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 (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. 

    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)


Parameters names and default values:

    root@vm0083:~/mydisk/ChIP-seq_SE_GSE20870# sickle se -h
    sickle: invalid option -- 'h'
    
    Usage: sickle se [options] -f <fastq sequence file> -t <quality type> -o <trimmed fastq file>
    
    Options:
    -f, --fastq-file, Input fastq file (required)
    -t, --qual-type, Type of quality values (solexa (CASAVA < 1.3), illumina (CASAVA 1.3 to 1.7), sanger (which is CASAVA >= 1.8)) (required)
    -o, --output-file, Output trimmed fastq file (required)
    -q, --qual-threshold, Threshold for trimming based on average quality in a window. Default 20.
    -l, --length-threshold, Threshold to keep a read based on length after trimming. Default 20.
    -x, --no-fiveprime, Don't do five prime trimming.
    -n, --trunc-n, Truncate sequences at position of first N.
    -g, --gzip-output, Output gzipped files.
    --quiet, Don't print out any trimming information
    --help, display this help and exit
    --version, output version information and exit

I would like to  know if this issue is likely related to sickle itself, or the VM I'm using, or something else...

Thank you 

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.