Hi all!
Using the command: bwa sampe refseq.fasta seq_1.aln.sai seq_2.aln.sai seq_1.fastq.gz seq_2.fastq.gz > output.sam , sometimes I get the error that you can see in the title. It looks like this:
[bwa_sai2sam_pe_core] 5505024 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (410, 437, 469)
[infer_isize] fail to infer insert size: weird pairing
[bwa_sai2sam_pe_core] time elapses: 0.82 sec
[bwa_sai2sam_pe_core] changing coordinates of 643 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
Segmentation fault
I did several very similar alignment tasks with BWA, most of them goes through fine, but with a few fastq files this happens. My data is from the 1000genomes, so that shouldn't be the problem I guess.
Please let me know, if you guys have an idea what's causing this!
Yours,
Attila Vikor
Using the command: bwa sampe refseq.fasta seq_1.aln.sai seq_2.aln.sai seq_1.fastq.gz seq_2.fastq.gz > output.sam , sometimes I get the error that you can see in the title. It looks like this:
[bwa_sai2sam_pe_core] 5505024 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (410, 437, 469)
[infer_isize] fail to infer insert size: weird pairing
[bwa_sai2sam_pe_core] time elapses: 0.82 sec
[bwa_sai2sam_pe_core] changing coordinates of 643 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
Segmentation fault
I did several very similar alignment tasks with BWA, most of them goes through fine, but with a few fastq files this happens. My data is from the 1000genomes, so that shouldn't be the problem I guess.
Please let me know, if you guys have an idea what's causing this!
Yours,
Attila Vikor
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