soedinglab
Stalled at prefitering?
I started 3 metaeuk jobs, all with different fasta input but same pfam_full database. They all seemed to stall at a prefiltering step (different step) but the jobs appearing as running (2 days since). Below is one of the caller scripts with the command line:
#!/bin/bash #$ -S /bin/bash . /etc/profile #$ -pe threaded 8
source activate metaeuk metaeuk easy-predict /path-to-input/contigs.fasta /path-to-db/pfam_msa_db.fasta predsResultProteinsOmSpadesClean.fas tempor
Below is the log attached:
Expected Behavior
Current Behavior
Steps to Reproduce (for bugs)
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MetaEuk Output (for bugs)
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Context
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Your Environment
Include as many relevant details about the environment you experienced the bug in.
- Git commit used (The string after "MetaEuk Version:" when you execute MetaEuk without any parameters):
- Which MetaEuk version was used (Statically-compiled, self-compiled, Homebrew, etc.):
- For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
- Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
- Operating system and version:
Sorry your issue fell a bit through the cracks. Did you have any progress with it?
What are the specs of the machine you were running MetaEuk? It looks like it didn't have enough RAM, so it had to split the database into many many smaller chunks which affects runtime quite badly. However, none of the smaller chunks were actually taking a long time. Was that the last piece of output of MetaEuk?
Hi, I have the same problem. The "prefilter" step takes a lot of time. More precisely, the CPU usage is very low and RAM usage increases then decreases in cyclic manner.
