Question: segmentation fault (core dumped) when running unikalow
0
gravatar for Yingzi Zhang
8 months ago by
Yingzi Zhang60
Beijing
Yingzi Zhang60 wrote:

Hi all, I was using unikalow to do denovo assembly. The test.config set as:

max_rd_len=100
[LIB]
avg_ins=57533
reverse_seq=0
asm_flags=3
rank=1
pair_num_cutoff=3
map_len=32
q1=1_1.fastq
q2=1_2.fastq

the command was:

unikalow -kmer 61 -trim 90 <test.config> test_assembly

The error reported as: Segmentation fault (core dumped)

So I looked "-help" and found no parameter to assign memory. I searched internet and followed the suggestion using gdb to see the core file. The core file reported: Core was generated by `/unikalow/bin/ssaha_reads -file 23 readfile_0000_trim'. Program terminated with signal 11, Segmentation fault.

Is there any advice how I should fix it please? Thank you.

Yingzi

assembly • 500 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by Yingzi Zhang60
1

seems memory issue. Is there any parameter to assign higher RAM, explore that

ADD REPLYlink written 8 months ago by pbpanigrahi180
1

Yes, it is a kind of memory issue.

ADD REPLYlink written 8 months ago by Mehmet460

Thank you for suggestion. I looked "-help" but found no parameter to assign memory. (but I don't know whether there are some codes to set in the software itself). I also tried to see core files. It was re-ediited in the question, if you have interest.

ADD REPLYlink modified 8 months ago • written 8 months ago by Yingzi Zhang60
1

Try using larger Kmer value, it will decrease the memory requirement.

Also did u mail the author: zn1@sanger.ac.uk

Explore this thread

ADD REPLYlink written 8 months ago by pbpanigrahi180

Explore kmerGenie (KmerGenie estimates the best k-mer length for genome de novo assembly.)

ADD REPLYlink written 8 months ago by pbpanigrahi180

yes, I took your advice and tried -kmer 101 and -kmer 127, but it didn't work. I did kmer frequency analysis using GCE developed by BGI, is the work similar to what kmerGenie do? I know the peak of the kmers are about 101, could it help? And yes, I didn't but I should email to the author :)

ADD REPLYlink written 8 months ago by Yingzi Zhang60
1

Silly suggestion, are you using latest version of SOAPdenovo? If some patches might fix any bug with the tool itself. Explore this thread

ADD REPLYlink written 8 months ago by pbpanigrahi180
1

Hi. I changed the SOAPdenovo in unikalow package to the latest version. It didn't help. The author answered me. He suggested me to use other pipelines such as bfc to get better results. The link is here if you need: bfc

Thanks a lot!

ADD REPLYlink written 8 months ago by Yingzi Zhang60

Good suggestion! I shall check it. I met the RAM error when using soapdenovo in a early version and it was solved when changing to use the latest version of SOAPdenovo. The unikalow software I use is based on soapdenovo. I should check the version of SOAPdenovo in its package.

ADD REPLYlink modified 8 months ago • written 8 months ago by Yingzi Zhang60
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