Segmentation fault with version 1.04 from conda
winni2k opened this issue · 1 comments
winni2k commented
I have installed SOAPdenovo-Trans version 1.04 from bioconda (https://bioconda.github.io/recipes/soapdenovo-trans/README.html)
When I run SOAPdenovo-Trans using this command:
OUTDIR=wd/soapdenovo_trans/
SOAPdenovo-Trans-31mer all -s $OUTDIR/config -o $OUTDIR/outputGraph
I get the following output followed by a segmentation fault:
The version 1.03: released on July 19th, 2013
With bug fixes by Chris Boursnell January 23rd, 2014
pregraph -s wd/soapdenovo_trans/config -o wd/soapdenovo_trans/outputGraph
In wd/soapdenovo_trans/config, 1 libs, max seq len 101, max name len 256
8 thread created in prlHashReads
read from file - type 2:
wd/SRR1153470/trimmed/fw-paired.fq.gz
read from file - type 2:
wd/SRR1153470/trimmed/rev-paired.fq.gz
Segmentation fault (core dumped)
The contents of my config file is:
#maximal read length
max_rd_len=101
[LIB]
#maximal read length in this lib
rd_len_cutof=101
#average insert size
avg_ins=200
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#fastq file for read 1
q1=wd/trimmed/fw-paired.fq.gz
#fastq file for read 2 always follows fastq file for read 1
q2=wd/trimmed/rev-paired.fq.gz
Does anyone have any idea what I can do to fix this?