ERROR-get_tx_seq : No genes were found on chromosomes defined in fasta file. about pygtftk HOT 6 OPEN

Hi Yasmina,
Yes. First, there is this issue related to " dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF" which has not been fixed yet. This is a known issue (#171). But, yes, deleting every character after "1" should work...
Maybe the problem is related to the fact that (at least in your example), the line does not start with ">".
Best

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Also, you forgot to paste the error message.
Denis

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oh yes sorry,

1- my lines start by > (I did'nt paste it) :

1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

2- the error message is the same in the subject :

|-- 16:50-ERROR-get_tx_seq : No genes were found on chromosomes defined in fasta file.

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Yes I found it
The probleme was in some unlocalized genomic contigs (like >GL456211.1 ...)
I deleted them and it works now

Thanks Denis!

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I will reopen it as it should not complain for additional chromose in the fasta file (but for additional chromosome in the gtf file).

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