mothur

Uchime issues with 1.42.1?

I have 2 jobs running on the cluster. Both died at uchime with no error in mother. I also write an error file. one job says 48063 Bus error. The other begins:

*** Error in `mothur': double free or corruption (fasttop): 0x0000000001935e90 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x7ffff6c0a489]
/lib64/libstdc++.so.6(_ZNSs6assignERKSs+0x9e)[0x7ffff7748dbe]
mothur[0x41b1e3]
mothur[0x8509a4]
mothur[0x10dda8c]
mothur[0xedbc39]
mothur[0x13da16f]
/lib64/libpthread.so.0(+0x7dd5)[0x7ffff6f5ddd5]
/lib64/libc.so.6(clone+0x6d)[0x7ffff6c86ead]
======= Memory map: ========
00400000-016c0000 r-xp 00000000 00:39 7866632213                         /isg/shared/apps/mothur/1.42.1/mothur
018c0000-018c2000 r--p 012c0000 00:39 7866632213                         /isg/shared/apps/mothur/1.42.1/mothur
018c2000-018c8000 rw-p 012c2000 00:39 7866632213                         /isg/shared/apps/mothur/1.42.1/mothur
018c8000-1d43d000 rw-p 00000000 00:00 0                                  [heap]
7fff60000000-7fff61518000 rw-p 00000000 00:00 0 
7fff61518000-7fff64000000 ---p 00000000 00:00 0 

this is the first set of jobs I’ve run since they upgraded to mothur 1.42.1

We had a bug in the count table remove functions that is causing this issue. It has been fixed in version 1.42.3. Can you give it a try, https://github.com/mothur/mothur/releases/tag/v.1.42.3?

sorry, was away. I’ve asked for the update and will give it another shot!

also failing with 1.42.3 at

mothur > 
chimera.uchime(fasta=current, count=current, dereplicate=t)
Using 2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.count_table as input file for the count parameter.
Using 2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.fasta as input file for the fasta parameter.

Using 32 processors.

uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

Checking sequences from 2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.fasta ...
Reducing processors to 8.

/******************************************/
Running command: split.groups(groups=0613HF1N.0613HF1N, fasta=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.fasta, count=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.count_table)

/******************************************/
Running command: split.groups(groups=0613HF1R.0613HF1R, fasta=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.fasta, count=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.count_table)

/******************************************/
Running command: split.groups(groups=0613Kelp2B.0613Kelp2B, fasta=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.fasta, count=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.count_table)

/******************************************/
Running command: split.groups(groups=0613Kelp2L.0613Kelp2L, fasta=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.fasta, count=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.count_table)

/******************************************/
Running command: split.groups(groups=0613Kelp2N.0613Kelp2N, fasta=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.fasta, count=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.count_table)

/******************************************/
Running command: split.groups(groups=0613Kelp2R.0613Kelp2R, fasta=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.fasta, count=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.count_table)

/******************************************/
Running command: split.groups(groups=0613HF1L.0613HF1L, fasta=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.fasta, count=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.count_table)

/******************************************/
Running command: split.groups(groups=RID633Blank.RID633Blank, fasta=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.fasta, count=2018KelpMouseStudy.trim.contigs.good.unique.good.filter.precluster.count_table)

That’s the end of the logfile. Here’s the top of the error log that I had sbatch write

*** Error in `mothur’: double free or corruption (fasttop): 0x00007fff94003620 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x7ffff6c0a489]
/lib64/libstdc++.so.6(_ZNSs6assignERKSs+0x9e)[0x7ffff7748dbe]
mothur[0x41b1e3]
mothur[0x850414]
mothur[0x10dd23c]
mothur[0xedb1b9]
mothur[0x13d991f]
/lib64/libpthread.so.0(+0x7dd5)[0x7ffff6f5ddd5]
/lib64/libc.so.6(clone+0x6d)[0x7ffff6c86ead]
======= Memory map: ========
00400000-016c0000 r-xp 00000000 00:39 8939607240 /isg/shared/apps/mothur/1.42.3/mothur
018bf000-018c1000 r–p 012bf000 00:39 8939607240 /isg/shared/apps/mothur/1.42.3/mothur
018c1000-018c7000 rw-p 012c1000 00:39 8939607240 /isg/shared/apps/mothur/1.42.3/mothur

I’ve been having trouble with the chimera step in 1.42.3 also - I accidentally posted about it in a different section: Pre.cluster error in 1.42.0