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Published 20 hours ago • verified publisher icon AntonBankevich

Crash in Uncompressing homopolymers in contigs | Child process crashed

Open cyycyj opened this issue 1 year ago • 6 comments

Dear developers,

I used LJA to assemble a plant genome (~500Mb, het≈1.05%, 2n=30), and after the one day's running, LJA met Child process crashed in Uncompressing homopolymers in contigs. Could you please tell me what has happened?

Please kindly find the attachments, they are stdout and the slurm script.

Best regards,

Andrew

lja_slurm_script.txt lja_stdout.txt

cyycyj avatar Oct 12 '23 12:10 cyycyj

my hifireads is about 180x

cyycyj avatar Oct 12 '23 13:10 cyycyj

Hi, have you solved this problem?

supermanwasd avatar Jan 03 '24 06:01 supermanwasd

I have the same issue.

SvitlanaLukicheva avatar Feb 20 '24 15:02 SvitlanaLukicheva

Hi, My first assumption about this crash would be running out of memory - can you check? How much memory was available?

Dmitry-Antipov avatar Feb 20 '24 23:02 Dmitry-Antipov

Hello @Dmitry-Antipov ,

This was the first thing that I checked, but I requested 30 Gb of memory and the job only used 21 Gb, also its exit code was 0.

SvitlanaLukicheva avatar Feb 21 '24 09:02 SvitlanaLukicheva

Update: I finally managed to run LJA successfully on another cluster node, after requesting more CPUs and memory. Not sure which of these parameters solved the issue though.

SvitlanaLukicheva avatar Feb 21 '24 12:02 SvitlanaLukicheva