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lh3 / yak

Yet another k-mer analyzer
MIT License
113 stars 8 forks source link

dumpped the hash table to file ".yak" #7

Closed Karimi-81 closed 3 years ago

Karimi-81 commented 3 years ago

Hi everybody, I encountered with this issue several times. Do you have any idea about this:

[M::worker_pipeline::837.296*10.33] processed 94 sequences; 2333500880 distinct k-mers in the hash table [M::main_count] 2333322325 distinct k-mers after shrinking [M::yak_ch_dump] dumpped the hash table to file 'ccs.yak'. [M::main] Version: 0.1-r56 [M::main] CMD: yak count -b37 -t32 -o ccs.yak ccs.fa [M::main] Real time: 963.551 sec; CPU: 8858.973 sec; Peak RSS: 48.784 GB yak: main.c:108: main_qv: Assertion ch' failed. /var/spool/slurmd/job62811721/slurm_script: line 16: 32703 Aborted (core dumped) yak qv -t32 -p -K3.2g -l100k sr.yak "/project/6049291/karimi81/Pacbio_data/wtdbg/mink.srp.fa" > asm-sr.qv.txt yak: main.c:108: main_qv: Assertionch' failed. /var/spool/slurmd/job62811721/slurm_script: line 17: 32706 Aborted (core dumped) yak qv -t32 -p sr.yak "/project/6049291/karimi81/Pacbio_data/lib1/ccs.fastq" > ccs-sr.qv.txt /var/spool/slurmd/job62811721/slurm_script: line 20: 32707 Segmentation fault (core dumped) yak inspect ccs.yak sr.yak > ccs-sr.kqv.txt [M::yak_ch_restore_core] inserted 2132336103 k-mers, of which 2132336103 are new

lh3 commented 3 years ago

What command lines were you running? Why did you generate ccs.yak but put sr.yak on the qv command line?

Karimi-81 commented 3 years ago

Thank you. You were right. I missed somethings in my commands. It was solved. Best wishes

Karim Karimi Ph.D in Animal Breeding & Genetics Postdoctoral Fellowship in Mink Genomics Department of Animal Science and Aquaculture

Dalhousie University Tel: (902) 814 4442

From: Heng Li notifications@github.com Sent: Sunday, February 28, 2021 9:56 PM To: lh3/yak yak@noreply.github.com Cc: Karim Karimi Karim.Karimi@dal.ca; Author author@noreply.github.com Subject: Re: [lh3/yak] dumpped the hash table to file ".yak" (#7)

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What command lines were you running? Why did you generate ccs.yak but put sr.yak on the qv command line?

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