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Old 01-09-2012, 06:52 PM   #1
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Location: Singapore

Join Date: Apr 2010
Posts: 1
Default 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.


tangzhonghui is offline   Reply With Quote
Old 10-09-2012, 05:32 PM   #2
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Location: New Zealand

Join Date: Jul 2011
Posts: 1

Hi Zhonghui,

Did you find a solution to this, as am having the same problems....
victoriat is offline   Reply With Quote

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