Hi, everybody. Now I am trying to de novo assembly by SOAP.
My excuted code is this.
~/Downloads/SOAPdenovo2-bin-LINUX-generic-r240/SOAPdenovo-63mer all -s SOAPdenovo.config -o K47 -K -R 1>/home/Assembly/Cyanea-nozakii/all.log 2>/home/Assembly/Cyanea-nozakii/all.err
After it finish, occur
Segmentation fault (core dumped)
Some people say the reason is max_rd_lenth, but I think my max_rd_length is ok. I checked by FastQC, sequence length is 301.
Here is my config file text.
#maximal read length max_rd_len=301 [LIB] #average insert size(400~800 illumina) avg_ins=400 #if sequence needs to be reversed reverse_seq=0 #in which part(s) the reads are used asm_flags=3 #use only first 100 bps of each read rd_len_cutoff=100 #in which order the reads are used while scaffolding rank=1 # cutoff of pair number for a reliable connection (at least 3 for short insert size) pair_num_cutoff=3 #minimum aligned length to contigs for a reliable read location (at least 32 for short insert size) map_len=32 #a pair of fastq file, read 1 file should always be followed by read 2 file q1=Cyanea-nozakii.R1.fq q2=Cyanea-nozakii.R2.fq
Please let me konw what's the problem of my job.;(((