Segmentation fault when running Minia v3 with some kmer values
1
0
Entering edit mode
2.7 years ago

Hi,

I am attempting to assemble a set of 151 bp paired end reads using Minia v3 on my university's cluster. I am using the precompiled linux binary.

I ran kmergenie on the data (~60 million reads) and it suggested setting kmer-size to 47. If I submit the job with 1 thread and 8G memory, it completes without problems. The maxRSS is 4.9G.

However, when I submit the job with 8 threads, I get a segmentation fault


Minia 3, git commit 4b32fec
setting storage type to hdf5
[Approximating frequencies of minimizers ]  100  %   elapsed:   0 min 26 sec   remaining:   0 min 0  sec   cpu: 100.0 % mem: [  29,   29,   29] MB
[DSK: nb solid kmers found : 439869125   ]  116  %   elapsed:  64 min 5  sec   remaining:   0 min 0  sec   cpu: 706.6 %   mem: [ 152, 50662, 50731] MB
bcalm_algo params, prefix:295-8.minia-k31-8c.unitigs.fa k:47 a:2 minsize:10 threads:8 mintype:1
DSK used 1 passes and 16 partitions
prior to queues allocation                      21:32:25     memory [current, maxRSS]: [ 159, 50731] MB
Starting BCALM2                                 21:32:25     memory [current, maxRSS]: [ 159, 50731] MB
[Iterating DSK partitions                ]  0    %   elapsed:   0 min 0  sec   remaining:   0 min 0  sec
Iterated 34589186 kmers, among them 2486370 were doubled
/var/spool/slurmd/job830979/slurm_script: line 11:  1446 Segmentation fault      ../minia-v3.2.0-bin-Linux/bin/minia -in 295-8_filenames -nb-cores 8 -max-memory 60000 -kmer-size 47 -out 295-8.minia-k31-8c

This has happened regardless of how much memory I allocate (here I gave it 60G).

But, if I use a smaller kmer size (say, 31), the job completes with 8 cores, no problem. For that job, the maxRSS was 22G.

Is the problem that the software runs out of memory, or something else?

Thanks,

Matt

Assembly software error minia • 764 views
ADD COMMENT
0
Entering edit mode
2.7 years ago
Rayan Chikhi ★ 1.5k

Hi,

Segfault is unlikely a memory error but rather a bug in the program or something else. Do you have enough disk space? Would it be possible to share the input data?

Best, Rayan

ADD COMMENT

Login before adding your answer.

Traffic: 2324 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6