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miniasm stop at step1 and error with 段错误(吐核)(core dump) #66

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y842739756 opened this issue Mar 26, 2019 · 0 comments
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y842739756 commented Mar 26, 2019

#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/Rrzz_pacbio/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::141001.418
17.57] 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/Rrzz_pacbio/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=,
d=d@entry=0x2136010, n=n@entry=0x7ffc2a5c83c8, bi_dir=bi_dir@entry=1,
excl=excl@entry=0x0) at hit.c:94
94 p->qns = (uint64_t)sd_put(d, r.tn, r.tl)<<32 | r.ts;

does that means there are some problem with my fastq head

Thanks in Advance!
xu

@y842739756 y842739756 changed the title miniasm stop at step1 and not any error message miniasm stop at step1 and error with 段错误(吐核)(core dump) Mar 29, 2019
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