Question: minia seg fault (core dump) after inability to unlink mphf temp files?
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gravatar for mmelendrez
17 days ago by
mmelendrez0
mmelendrez0 wrote:

hey! So I'm unsure of what the following means:

ubuntu@ubuntu-xenial:/vagrant/denovo$ ./minia-v2.0.7-bin-Linux/bin/minia -in minia-v2.0.7-bin-Linux/test_data/P4-P1S_12.fastq -kmer-size 31 -abundance-min 3 -out P4-P1S
[DSK: Collecting stats on P4-P1S_12     ]  100  %   elapsed:   0 min 9  sec    estimated remaining:   0 min 0  sec   cpu:   88.2 %   mem: [  11,   11,   11] MB
[DSK: nb solid kmers found : 1467480    ]  108  %   elapsed:   0 min 47 sec    estimated remaining:   0 min 0  sec   cpu:   86.7 %   mem: [  36,  114,  114] MB
WARNING: Error unlinking temporary file mphf.temp.Xi3OR8
WARNING: Error unlinking temporary file mphf.temp.XQvJoL
Segmentation fault (core dumped)

The output when I ls the dir:

ubuntu@ubuntu-xenial:/vagrant/denovo$ ls
trashme_25135_dsk_partitions.parts.1   trashme_25135_dsk_partitions.parts.15  trashme_25135_dsk_partitions.parts.20  trashme_25135_dsk_partitions.parts.26  trashme_25135_dsk_partitions.parts.4
minia-v2.0.7-bin-Linux                trashme_25135_dsk_partitions.parts.10  trashme_25135_dsk_partitions.parts.16  trashme_25135_dsk_partitions.parts.21  trashme_25135_dsk_partitions.parts.27  trashme_25135_dsk_partitions.parts.5
mphf.temp.Xi3OR8                      trashme_25135_dsk_partitions.parts.11  trashme_25135_dsk_partitions.parts.17  trashme_25135_dsk_partitions.parts.22  trashme_25135_dsk_partitions.parts.28  trashme_25135_dsk_partitions.parts.6
mphf.temp.XQvJoL                      trashme_25135_dsk_partitions.parts.12  trashme_25135_dsk_partitions.parts.18  trashme_25135_dsk_partitions.parts.23  trashme_25135_dsk_partitions.parts.29  trashme_25135_dsk_partitions.parts.7
P4-P1S.h5                             trashme_25135_dsk_partitions.parts.13  trashme_25135_dsk_partitions.parts.19  trashme_25135_dsk_partitions.parts.24  trashme_25135_dsk_partitions.parts.3   trashme_25135_dsk_partitions.parts.8
trashme_25135_dsk_partitions.parts.0  trashme_25135_dsk_partitions.parts.14  trashme_25135_dsk_partitions.parts.2   trashme_25135_dsk_partitions.parts.25  trashme_25135_dsk_partitions.parts.30  trashme_25135_dsk_partitions.parts.9

So lots of trashme files, mphf.temp.Xi30R8, mphf.temp.XQvJoL and P4-P1S.h5

UPDATE: I have fiddled with kmer size and converted from fastq to fasta and I get the same error each time.

I'm running on an Ubuntu VM. I'm sure I'm missing something obvious and I searched biostars and didn't find something similar.

Thanks!

minia assembly • 89 views
ADD COMMENTlink modified 17 days ago • written 17 days ago by mmelendrez0
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