WARNING Final process status is permanentFail

[Ahmer1122]

Hello, I am trying to run PGAP however, it ends with permanent fail. I have attached the CWLtool file.

Best regards,

Ahmer

errorCWLtool.txt

[azat-badretdin]

Thank you for your report, Ahmer!

The report says at the first permanentFail message:

[2023-01-16 14:10:45] DEBUG Could not collect memory usage, job ended before monitoring began.
[2023-01-16 14:10:45] WARNING [job fastaval] exited with status: 255
[2023-01-16 14:10:45] WARNING [job fastaval] completed permanentFail

The file fastaval.xml in the output/ directory should provide you with information about what failed. This stage tests genome nucleotide sequence for basic errors. Please let me know if you have trouble interpreting this file contents.

[Ahmer1122]

Dear Sir, many thanks for your response.

I have looked in the output folder as well as the each and every directory. However, I could not locate this file. Most probably the file does not exist. Secondly, I have run PGAP previously without any problem. This problem occurred yesterday after i updated PGAP.

Looking forward,

Best regards,

Ahmer

[azat-badretdin]

However, I could not locate this file

Could you please post the listing ls -l output/?

[azat-badretdin]

Hang on, I see already that you indeed do not have it. Could you please rerun your genome with ./pgap.py -d option? This will preserve intermediate files, include fastaval.xml.

[Ahmer1122]

Here is the screenshot.

[azat-badretdin]

Thanks for the screenshot, Ahmer, now please rerun your genome with ./pgap.py -d option. Thanks!

[Ahmer1122]

After running the command. I did not recover any files.

[azat-badretdin]

My apologies for not posting a complete line, I mean addition of -d parameter of course. Here is the complete line: ./pgap.py -r -d -o strain10_results /home/szweda/.pgap/strain10/input.yaml

[Ahmer1122]

Dear Sir, Here is the fastaval file.

fastaval.txt

[azat-badretdin]

Thanks! That was fast!

Here is the relevant part of this file

  <message tool="fastaval" severity="ERROR" seq_id="NODE34" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|NODE34">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="NODE35" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|NODE35">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="NODE36" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|NODE36">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="NODE37" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|NODE37">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="NODE38" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|NODE38">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="NODE39" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|NODE39">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="NODE40" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|NODE40">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="NODE41" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|NODE41">Sequence is shorter than 200 nucleotides</message>

as you can see, some of your input sequences (contigs) are too short. You can either edit your genome or run pgap.py with addition of --ignore-all-errors flag.

[Ahmer1122]

Dear Sir, thanks for your help. it worked.

Best regards,

Ahmer