Taxonomy Check error

[Leobpfbac]

Hi,
I installed PGAP, tested it with the suggested genome and everything worked as expected.
I have a de novo assembled genome and ran PGAP just for --taxcheck but it didn't seem to work. I ran another time using --ignore-all-error and it worked. Could you help me identify what the problem might be? Here is the cwltool.log file of the first run.

Thank you

cwltool.log

[azat-badretdin]

Thank you for your request, user @Leobpfbac

The general rule of interpreting cwltool.log output is to search for the first occurrence of permanentFail then scroll up to see the first error after the first command line echo message like this:

....$ executable \
continuation \
of command \
line

In this case, it's

  <message tool="fastaval" severity="ERROR" seq_id="58" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|58">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="59" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|59">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="60" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|60">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="61" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|61">Sequence is shorter than 200 nucleotides</message>
  <message tool="fastaval" severity="ERROR" seq_id="62" code="SEQ_SHORT_LENGTH" fasta_seq_id="lcl|62">Sequence is shorter than 200 nucleotides</message>

We accept only contigs with length larger than 200 nucleotides for official submissions to GenBank, so your choice of running this with --ignore-all-errors is a valid choice if you use this annotation for your purposes, but in case you want to submit it to Genbank, you will have to somehow get rid of short contigs.

[Leobpfbac]

Oh, you're right.
I'll work on this and run pgap later.
Thanks @azat-badretdin

[azat-badretdin]

Happy landings, user @Leobpfbac !