Question: bowtie2-build index files missing
0
gravatar for juan.crescente
20 months ago by
juan.crescente20 wrote:

I'm trying to use bowtie2 for mapping reads agains a large genome (17Gb). I'm getting an error. It seems like an issue in the index / or some files missing:

./bowtie2 -x refseq -1w_paired.fq -2 rv_paired.fq -S outrefseq --no-unal
Could not open index file refseq.rev.1.bt2l
Could not open index file refseq.rev.2.bt2l
Segmentation fault (core dumped)
(ERR): bowtie2-align exited with value 139

I built the index this way:

nohup ./bowtie2-build /Data/refseq.fasta refseq &

These seems to be the output files

refseq.1.bt2l
refseq.2.bt2l
refseq.3.bt2l
refseq.4.bt2l

This is the last output of build

tail nohup
      bucket 7: 60%
      bucket 7: 70%
      bucket 7: 80%
      bucket 7: 90%
      bucket 7: 100%
      Sorting block of length 2029111534 for bucket 7
      (Using difference cover)
      Sorting block time: 03:54:26
    Returning block of 2029111535 for bucket 7

Is there anything I'm missing?

ADD COMMENTlink written 20 months ago by juan.crescente20
2

Segmentation fault (core dumped) is a typical memory error. You should increase memory for that.

ADD REPLYlink modified 20 months ago • written 20 months ago by Mehmet500

Can I specify the memory in the job? What about this error? Could not open index file refseq.rev.1.bt2l

ADD REPLYlink written 20 months ago by juan.crescente20

Do you use a SuperComputer system? If yes, you can specify memory during qsub submission. If not, you need to assign more memory to this analysis in your personal computer. There may have an error during indexing files because of lack of memory, so bowtie could not open index file reqseq.rev.1.bt2l.

ADD REPLYlink written 20 months ago by Mehmet500

It looks like bowtie-build did not produce all the files for the index, and you are missing the ones mentioned in the error message, so the bowtie-build command did not complete successfully. Since you are working with a large genome, you may need more memory, as already mentioned by Mehmet, segmentation faults often mean the computer ran out of memory.

ADD REPLYlink written 20 months ago by mastal5112.0k

So the seg fault was when running bowtie2, not build. Maybe build was killed and did not finish. I'll re-run and update results in a few days.

ADD REPLYlink written 20 months ago by juan.crescente20
1

Can you specify how much RAM you are using for the job/have available?

ADD REPLYlink written 20 months ago by genomax78k

47GB is the RAM in the machine, can I increase the assigned memory?

ADD REPLYlink modified 20 months ago • written 20 months ago by juan.crescente20
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