I followed the issues before and check with
cat ../../data/Rrzz_pacbio/all.fastq | perl -ne 'print "$1\n" if />(\S+)/' | sort | uniq -d
and print nothing
I use gdb ./miniasm/miniasm core.264457 try to find out what happened and show the info
_Program terminated with signal 11, Segmentation fault.
0 ma_hit_read (fn=, min_span=2000, min_match=,
d=d@entry=0x2136010, n=n@entry=0x7ffc2a5c83c8, bi_dir=bi_dir@entry=1,
excl=excl@entry=0x0) at hit.c:94
I have serval fq file and i cat them into one fq file
cat *.fastq >all.fastq
then i use minimap2 mapping to themselfs
_./minimap2/minimap2 -x ava-pb -t 50 /home/yanxu2016/Documents/data/Rrzz_pacbio/all.fastq /home/yanxu2016/Documents/data/Rrzzpacbio/all.fastq |gzip -1 >Rrzz.paf.gz
by the way ,the mem of computer is 500G and got 974 cpu tasks
it seems like minimap2 run successfully
[M::worker_pipeline::140990.20417.57] mapped 51289 sequences [M::worker_pipeline::141001.41817.57] mapped 45788 sequences [M::main] Version: 2.16-r922 [M::main] CMD: ./minimap2/minimap2 -x ava-pb -t 50 /home/yanxu2016/Documents/data/Rrzz_pacbio/all.fastq /home/yanxu2016/Documents/data/Rrzz_pacbio/all.fastq [M::main] Real time: 141002.732 sec; CPU: 2476745.891 sec; Peak RSS: 39.739 GB
And got a 2.4TB paf.gz file
then run miniasm
_./miniasm/miniasm -f ../../data/Rrzzpacbio/all.fastq Rrzz.paf.gz > Rrzz.gfa
[M::main] ===> Step 1: reading read mappings <=== 段错误（吐核） : Aborted (core dumped)
I followed the issues before and check with cat ../../data/Rrzz_pacbio/all.fastq | perl -ne 'print "$1\n" if />(\S+)/' | sort | uniq -d and print nothing
I use gdb ./miniasm/miniasm core.264457 try to find out what happened and show the info
_Program terminated with signal 11, Segmentation fault.
0 ma_hit_read (fn=, min_span=2000, min_match=,
94 p->qns = (uint64_t)sdput(d, r.tn, r.tl)<<32 | r.ts;
does that means there are some problem with my fastq head
Thanks in Advance! xu