stampy error with bwa

[pankajsvats]

./stampy.py --bwaoptions="-q10 /data/bwa/bwa_human" -g hg_rna -h hg_rna -M /data/3_1.fq /data/3_2.fq
stampy: Mapping...
stampy: [bwa_aln] 17bp reads: max_diff = 2
stampy: [bwa_aln] 38bp reads: max_diff = 3
stampy: [bwa_aln] 64bp reads: max_diff = 4
stampy: [bwa_aln] 93bp reads: max_diff = 5
stampy: [bwa_aln] 124bp reads: max_diff = 6
stampy: [bwa_aln] 157bp reads: max_diff = 7
stampy: [bwa_aln] 190bp reads: max_diff = 8
stampy: [bwa_aln] 225bp reads: max_diff = 9
stampy: [bwt_restore_bwt] fail to open file '/data/bwa/bwa_human.rbwt'. Abort!

stampy: Error: Executing 'bwa aln -q10 /data/bwa/bwa_human /tmp/tmpbwaoA8298.fq' exits with returncode -6

[colindaven]

Does the file
'/data/bwa/bwa_human.rbwt'.
exist ?

Is it readable - check permissions.

Perhaps recreate the reference if all else fails

[pankajsvats]

Thanks

The stampy is having some problem with bwa-0.6
version so i tried with bwa 0.5 and rebuilt all the index's
now its working

[NGSfan]

Does anybody know what returncode -11 means?

I have created an index for both bwa and stampy. This command works with my hg18.fa but now it is crashing with my hg19.fa


stampy.py -g /net/ngs/HumanGenome/hg19/hg19 -h /net/ngs/HumanGenome/hg19/hg19 -o my.sam --sanger --bwa=/bin/bwa-0.5.9/bwa --bwaoptions="-q10 /net/ngs/HumanGenome/hg19/hg19.fa" --bwatmpdir=/tmp --keepreforder -M my.fastq.gz

stampy: Mapping...
stampy: [bwa_aln] 17bp reads: max_diff = 2
stampy: [bwa_aln] 38bp reads: max_diff = 3
stampy: [bwa_aln] 64bp reads: max_diff = 4
stampy: [bwa_aln] 93bp reads: max_diff = 5
stampy: [bwa_aln] 124bp reads: max_diff = 6
stampy: [bwa_aln] 157bp reads: max_diff = 7
stampy: [bwa_aln] 190bp reads: max_diff = 8
stampy: [bwa_aln] 225bp reads: max_diff = 9
stampy: [bwa_read_seq] 2.0% bases are trimmed.
stampy: [bwa_aln_core] calculate SA coordinate...

stampy: Error: '/net/ngs/NGS.analysis/bin/bwa-0.5.9/bwa aln -q10 /net/ngs/HumanGenome/hg19/hg19.fa /tmp/tmpbwaZSXe_i.fq' exits with returncode -11

[NGSfan]

actually it looks like a BWA problem. I get a core dump when I run BWA by itself. I will check to see if my index is bad.

[pankajsvats]

Rebuilt your bwa index and try again hope it will work

[NGSfan]

I think I have found the problem - it is the index. I think the default "is" indexing method worked with hg18, but it will not work on hg19 (it is too large).

It took some digging, but this thread mentions it:

http://seqanswers.com/forums/showthread.php?t=7799

I am now running the index with:

bwa index -a bwtsw hg19.fa