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?