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Old 05-10-2018, 07:50 AM   #1
eilosei
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Location: New York

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Default bwa samse problem

Hi there,

I'm trying to use bwa to align Paired-end reads to mouse genome. The alignment step goes well, but the bwa samse failed and generated error message like:

[bwa_sai2sam_pe_core] convert to sequence coordinate...
[infer_isize] (25, 50, 75) percentile: (133, 164, 201)
[infer_isize] low and high boundaries: 51 and 337 for estimating avg and std
[infer_isize] inferred external isize from 210397 pairs: 167.836 +/- 42.264
[infer_isize] skewness: 0.224; kurtosis: -0.815; ap_prior: 1.00e-05
[infer_isize] inferred maximum insert size: 462 (6.97 sigma)
[bwa_sai2sam_pe_core] time elapses: 111.90 sec
[bwa_sai2sam_pe_core] changing coordinates of 13666 alignments.
[bwa_sai2sam_pe_core] align unmapped mate...
[bwa_paired_sw] 5674 out of 6128 Q17 singletons are mated.
[bwa_paired_sw] 1650 out of 2146 Q17 discordant pairs are fixed.
[bwa_sai2sam_pe_core] time elapses: 1.93 sec
[bwa_sai2sam_pe_core] refine gapped alignments... 0.41 sec
[bwa_sai2sam_pe_core] print alignments... 2.58 sec
[bwa_sai2sam_pe_core] 262144 sequences have been processed.
[bwa_sai2sam_pe_core] convert to sequence coordinate...
bwa(88853,0xa70dc1c0) malloc: *** mach_vm_map(size=1022164992) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

There is no problem to align that file by "bwa samse" from one end.

Could anyone tell what is the problem? How may I get it to work? Thank you!
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Old 05-10-2018, 06:58 PM   #2
Richard Finney
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Your mac is out of memory.
Close your other programs and try again.
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Old 05-11-2018, 08:59 AM   #3
eilosei
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Thank you for the suggestion. I tried to release the memory and hard drive space. The program processed a little bit more reads but it still stopped with the same error message. Is that because I still don't have enough memory and hard drive space to complete the job? I'm using my mac (16GB) to do the alignment. I've never got problem with single reads. What's the minimum requirement for running BWA on paired-end reads?

Quote:
Originally Posted by Richard Finney View Post
Your mac is out of memory.
Close your other programs and try again.
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Old 05-11-2018, 10:27 AM   #4
Richard Finney
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16 GB should be fine. What is your command line? How much free memory do you have? (not total memory).
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Old 05-11-2018, 11:08 AM   #5
eilosei
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Here is my command:
bwa sampe RefGenome/mm9bwaidx file_1.bwa file_2.bwa file_1.fastq.gz file_2.fastq.gz > file.sam

This is the memory in my mac when I run the command.

Physical Memory: 16.00 GB
- Available Memory: 9.63 GB
- Memory Used: 6.37 GB
App Memory: 4.76 GB
Wired Memory: 1.27 GB
Compressed: 330.88 MB
- Catched Files: 5.01 GB


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Originally Posted by Richard Finney View Post
16 GB should be fine. What is your command line? How much free memory do you have? (not total memory).
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