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NCBI Prokaryotic Genome Annotation Pipeline
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Completed permanentFail when using test_genomes/C_jejuni/input.yaml #200

Closed zhuofeih closed 2 years ago

zhuofeih commented 2 years ago

Describe the bug Firstly thank you so much for offering PGAP! I downloaded the latest 2022-04-14.build6021 following https://github.com/ncbi/pgap/wiki/Quick-Start . I ran it on a Linux HPC cluster at our institution. It completed successfully when I ran pgap.py with test_genomes/MG37/input.yaml . However, when I ran it with test_genomes/C_jejuni/input.yaml , it failed with "completed permanentFail" at [step screen_evaluate] and [step vecscreen].

My command lines are: pwd /scratch/zhuofei/PGAP

export PGAP_INPUT_DIR=/scratch/zhuofei/PGAP

./pgap.py --update PGAP version 2022-04-14.build6021 is up to date.

./pgap.py --version PGAP version 2022-04-14.build6021 is up to date.

./pgap.py -r -c 8 -o ./cjejuni_results ./test_genomes-2022-04-14.build6021/C_jejuni/input.yaml

Before the first permanentFail, in cwltool.log I received a debug info: "DEBUG Could not collect memory usage, job ended before monitoring began" After I started my command line, I received a warning message: "WARNING: open files is less than the recommended value of 8000"

Could you please help to take a look at cwltool.log attached in this ticket? Any help would be greatly appreciated!

Software versions (please complete the following information):

Log Files cwltool.log

azat-badretdin commented 2 years ago

It's OK. Some of the test genomes are for testing if we detect their failure, so is, for example, C_jejuni.

If you look at the first permenanetFail in the posted cwltool.log you will see that screen_evaluate failed and the result is in the calls.tab that lists regions contaminated by sequences that are foreign to it.

zhuofeih commented 2 years ago

I see. I will let our user know. Thank you so much for your prompt response. Have a good day!