Question: minia seg fault (core dump) after inability to unlink mphf temp files?
1
gravatar for mmelendrez
7 months ago by
mmelendrez10
mmelendrez10 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 • 299 views
ADD COMMENTlink modified 4 months ago by malaya770 • written 7 months ago by mmelendrez10
0
gravatar for malaya77
4 months ago by
malaya770
malaya770 wrote:

Did you get it solved yet ? One work around that worked for me earlier was : Copy the fastq file into your virtual box (Desktop or elsewhere, instead of keeping in the shared folder in windows host side). And then run minia command.

It seems like the problem in the unlinking error is because windows does not allow to rename the file. "... the problem is in the way glib saves a file by writing to a temporary file and renaming to the final name. This is don't without closing the file, which is ok on most linux file systems but not on windows." Source

ADD COMMENTlink written 4 months ago by malaya770
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