4G, right away. Does samse use the same memory as aln?
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Originally posted by carolW View Post4G, right away. Does samse use the same memory as aln?
You may need to find a computer/server with more available RAM or upgrade the RAM in your own.
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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?
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Originally posted by carolW View PostThe 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.
BWA-MEM is a new alignment algorithm (for long reads). See pre-print here: http://arxiv.org/abs/1303.3997
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Originally posted by GenoMax View PostAre 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
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.
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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
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If you just issue the following commands (highlighted in red) do you see an output similar to what is posted here:
Code:$ [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)
Did you create the human genome index or download it from somewhere else?
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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
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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?
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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)
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Originally posted by carolW View PostNote that no core file is generated after segmentation fault if this could answer your question.
Originally posted by carolW View PostJust a question, to compile and generated the bw exec file, I just invoked "make". Was it sufficient to compile the files?
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?
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