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Old 01-03-2013, 02:30 AM   #1
dd_genome
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Default "refine gapped alignments... Segmentation fault" while using bwa sampe

Dear all,
I got struck to convert sai files (generated using bwa aln) to sam files using bwa sampe command.
I have downloaded one sra file (SRR015553.sra) from sequence read archive of ncbi. Then I converted the SRR015553.sra file to two fastq files (as it contains pair end reads) by using sratoolkit.2.1.16 command:

fastq-dump.2.1.18 --split-3 SRR015553.sra

Then I converted the two fastq files thus generated viz. SRR015553_1.fastq and SRR015553_2.fastq to the respective sai files viz. SRR015553_sa1.sai and SRR015553_sa2.sai using the bwa aln command with no error. Finally when I was trying to convert the sai files to the sam file (by bwa sampe) using the command line:

bwa sampe hg19.fa SRR015553_sa1.sai SRR015553_sa2.sai SRR015553_1.fastq SRR015553_2.fastq > SRR015553.sam

I got the error in the form of segmentation error. The details of the last few lines before exit from the program are as follows:

[bwa_paired_sw] 3 out of 8338 Q17 singletons are mated.
[bwa_paired_sw] 0 out of 215506 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 3.63 sec
[bwa_sai2sam_pe_core] refine gapped alignments... Segmentation fault

I have repeated the entire process several times but in vain. I am using a CentOs Linux machine with ram 64Gb and enough memory, so probably memory is not an issue in my case.
Can you help me in solving my problem, where the error could appear. I did the same process of converting sra files to sam files with success for some other sra files but NOT in case of this sra file. Where I am wrong? Is there any problem in converting sra files to fastq files or elsewhere. Please help me to find the way out. Thank you.
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Old 01-03-2013, 03:06 AM   #2
GenoMax
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Did you create the hg19 indexes yourself or are you using indexes downloaded from elsewhere?

Check post #51 if you are using "nohup" to run this analysis to capture additional error info (http://seqanswers.com/forums/showpos...2&postcount=51). Parent thread is here: http://seqanswers.com/forums/showthread.php?t=2077
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Old 01-03-2013, 09:21 AM   #3
dd_genome
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Hi GenoMax,
Thanks for your reply. Yes I did indexing of hg19.fa by using bwa. I am surprised to say that except that sra file (SRR015553.sra) as mentioned by me other sra files from the same run (Illumina) of the same individual viz. SRR015551.sra, SRR015552.sra etc worked perfectly. What and where should be the problem then?
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Old 01-03-2013, 10:42 AM   #4
GenoMax
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It is possible that perhaps the file in question (SRR015553.sra) was corrupted somewhere along the way. Have you tried to re-download from SRA and reanalyze? In the worst case scenario the original file at SRA may be corrupt.
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