Pipeline Report

Created by Bpipe, Wed Dec 10 16:33:30 GMT 2014

Result

Timeline

Pipeline Stages

Total Runtime = 4 minutes, 45.515 seconds

1. index_reference ✓

   Inputs	input/nanopore/Ecoli_R73_2D_wf19.fasta
   Commands	lastdb output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.lastindex input/refs/NC_000913.fna && touch output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.lastindex
   Outputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.lastindex
   Execution Time	2014-12-10 16:28:48 - 2014-12-10 16:28:50 (1.790 seconds)

2. align ✓

   Inputs	input/nanopore/Ecoli_R73_2D_wf19.fasta
   Commands	lastal -q 2 -a 1 -b 1 output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.lastindex input/nanopore/Ecoli_R73_2D_wf19.fasta > output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.align.maf
   Outputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.align.maf
   Execution Time	2014-12-10 16:28:50 - 2014-12-10 16:32:50 (4 minutes, 0.392 seconds)

3. convert ✓

   Inputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.align.maf
   Commands	maf-convert sam output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.align.maf | samtools view -T input/refs/NC_000913.fna -bS - | samtools sort -@ 16 - output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.align.convert
   Outputs	output/alignment/nickloman-last-q2/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 16:32:50 - 2014-12-10 16:33:16 (26.467 seconds)

4. finalise_bam ✓

   Inputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.align.convert.bam
   Commands	cp output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.index_reference.align.convert.bam output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.bam
   Outputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.bam
   Execution Time	2014-12-10 16:33:16 (0.196 seconds)

5. histo ✓

   Inputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.bam
   Commands	genomeCoverageBed -ibam output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.bam | grep ^genome > output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.bam.cov.txt
   Outputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.bam
   Execution Time	2014-12-10 16:33:17 - 2014-12-10 16:33:20 (2.957 seconds)

6. draw_histo ✓

   Inputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.bam
   Commands	cov_histogram.R output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.bam.cov.txt output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.draw_histo.png
   Outputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.draw_histo.png
   Execution Time	2014-12-10 16:33:20 - 2014-12-10 16:33:21 (1.572 seconds)

7. count_errors ✓

   Inputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.draw_histo.png
   Commands	count-errors.py output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.bam > output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Outputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Execution Time	2014-12-10 16:33:21 - 2014-12-10 16:33:28 (6.499 seconds)

8. draw_alignment_length_histogram ✓

   Inputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.count_errors.errors.txt
   Commands	aln_histogram.R output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.count_errors.errors.txt output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.count_errors.errors.draw_alignment_length_histogram.png
   Outputs	output/alignment/nickloman-last-q2/Ecoli_R73_2D_wf19.final.count_errors.errors.draw_alignment_length_histogram.png
   Execution Time	2014-12-10 16:33:28 - 2014-12-10 16:33:30 (1.740 seconds)