Segmentation fault (core dumped) at contig step during SOAP denovo assembly

tangzhonghui · 01-09-2012, 07:52 PM

Hi all,
I intend to assembly a 2.5G-sized genome with 2.4 G shut gun reads (100 bp) and 2.9 G mate-paried reads (75 bp). I run the SOAP denovo (v 1.05) step by step. The first step, pregraph, succeed in running. However, at the second step, the contig step, SOAP denovo reported the error message. The command line and error message are shown as below:

SOAPdenovo-31mer pregraph -s shutgun_Q.gPET_Q.SOAP.kmer_21.config_1 -K 21 -a 650 -p 40 -R -o shutgun_Q.gPET_Q.K21

SOAPdenovo-31mer contig -g shutgun_Q.gPET_Q.K21 -R
Version 1.05: released on July 29th, 2010

there're 415826527 kmers in vertex file
there're 1447198408 edge in edge file
done sort
input 1447198408 edges
1976892894 pre-arcs loaded
66317675738 markers overall
66317675738 markers loaded
11919701 repeats solvable, 23896696 more edges
47793392 dead arcs removed
time spent on solving repeat: 53867s
start to pinch bubbles, cutoff 0.100000, MAX NODE NUM 3, MAX DIFF 2
Segmentation fault (core dumped)

I am eagerly looking forward for your help.

Yours,

Zhonghui

victoriat · 10-09-2012, 06:32 PM

Hi Zhonghui,

Did you find a solution to this, as am having the same problems....

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01-09-2012, 07:52 PM	#1
tangzhonghui Junior Member Location: Singapore Join Date: Apr 2010 Posts: 1	Segmentation fault (core dumped) at contig step during SOAP denovo assembly Hi all, I intend to assembly a 2.5G-sized genome with 2.4 G shut gun reads (100 bp) and 2.9 G mate-paried reads (75 bp). I run the SOAP denovo (v 1.05) step by step. The first step, pregraph, succeed in running. However, at the second step, the contig step, SOAP denovo reported the error message. The command line and error message are shown as below: SOAPdenovo-31mer pregraph -s shutgun_Q.gPET_Q.SOAP.kmer_21.config_1 -K 21 -a 650 -p 40 -R -o shutgun_Q.gPET_Q.K21 SOAPdenovo-31mer contig -g shutgun_Q.gPET_Q.K21 -R Version 1.05: released on July 29th, 2010 there're 415826527 kmers in vertex file there're 1447198408 edge in edge file done sort input 1447198408 edges 1976892894 pre-arcs loaded 66317675738 markers overall 66317675738 markers loaded 11919701 repeats solvable, 23896696 more edges 47793392 dead arcs removed time spent on solving repeat: 53867s start to pinch bubbles, cutoff 0.100000, MAX NODE NUM 3, MAX DIFF 2 Segmentation fault (core dumped) I am eagerly looking forward for your help. Yours, Zhonghui

10-09-2012, 06:32 PM	#2
victoriat Junior Member Location: New Zealand Join Date: Jul 2011 Posts: 1	Hi Zhonghui, Did you find a solution to this, as am having the same problems....