abyss de novo asssembly exited on signal 9 error
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8.3 years ago
sun.nation ▴ 140

I am getting this error several time: mpirun noticed that process rank 3 with PID 24999 on node exited on signal 9 (Killed).

with this command: abyss-pe np=28 k=64 lib='pe' pe='230.109bp-trim_1.paired.trimmed.fq 230.109bp-trim_2.paired.trimmed.fq' se='230.109bp-trim_1.unpaired.trimmed.fq 230.109bp-trim_2.unpaired.trimmed.fq' name=taro230_190

I was not able to figure out the problem. Please anybody has idea what is going on? Thank you

abyss de novo assembly • 1.6k views
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8.3 years ago
mastal511 ★ 2.1k

It looks like you're running this on a cluster. Perhaps the program was still running when the requested wall-clock time ran out so the job was killed.

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No, this is a ubuntu server with 32 cores and 64 gb ram.

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8.3 years ago
GenoMax 144k

The program may have requested more resources than what you are allowed/were available on the node in question, which led to the program getting killed (signal 9).

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This server has 32 cores with 2gb of ram each. I used 28 of them in the job.

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