segfault in summary.seqs

mothur bugs
1

We’re fairly new to mothur so this is as likely to be user error as a bug. The first part of the workflow looks like this:

make.contigs(file=PracticeSmithMiSeq.files, processors=8)
summary.seqs(fasta=current)
screen.seqs(fasta=130819_M01529_0018_2012_1.R1.trim.contigs.fasta, group=130819_M01529_0018_2012_1.R1.contigs.groups, summary=130819_M01529_0018_2012_1
.R1.trim.contigs.summary, maxambig=0, maxlength=275)
unique.seqs(fasta=130819_M01529_0018_2012_1.R1.trim.contigs.good.fasta)
count.seqs(name=130819_M01529_0018_2012_1.R1.trim.contigs.good.names, group=130819_M01529_0018_2012_1.R1.contigs.good.groups)
summary.seqs(count=current)
pcr.seqs(fasta=silva.bacteria.fasta, start=13862, end=23444, keepdots=F)
system(mv silva.bacteria.pcr.fasta silva.v4.fasta)
summary.seqs(fasta=silva.v4.fasta)
align.seqs(fasta=130819_M01529_0018_2012_1.R1.trim.contigs.good.unique.fasta, reference=silva.v4.fasta)
summary.seqs(fasta=130819_M01529_0018_2012_1.R1.trim.contigs.good.unique.fasta, count=130819_M01529_0018_2012_1.R1.trim.contigs.good.count_table)
screen.seqs(fasta=current, count=current, start=8, end=9582, maxhomop=8)

This segfaults with processors=8 and processors=1, both in the pthread library

summary.seqs(fasta=current, count=current, processors=1)
[as12:26348] *** Process received signal ***
[as12:26348] Signal: Segmentation fault (11)
[as12:26348] Signal code: Address not mapped (1)
[as12:26348] Failing at address: (nil)
[as12:26348] [ 0] /lib64/libpthread.so.0 [0x327a00eca0]
[as12:26348] [ 1] /mounts/al-salam/software/Mothur/mothur(_ZN17SeqSummaryCommand7executeEv+0xdf6) [0xc53206]
[as12:26348] [ 2] /mounts/al-salam/software/Mothur/mothur(_ZN11BatchEngine8getInputEv+0x8db) [0x76ce2b]
[as12:26348] [ 3] /mounts/al-salam/software/Mothur/mothur(main+0x121c) [0x9cf9ac]
[as12:26348] [ 4] /lib64/libc.so.6(__libc_start_main+0xf4) [0x327981d9c4]
[as12:26348] [ 5] /mounts/al-salam/software/Mothur/mothur(_ZNSt8ios_base4InitD1Ev+0x49) [0x49adf9]
[as12:26348] *** End of error message ***

I’ve looked around and couldn’t find anything in the forums or on the net that seemed to be related to this. Is this the result of a mistake we made in the workflow?

thanks,
charlie peck

2

summary.seqs(fasta=130819_M01529_0018_2012_1.R1.trim.contigs.good.unique.fasta, count=130819_M01529_0018_2012_1.R1.trim.contigs.good.count_table)


screen.seqs(fasta=current, count=current, start=8, end=9582, maxhomop=8) - the current file will be the 130819_M01529_0018_2012_1.R1.trim.contigs.good.unique.fasta which is not aligned. I think you wanted 130819_M01529_0018_2012_1.R1.trim.contigs.good.unique.align, which is the result of the align.seqs command.
summary.seqs(fasta=current, count=current, processors=1) - I suspect this is failing because the screen.seqs command create a blank fasta file in before it died and summary.seqs is reading that.
3

That fixed it, thank you very much.

Is there a more appropriate place to ask newbie questions than this?

thanks,
charlie

4

Nope, you are in the right place. Happy to help, :slight_smile: