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Hi,
Thank you for the WGS annotation tool. I have installed and run the example data (MG37) with only one issue "WARNING: open files is less than the recommended value of 8000" though the annotation…
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Currently we skip all-reduce if it is for gradient accumulation and rewritten (call them grad-acc all-reduce). However, after that, such an all-reduce can be merged with all-reduce not for grad-acc. S…
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Greetings,
I am not able to run PGAP with my assembled genomes. I ran it with the MG37 test genome and it ran successfully although it gave me the warning of having low space in the tmp outdir (1 G…
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Hi,
i'm using PGAP for the first time. I try running the pipeline with mg37 test_genome and encounter the following issue: permanent fail.
d-i89-241-243:~ s4251484$ /Users/s4251484/pgap.py -r -o m…
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### 🐛 Describe the bug
distributed/pipeline/sync/skip/test_gpipe.py::test_1to3[always-1:1:1]
distributed/pipeline/sync/skip/test_gpipe.py::test_1to3[always-1:2]
distributed/pipeline/sync/skip/tes…
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I have pgap installed as a module
module load pgap/20220414
pgap.py -h
usage: pgap.py [-h] [-V] [-v] [--prod] [--taxcheck | --taxcheck-only] [-l | -u] [-r | -n] [--container-name CONTAINER_NAME] [-…
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Hi @azat-badretdin ,
The problem I mentioned in [https://github.com/ncbi/pgap/issues/205](https://github.com/ncbi/pgap/issues/205) before, according to your suggestion, I modify `--cpus` parameter:…
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https://papers.nips.cc/paper/2019/file/093f65e080a295f8076b1c5722a46aa2-Paper.pdf
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hello there:
When i run pgap.py with "test_genome/MG37/input.yaml", but finished with "**WARNING Final process status is permanentFail**" and there are no valued result.
Apparently I set the `-…
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