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ncbi / pgap

NCBI Prokaryotic Genome Annotation Pipeline
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[FEATURE REQUEST] Provide genome assembly/FASTA file name in ani-tax-report.txt #241

Closed aboffin closed 1 year ago

aboffin commented 1 year ago

Is your feature request related to a problem? Please describe. The generated ANI report has a generic id for the assembly/FASTA file:

ANI report for assembly: my_gc_assm_name
Submitted organism: Pyrococcus furiosus (taxid = 2261, rank = species, lineage = Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae; Pyrococcus)
Predicted organism: (none)
Submitted organism has type: Yes
Status: INCONCLUSIVE
Confidence: LOW

Describe the solution you'd like It will be useful for debugging, if instead of my_gc_assm_name, the name of the input genome FASTA file is provided in the ani-tax-report.txt file.

Describe alternatives you've considered Redirecting the console output to a file, then identifying the annotations that failed due to ANI/taxa check, opening the ANI report file indicated there to see why the taxonomy cannot be assigned confidently.

Additional context None.

thibaudnis commented 1 year ago

Hi @aboffin , sorry for the delay in responding; this ticket fell through the cracks. Your request is something we should have done already. We will try to add this to our next release. Thanks!