Pipeline Report

Created by Bpipe, Wed Dec 10 16:42:38 GMT 2014

Result

Timeline

Pipeline Stages

Total Runtime = 9 minutes, 2.843 seconds

1. index_reference ✓

   Inputs	input/nanopore/Ecoli_R73_2D_wf19.fasta
   Commands	lastdb output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.lastindex input/refs/NC_000913.fna && touch output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.lastindex
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.lastindex
   Execution Time	2014-12-10 16:33:38 - 2014-12-10 16:33:40 (1.798 seconds)

2. align ✓

   Inputs	input/nanopore/Ecoli_R73_2D_wf19.fasta
   Commands	lastal -q 1 -a 1 -b 1 output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.lastindex input/nanopore/Ecoli_R73_2D_wf19.fasta > output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.align.maf
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.align.maf
   Execution Time	2014-12-10 16:33:40 - 2014-12-10 16:41:53 (8 minutes, 13.083 seconds)

3. convert ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.align.maf
   Commands	maf-convert sam output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.align.maf | samtools view -T input/refs/NC_000913.fna -bS - | samtools sort -@ 16 - output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.align.convert
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.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 16:41:53 - 2014-12-10 16:42:23 (30.600 seconds)

4. finalise_bam ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.align.convert.bam
   Commands	cp output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.index_reference.align.convert.bam output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.bam
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.bam
   Execution Time	2014-12-10 16:42:23 (0.192 seconds)

5. histo ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.bam
   Commands	genomeCoverageBed -ibam output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.bam | grep ^genome > output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.bam.cov.txt
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.bam
   Execution Time	2014-12-10 16:42:24 - 2014-12-10 16:42:27 (3.366 seconds)

6. draw_histo ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.bam
   Commands	cov_histogram.R output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.bam.cov.txt output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.draw_histo.png
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.draw_histo.png
   Execution Time	2014-12-10 16:42:27 - 2014-12-10 16:42:29 (1.662 seconds)

7. count_errors ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.draw_histo.png
   Commands	count-errors.py output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.bam > output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Execution Time	2014-12-10 16:42:29 - 2014-12-10 16:42:35 (6.526 seconds)

8. draw_alignment_length_histogram ✓

   Inputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Commands	aln_histogram.R output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.count_errors.errors.txt output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.count_errors.errors.draw_alignment_length_histogram.png
   Outputs	output/alignment/nickloman-last-q1/Ecoli_R73_2D_wf19.final.count_errors.errors.draw_alignment_length_histogram.png
   Execution Time	2014-12-10 16:42:35 - 2014-12-10 16:42:37 (1.653 seconds)