Comments (7)
Do you use a grid engine and the job might have timed out? Your log outputs "killed" after the 6th iteration. So the OS or the grid engine might have killed the job.
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Another idea: Could you try to run the assembly with less threads?
I think we assume about 4-8GB RAM per thread, at least that are the conditions in which we developed our software.
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Thank you for the answers!
I'm not using a grid engine. This execution was performed in an AWS instance.
I'll try using less threads in my next assemblies. In any case, I could finish this assembly by starting it again in the same server (I needed three additional executions after this first one).
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@milot-mirdita I reduced the number of cores so that I had ~5GB of memory per thread, but the problem persisted. I got the same error across multiple tries.
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Something else that I've noticed: After finishing the assembly of a sample I started assembling the second one. The "generate k-mers list" step was very slow and eventually died. After deleting the PLASS directory and re-compiling it, the "generate k-mers list" of the first step was quick again, until eventually getting slow and dying in the 6th step.
I noticed this behavior several times already. After re-compiling PLASS gets fast again and doesn't die until it has processed several steps.
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@apcamargo I really do not know whats the issues. Some times it runs only one iteration and then six. Is it possible to share the data? I would try to reproduce the issues.
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Sure @martin-steinegger! I'll email the data to you.
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Related Issues (20)
- map of input sequences to assembled sequence
- missing handling of small number of input reads HOT 7
- Error running mpi job with class HOT 1
- Use Plass for euk metagenomics data HOT 2
- The output file is empty HOT 1
- Segmentation fault translatenucs HOT 2
- Some Issues about the length of protein sequences HOT 2
- Empty (len:0) sequences in plass output HOT 4
- Issue with Docker image soedinglab/plass:latest HOT 2
- Use PLASS in metatranscriptomic data HOT 5
- Update MMseqs2 submodule
- Install issues HOT 6
- Paired read prediction - mergereads failed HOT 3
- Quantification
- High level of duplicated protein sequences HOT 1
- mmseqs extractorfs can tranlate orfs but CLI does not allow to specify tranlation table HOT 2
- general question to gauge dev opinion/advice on selecting proteins for gene phylogenies HOT 2
- Quality trimming reads? HOT 2
- Alternative codon table HOT 2
- Insights needed for comparison with other assemblers HOT 1
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