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!!!
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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