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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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wtpoa-cns bam correction stage segmentation fault #28

Closed yuwwu closed 5 years ago

yuwwu commented 5 years ago

Dear colleague, Greetings. I am trying your wtdbg2 v2.2 on my data. I have about two million long reads, and wtdbg2/wtpoa-cns successfully assemble them into several thousands of contigs. I however encountered some difficulties trying to correct the assembly using bam file generated using minimap2. The command that I issued is exactly the same as specified in the wiki, which is

samtools view profile.ctg.lay.map.srt | ./wtpoa-cns -t 16 -d profile.ctg.lay.fa -i - -fo profile.ctg.lay.2nd.fa -v

I added "-v" for more verbose output and see the program stops here

(omitted) JOINT 222259 qe = 2005 -> 2005 te = 497 -> 497 [ 2005, 2015] [ 499, 496,1,2,0] Segmentation fault (core dumped)

Please kindly let me know if you have any suggestions. Thank you.

ruanjue commented 5 years ago

I will polish the short reads consensus codes.

BTW, please open issue under wtdbg2. SMARTdenovo is infrequently maintained now.