Test ConvertGDb genbank in Windows
There is some glitch with ConvertDb genbank and the wrapping of tbl2asn. Need to test this function in Windows.
Sometimes tbl2asn fails to recognize the input fasta (see also #137):
There is a known issue with the
--asn
argument. In some environments, for reasons that are presently unknown, tbl2asn may fail to recongizing the input fasta file and report an error stating Unable to read any FASTA records. Running tbl2asn manually should resolve the issue.
Sometimes some sequences are missing in the output (see also #162):
It is recommended that the number of sequences in the output
sqn
file be verified against the number of sequences in the inputtab
ortsv
file. From the command line, this can be achieved viagrep -c iupacna *.sqn
. This step is not necessary if running tbl2asn outside ConvertDb.
Comments (3)
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The console log says all passed. But when you actually look in the
sqn
, not all sequences are there. Problem goes away when runningtbl2asn
by itself outsideConvertDb
. Also, since I ranConvertDb
a few times with--asn
on as I was doing resubmission multiple times, I eventually noticed that the number of sequences insqn
varied slightly from submission to submission, suggesting that the number of sequences being omitted each time was different. -
- changed status to resolved
Tested and it works well
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For the missing sequences, is there a discrepancy between the number of records in the output and the PASS/FAIL counts shown in the console log? Filtering of incomplete sequences is intentional.