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NCBI Prokaryotic Genome Annotation Pipeline
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Fail to annotate a sequence construct by GATK #167

Closed JakeSLLeung closed 3 years ago

JakeSLLeung commented 3 years ago

Dear all,

I tried to annotate a sequence of A. baumannii which is construct by GATK, but I eventually fail and get the log file attached below. Could you please offer a help, or point out whats wrong? Thank you for your kindly attention cwltool.log

Best regards, Jake

azat-badretdin commented 3 years ago

Thank you for your report, user JakeSLLeung!

The first occurrence of "permanentFail" message is in "fastaval" node.

Please examine your output directory for a corresponding XML file (fastaval.xml) it should contain useful hints on what was wrong in the input file.

JakeSLLeung commented 3 years ago

sorry, my output folder only contains 3 file.

  1. cwltool.log
  2. MDRA_21M1005170_GCF_008632635.1_renamed_header_chromosome.consensus.fasta
  3. pgap_submol_6mj0jc_x.yaml I cannot see any XML file. (fastaval.xml)

And this is my command line to work for. ./pgap.py -r -o Results/20210822_MDRA_pyneh/compare/21M1005170_GCF_008632635.1 Input/20210822_MDRA_pyneh/compare/MDRA_21M1005170_GCF_008632635.1_input.yaml

thibaudnis commented 3 years ago

Hi! Do the inputs conform to the guidelines in the wiki ?

azat-badretdin commented 3 years ago

Thanks! Could you please rerun it with --debug flag? The output should be under a directory that starts with debug*, please use find debug* --name \*.xml

JakeSLLeung commented 3 years ago

Thanks. I found out the failure is due to my fasta header, so the problem is solved.

However, I would like to ask one more question. If my sequence has a number of N at either beginning or end, is there any alternate way to annotate it? Thank you.

azat-badretdin commented 3 years ago

You can try --ignore-all-errors parameter

JakeSLLeung commented 3 years ago

Thank you for your help, @azat-badretdin All problems are well solved. If there is a new issue, I will raise it again. Thank you again!

azat-badretdin commented 3 years ago

You are welcome!