when I used soapdenovo, i got the following results:
*********
In /bio/taupo/kang138/SOAPdenovo-V1.05/test.config, 1 libs, max seq len 100, max name len 256
8 thread created
time spent on hash reads: 0s, 0 reads processed
[LIB] 0, avg_ins 2000, reverse 1
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 1
Start to remove tips of single frequency kmers short than 46
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: /bio/taupo/kang138/SOAPdenovo-V1.05/test.config, max seq len 100, max name len 256
8 thread created
0 reads processed
time 0,0,0,0,0,0,0
0 markers outputed
done mapping reads, 0 reads deleted, 0 arcs created
[LIB] 0, avg_ins 2000, reverse 1
time spent on mapping reads: 0s
0 vertex outputed
overall time for lightgraph: 0m
*****************************
it seems wrong. so can you help figure out the reason? thanks a lot.
BTW, my command line is:./SOAPdenovo-127mer pregraph -s ~/SOAPdenovo-V1.05/test.config -o out
and the config file is:
max_rd_len=100
[LIB]
rank=2
avg_ins=2000
reverse_seq=1
asm_flags=2
q1=/bio/taupo/kang138/Dugong-COV-NGS-1_MPS017399_PELib_T_L005_R1_001.fastq
q2=/bio/taupo/kang138/Dugong-COV-NGS-2_MPS017400_PELib_G_L006_R1_001.fastq
*********
In /bio/taupo/kang138/SOAPdenovo-V1.05/test.config, 1 libs, max seq len 100, max name len 256
8 thread created
time spent on hash reads: 0s, 0 reads processed
[LIB] 0, avg_ins 2000, reverse 1
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 1
Start to remove tips of single frequency kmers short than 46
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: /bio/taupo/kang138/SOAPdenovo-V1.05/test.config, max seq len 100, max name len 256
8 thread created
0 reads processed
time 0,0,0,0,0,0,0
0 markers outputed
done mapping reads, 0 reads deleted, 0 arcs created
[LIB] 0, avg_ins 2000, reverse 1
time spent on mapping reads: 0s
0 vertex outputed
overall time for lightgraph: 0m
*****************************
it seems wrong. so can you help figure out the reason? thanks a lot.
BTW, my command line is:./SOAPdenovo-127mer pregraph -s ~/SOAPdenovo-V1.05/test.config -o out
and the config file is:
max_rd_len=100
[LIB]
rank=2
avg_ins=2000
reverse_seq=1
asm_flags=2
q1=/bio/taupo/kang138/Dugong-COV-NGS-1_MPS017399_PELib_T_L005_R1_001.fastq
q2=/bio/taupo/kang138/Dugong-COV-NGS-2_MPS017400_PELib_G_L006_R1_001.fastq