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NCBI Prokaryotic Genome Annotation Pipeline
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Annotation for A_baumannii_AC12 [PGAP failed, docker exited with rc = 1] #162

Closed wmml1234567890 closed 3 years ago

wmml1234567890 commented 3 years ago

cwltool.log cwltool.log

Input.yaml

fasta:
  class: File
  location: A_baumannii_AC12_CP007549_3.fna
submol:
  class: File
  location: submol.yaml

submol.yaml

organism:
    genus_species: 'Acinetobacter baumannii'

Fasta CP007549.3

Dear all,

We tried to use pgap to annotate the A. baumannii, but we get the above errors in the log file. The log file is attached above. Since the yaml and fna file is not supported, we just paste the information of these files here.

Thank you very much in advance.

Eddie

azat-badretdin commented 3 years ago

Thank you for your report, user wmml1234567890!

The log file indicates to contamination problem in your input file (see the name of the step before first permanentFail message in it). In this case PGAP produces calls.tab in the output directory, could you please post it here?

Thanks!

wmml1234567890 commented 3 years ago

Dear @azat-badretdin,

Thank you for your prompt reply.

calls.tab """ lcl|CP007549.3 M 3811326..3811426 pBR322 contam_in_prok
"""

Btw, We used the --ignore-all-errors and it completed successfully!

Thanks you very much.

azat-badretdin commented 3 years ago

You are welcome!