Question: Segmentation fault (core dumped) in SOAP
0
gravatar for choi.yisoo.hi
5 weeks ago by
choi.yisoo.hi0 wrote:

Hi, everybody. Now I am trying to de novo assembly by SOAP.

My excuted code is this.

~/Downloads/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-63mer all -s SOAPdenovo.config -o K47 -K -R 1>/home/Assembly/Cyanea-nozakii/all.log 2>/home/Assembly/Cyanea-nozakii/all.err

After it finish, occur Segmentation fault (core dumped)

Some people say the reason is max_rd_lenth, but I think my max_rd_length is ok. I checked by FastQC, sequence length is 301.

Here is my config file text.

#maximal read length
max_rd_len=301
[LIB]
#average insert size(400~800 illumina)
avg_ins=400
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
#use only first 100 bps of each read
rd_len_cutoff=100
#in which order the reads are used while scaffolding
rank=1
# cutoff of pair number for a reliable connection (at least 3 for short insert size)
pair_num_cutoff=3
#minimum aligned length to contigs for a reliable read location (at least 32 for short insert size)
map_len=32
#a pair of fastq file, read 1 file should always be followed by read 2 file
q1=Cyanea-nozakii.R1.fq
q2=Cyanea-nozakii.R2.fq

Please let me konw what's the problem of my job.;(((

soap sequence fastq assembly • 143 views
ADD COMMENTlink modified 4 weeks ago • written 5 weeks ago by choi.yisoo.hi0
1

Segmentation faults typically relate to memory / RAM, and may occur for diverse reasons. Developers ought to catch these errors better, and output more intelligent error messages. You said that it "works", though (?); do you mean that it runs to completion and then produces an error while outputting results?

ADD REPLYlink written 5 weeks ago by Kevin Blighe42k

Yes it was. I edited!

ADD REPLYlink written 4 weeks ago by choi.yisoo.hi0

It is likely an issue related to memory / RAM. How much do you have available? Also, take a look at the comment here: https://github.com/aquaskyline/SOAPdenovo2/issues/10

ADD REPLYlink written 4 weeks ago by Kevin Blighe42k
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