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Old 06-15-2011, 04:27 PM   #1
sweet_dna_girl
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Location: San Diego, CA

Join Date: Apr 2011
Posts: 11
Default running soap denovo

Hi,
I am trying to run SOAP Denovo, and I am following their manual instructions to run the example. Here is the command I am using:

./SOAPdenovo-63mer pregraph -s ecoli2.config -K 36 -p 8 -o testOut.txt

the contents of ecoli2.config are:
"q=/home/pyang/soapDenovo/SOAPdenovo-V1.05/bin/s_1_1_sequence.fastq"

However, I keep getting a segmentation fault for the output:

Version 1.05: released on July 29th, 2010

K should be an odd number
In ecoli2.config, 0 libs, max seq len 100, max name len 256

8 thread created
time spent on hash reads: 0s, 0 reads processed
0 nodes allocated, 0 kmer in reads, 0 kmer processed
0 linear nodes
time spent on marking linear nodes 0s
time spent on pre-graph construction: 0s

deLowKmer 0, deLowEdge 0
Start to remove tips of single frequency kmers short than 74
0 tips off
8 thread created
0 linear nodes
Start to remove tips which don't contribute the most links
kmer set 0 done
kmer set 1 done
kmer set 2 done
kmer set 3 done
kmer set 4 done
kmer set 5 done
kmer set 6 done
kmer set 7 done
0 tips off
8 thread created
0 linear nodes
time spent on cutTipe: 0s

0 (0) edges 0 extra nodes
time spent on making edges: 0s

In file: ecoli2.config, max seq len 100, max name len 256

8 thread created
Segmentation fault


Can someone help me with this?? Thanks!!!
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Old 06-16-2011, 07:57 PM   #2
cliffbeall
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As the program says, you have to make k an odd number, so try 35 or 37 instead of 36. Something about the algorithm not liking palindromes.

Not sure if that caused the segmentation fault, but it couldn't hurt.
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Old 10-16-2012, 10:57 PM   #3
Niloofar
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Location: Australia

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Posts: 7
Default Segmentation problem

Hi Sweet DNA girl
Didi you find a solution to your problem? I'm having the same problem
Cheers,
Niloofar
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Old 07-26-2013, 05:01 AM   #4
adilef
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hye,

Someone find a solution ?

Thanks.
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Old 07-26-2013, 06:24 AM   #5
mastal
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Default running soap denovo

segmentation faults often happen when the computer runs out of memory,
and de novo assembly can use quite a lot of memory.
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Old 07-30-2013, 04:37 AM   #6
adilef
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But when i try in the cluster, i have this output without segmentation fault:

********************
Pregraph
********************

Parameters: pregraph -s test_solexa.config -R -o assembly_SOAP

In test_solexa.config, 2 lib(s), maximum read length 76, maximum name length 256.

8 thread(s) initialized.
Time spent on hashing reads: 0s, 0 read(s) processed.
LIB(s) information:
[LIB] 0, avg_ins 76, reverse 1.
[LIB] 1, avg_ins 76, reverse 1.
0 node(s) allocated, 0 kmer(s) in reads, 0 kmer(s) processed.
done hashing nodes
0 linear node(s) marked.
Time spent on marking linear nodes: 0s.
Time spent on pre-graph construction: 1s.

Start to remove frequency-one-kmer tips shorter than 46.
Total 0 tip(s) removed.
8 thread(s) initialized.
0 linear node(s) marked.
Start to remove tips with minority links.
0 tip(s) removed in cycle 1.
Total 0 tip(s) removed.
8 thread(s) initialized.
0 linear node(s) marked.
Time spent on removing tips: 0s.

0 (0) edge(s) and 0 extra node(s) constructed.
Time spent on constructing edges: 0s.

In file: test_solexa.config, max seq len 76, max name len 256.
8 thread(s) initialized.
0 read(s) processed.
Time spent on:
importing reads: 0s,
chopping reads to kmers: 0s,
searching kmers: 0s,
aligning reads to edges: 0s,
searching (K+1)mers: 0s,
adding pre-arcs: 0s,
recording read paths: 0s.
0 marker(s) output.
Reads alignment done, 0 read(s) deleted, 0 pre-arc(s) added.
LIB(s) information:
[LIB] 0, avg_ins 76, reverse 1.
[LIB] 1, avg_ins 76, reverse 1.
Time spent on aligning reads: 0s.

0 vertex(es) output.
Overall time spent on constructing pre-graph: 0m.
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Old 07-30-2013, 07:30 AM   #7
klduong
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I had a similar problem. My solution was to go back to the SOAPdenovo2 Sourceforge page and download the separate bin folder that is available. The executables in the downloaded bin worked for me instead of the ones in the src download.
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