hi,
I am interested in taking advantage of the parallelised approach of running bwa using pBWA:http://pbwa.sourceforge.net/
to speed up the sampe step which uses one thread in bwa.
My interpretation of the guidance is that to useit I just need to adapt my existing bwa command:
The command that I am using is:
pBWA aln -t 8 -q 15 -f .R2.sai $ref_genome_folder $input_fastq_R2_untrimmed
PC is a 4 core (virtualised to 8) with 16GB ram
but I get the following error:
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
Proc 0: [bwa_seq_open] seeked to 0 in /PathTo_raw_data/s_5_1_sequence.txt
Broadcasting BWT (this may take a while)... done!
Broadcasting BWT (this may take a while)... [bwt_restore_bwt] fail to open file '/pathTo_ref_genomes/ucsc_hg19/ucsc_hg19.fa.rbwt'. Abort!
Aborted (core dumped)
The indexed genome that I successfully with bwawas generated by the bwa index refGenome.fasta command. Do I need to do anything different with respect to the ref genome index for pBWA?
Any pointers would be appreciated
I am interested in taking advantage of the parallelised approach of running bwa using pBWA:http://pbwa.sourceforge.net/
to speed up the sampe step which uses one thread in bwa.
My interpretation of the guidance is that to useit I just need to adapt my existing bwa command:
The command that I am using is:
pBWA aln -t 8 -q 15 -f .R2.sai $ref_genome_folder $input_fastq_R2_untrimmed
PC is a 4 core (virtualised to 8) with 16GB ram
but I get the following error:
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
Proc 0: [bwa_seq_open] seeked to 0 in /PathTo_raw_data/s_5_1_sequence.txt
Broadcasting BWT (this may take a while)... done!
Broadcasting BWT (this may take a while)... [bwt_restore_bwt] fail to open file '/pathTo_ref_genomes/ucsc_hg19/ucsc_hg19.fa.rbwt'. Abort!
Aborted (core dumped)
The indexed genome that I successfully with bwawas generated by the bwa index refGenome.fasta command. Do I need to do anything different with respect to the ref genome index for pBWA?
Any pointers would be appreciated
), and create a new index. And make sure you have the following files before executing pBWA: 
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