Pipeline Report

Created by Bpipe, Wed Dec 10 16:28:40 GMT 2014

Result

Timeline

Pipeline Stages

Total Runtime = 4 minutes, 59.872 seconds

1. index_reference ✓

   Inputs	input/nanopore/Ecoli_R73_2D_wf19.fasta
   Commands	bwa-0.7.10-r789 index input/refs/NC_000913.fna
   Outputs	input/nanopore/Ecoli_R73_2D_wf19.fasta
   Execution Time	2014-12-10 16:23:43 - 2014-12-10 16:23:46 (3.276 seconds)

2. align ✓

   Inputs	input/nanopore/Ecoli_R73_2D_wf19.fasta
   Commands	bwa-0.7.10-r789 mem -t 16 -x pacbio input/refs/NC_000913.fna input/nanopore/Ecoli_R73_2D_wf19.fasta > output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.align.sam
   Outputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.align.sam
   Execution Time	2014-12-10 16:23:46 - 2014-12-10 16:28:17 (4 minutes, 30.877 seconds)

3. sort ✓

   Inputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.align.sam
   Commands	samtools view -bS output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.align.sam | samtools sort -@ 16 - output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.align.sort
   Outputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.align.sort.bam
   Tools	samtools : 1.1 - A suite of utilities for sorting, indexing, viewing and calling variants on NGS data
   Execution Time	2014-12-10 16:28:17 - 2014-12-10 16:28:26 (9.129 seconds)

4. finalise_bam ✓

   Inputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.align.sort.bam
   Commands	cp output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.align.sort.bam output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.bam
   Outputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.bam
   Execution Time	2014-12-10 16:28:27 (0.223 seconds)

5. histo ✓

   Inputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.bam
   Commands	genomeCoverageBed -ibam output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.bam | grep ^genome > output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.bam.cov.txt
   Outputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.bam
   Execution Time	2014-12-10 16:28:27 - 2014-12-10 16:28:30 (2.933 seconds)

6. draw_histo ✓

   Inputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.bam
   Commands	cov_histogram.R output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.bam.cov.txt output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.draw_histo.png
   Outputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.draw_histo.png
   Execution Time	2014-12-10 16:28:30 - 2014-12-10 16:28:31 (1.391 seconds)

7. count_errors ✓

   Inputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.draw_histo.png
   Commands	count-errors.py output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.bam > output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Outputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Execution Time	2014-12-10 16:28:31 - 2014-12-10 16:28:38 (6.754 seconds)

8. draw_alignment_length_histogram ✓

   Inputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Commands	aln_histogram.R output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.count_errors.errors.txt output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.count_errors.errors.draw_alignment_length_histogram.png
   Outputs	output/alignment/nickloman-bwa-pacbio/Ecoli_R73_2D_wf19.final.count_errors.errors.draw_alignment_length_histogram.png
   Execution Time	2014-12-10 16:28:38 - 2014-12-10 16:28:39 (1.610 seconds)