fasta
   Commands	bwa-0.7.10-r1017-dirty index input/refs/NC_000913.fna
   Outputs	input/nanopore/Ecoli_R73_2D_wf19.fasta
   Execution Time	2014-12-10 16:42:45 - 2014-12-10 16:42:49 (3.637 seconds)

2. align ✓

   Inputs	input/nanopore/Ecoli_R73_2D_wf19.fasta
   Commands	bwa-0.7.10-r1017-dirty mem -t 16 -x ont2d input/refs/NC_000913.fna input/nanopore/Ecoli_R73_2D_wf19.fasta > output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.align.sam
   Outputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.align.sam
   Execution Time	2014-12-10 16:42:49 - 2014-12-10 16:44:5 (1 minutes, 16.246 seconds)

3. sort ✓

   Inputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.align.sam
   Commands	samtools view -bS output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.align.sam | samtools sort -@ 16 - output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.align.sort
   Outputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.align.sort.bam
   Tools	samtools : - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
   Execution Time	2014-12-10 16:44:5 - 2014-12-10 16:44:12 (7.258 seconds)

4. finalise_bam ✓

   Inputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.align.sort.bam
   Commands	cp output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.align.sort.bam output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.bam
   Outputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.bam
   Execution Time	2014-12-10 16:44:12 (0.194 seconds)

5. histo ✓

   Inputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.bam
   Commands	genomeCoverageBed -ibam output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.bam | grep ^genome > output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.bam.cov.txt
   Outputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.bam
   Execution Time	2014-12-10 16:44:13 - 2014-12-10 16:44:15 (2.502 seconds)

6. draw_histo ✓

   Inputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.bam
   Commands	cov_histogram.R output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.bam.cov.txt output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.draw_histo.png
   Outputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.draw_histo.png
   Execution Time	2014-12-10 16:44:15 - 2014-12-10 16:44:17 (1.330 seconds)

7. count_errors ✓

   Inputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.draw_histo.png
   Commands	count-errors.py output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.bam > output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Outputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Execution Time	2014-12-10 16:44:17 - 2014-12-10 16:44:21 (4.416 seconds)

8. draw_alignment_length_histogram ✓

   Inputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Commands	aln_histogram.R output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.count_errors.errors.txt output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.count_errors.errors.draw_alignment_length_histogram.png
   Outputs	output/alignment/nickloman-bwa-ont2d/Ecoli_R73_2D_wf19.final.count_errors.errors.draw_alignment_length_histogram.png
   Execution Time	2014-12-10 16:44:21 - 2014-12-10 16:44:23 (1.601 seconds)