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Old 04-17-2012, 05:38 AM   #6
Location: St. Louis

Join Date: Jan 2012
Posts: 15

A FASTQ has 4 lines per read. When it segfaults at 25034752 it means that it has gone through 12517376 reads from reads_1 and 12517376 from reads 2. And something in the next 131072 reads makes it choke. At least that is what I think I am getting from the evidence here.

When I removed the first chunk it did continue further than it had before and then dropped out again.

I thought it was a memory issue, but then I saw it was failing in the same place no matter how much memory I threw at it.

Luckily, I think I have a small dataset that chokes on this. I will try the idea of separating it into files 65536 from each of the reads files and seeing if there is something there.

Now I'm really new to soapaligner and I'm not familiar with all of the options, so it is not out of the realm of possibility that my problem could be a max size of insert problem.

Could it be that soapaligner expects a certain insert size and if those qualifications aren't met it can segfault (point 3)?

I hope I have more helpful info today.
cwisch88 is offline   Reply With Quote