[BUG] <title>A warning Warning: Field `location` contains undefined reference to `file:///pgap/pgap/input`, then after run 15 min, it reports permanent FAIL!

ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline

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[BUG] <title>A warning Warning: Field `location` contains undefined reference to `file:///pgap/pgap/input`, then after run 15 min, it reports permanent FAIL! #189

Closed minhtrung1997 closed 2 years ago

minhtrung1997 commented 2 years ago

I've downloaded and run successfully PGAP in the November 2021. After then I move pgap folder to 2.Tool folder. Recently when I return to run pgap on a Salmonella dataset, it consistently fails. This is the last attempt cwl.log

Software versions I run PGAP on Linux Ubuntu RAM 32 GB and 251GB Disk. CPU is Intel® Xeon(R) CPU E5-2620 0 @ 2.00GHz × 24 the docker is the latest image: ncbi/pgap 2022-02-10.build5872 Could you please take a glance at those input and log files and give us recommendations Thanks

Debug zip Files `. debug.zip

CWL log file

azat-badretdin commented 2 years ago

Thank you for your report! Do you see any errors in debug/tmp-outdir/m5gw6ux2/fastaval.xml?

azat-badretdin commented 2 years ago

I see that you posted the whole thing.

Your fastaval.xml output has lines like:


[<message fasta_seq_id="lcl|NODE_100_length_155_cov_95.935897" code="SEQ_SHORT_LENGTH" seq_id="NODE_100_length_155_cov_95.935897" severity="ERROR" tool="fastaval">]()Sequence is shorter than 200 nucleotides</message>

Contigs less than 200 bases are not allowed. You can either try to bypass this error by specifying pgap.py --ignore-all-errors or you can edit your input assembly.

minhtrung1997 commented 2 years ago

thank you, I've fix that bug ^^. I'll close now

azat-badretdin commented 2 years ago

You are welcome!