"Segmentation fault (core dumped)" depending on parameters naming

[rioualen]

Hello,

I'm running into "Segmentation fault (core dumped)" error when running a workflow with (or without) snakemake. I've used the same data, same tools and same parameters on several machines without a problem before.

Now the problem arises on a Ubuntu 14.04 virtual machine (using 4 CPU + 8Go RAM), when executing sickle. I've noticed that it depends on the parameters that I use, even when I'm specifying parameters that are supposed to be the default ones.

Not sure if the issue is related to sickle, but here it is:

root@vm0083:~/mydisk/ChIP-seq_SE_GSE20870# sickle se -f fastq/GSM521934/GSM521934.fastq -t sanger -o sickle.fastq -q 20 -l 20

FastQ records kept: 2449731
FastQ records discarded: 1137314

root@vm0083:~/mydisk/ChIP-seq_SE_GSE20870# sickle se -f fastq/GSM521934/GSM521934.fastq -t sanger -o sickle.fastq -q 20 --length-threshold 20
Segmentation fault (core dumped)

root@vm0083:~/mydisk/ChIP-seq_SE_GSE20870# sickle se -f fastq/GSM521934/GSM521934.fastq -t sanger -o sickle.fastq --qual-threshold 20 -l 20
Segmentation fault (core dumped)

This happens in a Ubuntu 14.04.4 virtual machine, but not on my host computer under LMDE 2, nor on a Ubuntu 14.04.5 server, all with sickle version 1.330.

[rioualen]

In case someone else is running into this issue, using shortcuts for params names avoids the problem: -q instead of --qual-threshold and -l instead of --length-threshold, specifically.

So in my case the problem was not related to my VM, but to the fact that my VM was using another version of my code which included full params names.

[guillaumecharbonnier]

I am seeing the same issue with sickle build from bioconda whereas I have no issue with a build from git source. If we really want to use long names, using '=' instead of a space seems to do the job for numeric values, although I have no idea why.

$ sickle se --fastq-file tmpin.fastq --qual-threshold=20 --qual-type=sanger -o tmpout.fastq
FastQ records kept: 24
FastQ records discarded: 1

$ sickle se --fastq-file tmpin.fastq --qual-threshold 20 --qual-type=sanger -o tmpout.fastq
Segmentation fault (core dumped)

$ sickle se --fastq-file tmpin.fastq --qual-threshold=20 --qual-type sanger -o tmpout.fastq
FastQ records kept: 24
FastQ records discarded: 1