[carolW]

4G, right away. Does samse use the same memory as aln?

[GenoMax]

4G, right away. Does samse use the same memory as aln?

If you only have 4GB of RAM then you are probably running out of memory. BWA will need between ~3-5GB of RAM for human data as indicated here.

You may need to find a computer/server with more available RAM or upgrade the RAM in your own.

[carolW]

The problem is that bwa doesn't even start. Should it not start and then, crash if it is due to lack of memory? I don't see it in the list of process when I run top.

Another question is that I didn't finally need to run bwa mem as in one of the answers was suggested?

[GenoMax]

The problem is that bwa doesn't even start. Should it not start and then, crash if it is due to lack of memory? I don't see it in the list of process when I run top.

Are you using 32-bit or 64-bit OS? Did you compile bwa on this machine yourself?

BWA-MEM is a new alignment algorithm (for long reads). See pre-print here: http://arxiv.org/abs/1303.3997

[carolW]

Are you using 32-bit or 64-bit OS? Did you compile bwa on this machine yourself?

BWA-MEM is a new alignment algorithm (for long reads). See pre-print here: http://arxiv.org/abs/1303.3997

64-bit and I compiled bwa on this machine.

Mastal thought that the segmentation fault comes from the number of bp and suggested me to use bwa mem because there are more than 100bp in the seqence based on the output that was generated from bwa aln (see below). Do you agree with this argument?

[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
[bwa_aln_core] 109811 sequences have been processed.

[carolW]

Is there anything else that could be done?

Look forward to your reply,

Carol

[carolW]

I executed the following command many times, I didn't see bwa in the list of processes. So it doesn't even start. Is it able to evaluate the memory before starting? What prevents to start?

../pgm/bwa-0.7.3a/bwa samse ../hg19/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa SRR062641.filt.sai SRR062641.filt.fastq > SRR062641.filt.sam

Thanks,

Carol

[GenoMax]

If you just issue the following commands (highlighted in red) do you see an output similar to what is posted here:

$ [COLOR="Red"]bwa samse[/COLOR]
Usage: bwa samse [-n max_occ] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>
$ [COLOR="Red"]bwa[/COLOR]

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.4-r385
Contact: Heng Li <[email protected]>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)

(output for second command truncated)

Did you create the human genome index or download it from somewhere else?

[carolW]

I get the same output

../pgm/bwa-0.7.3a/bwa samse
Usage: bwa samse [-n max_occ] [-f out.sam] [-r RG_line] <prefix> <in.sai> <in.fq>

../pgm/bwa-0.7.3a/bwa

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.3a-r367
Contact: Heng Li <[email protected]>

Usage: bwa <command> [options]

Command: index index sequences in the FASTA format
mem BWA-MEM algorithm
fastmap identify super-maximal exact matches
pemerge merge overlapping paired ends (EXPERIMENTAL)
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries

fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generating BWT
bwtupdate update .bwt to the new format
bwt2sa generate SA from BWT and Occ


I downloaded the HG index from http://cufflinks.cbcb.umd.edu/igenomes.html. I used it with bwa aln without any problem. I use only the following file from the uncompressed untared file
hg19/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa

[GenoMax]

Just wanted to verify that the bwa is executing properly on your system .. which it seems to be doing.

Are you issuing the samse command from the directory where you have the "SRR062641*" files? Have you tried to add ./SRR062641.filt.sai and ./SRR062641.filt.fastq to explicitly locate the files as being in current directory?

[carolW]

yes, I added ./ and get segmentation fault right away

[GenoMax]

Are you generating files that contain word "core" in the name after you get the seg fault?

[carolW]

I'm not sure to have understood your question. I don't generate files that contain "core" in the name. This is what I did

../pgm/bwa-0.7.3a/bwa samse ../hg19/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/genome.fa ./SRR062641.filt.sai ./SRR062641.filt.fastq > ./SRR062641.filt.sam
Segmentation fault (core dumped)

[carolW]

Note that no core file is generated after segmentation fault if this could answer your question.

Just a question, to compile and generated the bw exec file, I just invoked "make". Was it sufficient to compile the files?

[GenoMax]

Note that no core file is generated after segmentation fault if this could answer your question.

So we know that the process is not aborting resulting in a core dump.

Just a question, to compile and generated the bw exec file, I just invoked "make". Was it sufficient to compile the files?

That should be all you need as long as you have the compiler and libraries available.

Have you been able to successfully use the bwa program on a different data set (look for some E coli data from SRA if you need a test case) so we are sure it works otherwise.

Are you the "administrator" of this machine? What does the output of command "limit" show?