Dear all,
I'm having some difficulties trying to index a reference genome using BWA -a bwtsw.
I am using BWA 0.6.2 version and I tried to index the Hg19 but BWA fails to complete the index.
The error looks like this:
I am currently using a 4 CPU server with 8Gb RAM.
In the BWA manual it says that BWA uses approx. 2.5 Gb of memory to align the whole human genome, so I wasn't expecting this type of error.
I checked the memory usage (using system monitor) during BWA index and in fact it showed that only 2.4 Gb out of 7.9Gb were being used in the process.
Do you have any idea of what might be the problem?
I tried looking at the different seqanswers threads reporting "segmentation fault" with BWA but none of them had an answer to my question.
I have 250Gb of disk space left so I don't think that this is the problem.
I'm having some difficulties trying to index a reference genome using BWA -a bwtsw.
I am using BWA 0.6.2 version and I tried to index the Hg19 but BWA fails to complete the index.
The error looks like this:
[BWTIncConstructFromPacked] 620 iterations done. 1697352406 characters processed.
[BWTIncConstructFromPacked] 630 iterations done. 1740074246 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 1778041526 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 1811782918 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 1841768294 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 1868415350 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 1892095270 characters processed.
[bwt_gen] Finished constructing BWT in 688 iterations.
[bwa_index] 886.42 seconds elapse.
[bwa_index] Update BWT... Segmentation fault (core dumped)
[BWTIncConstructFromPacked] 630 iterations done. 1740074246 characters processed.
[BWTIncConstructFromPacked] 640 iterations done. 1778041526 characters processed.
[BWTIncConstructFromPacked] 650 iterations done. 1811782918 characters processed.
[BWTIncConstructFromPacked] 660 iterations done. 1841768294 characters processed.
[BWTIncConstructFromPacked] 670 iterations done. 1868415350 characters processed.
[BWTIncConstructFromPacked] 680 iterations done. 1892095270 characters processed.
[bwt_gen] Finished constructing BWT in 688 iterations.
[bwa_index] 886.42 seconds elapse.
[bwa_index] Update BWT... Segmentation fault (core dumped)
In the BWA manual it says that BWA uses approx. 2.5 Gb of memory to align the whole human genome, so I wasn't expecting this type of error.
I checked the memory usage (using system monitor) during BWA index and in fact it showed that only 2.4 Gb out of 7.9Gb were being used in the process.
Do you have any idea of what might be the problem?
I tried looking at the different seqanswers threads reporting "segmentation fault" with BWA but none of them had an answer to my question.
I have 250Gb of disk space left so I don't think that this is the problem.
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