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

[yaskermezli]

Hi,

I'm using the get_tx_seq function from gtftk and I'm getting this error

Here the header of my genome_fasta.fa file :

1 dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

to test that I deleted headers after chr [dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF] but still getting the same error

Any help/suggestion ?

Thank you

[dputhier]

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

[dputhier]

Also, you forgot to paste the error message.
Denis

[yaskermezli]

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.

[dputhier]

Ah yes, this error is handled. Maybe this is a story about a file having chr prefix not found in the other file ? Denis Le ven. 31 mars 2023 à 16:51, Yasmina Kermezli ***@***.***> a écrit :

…

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. — Reply to this email directly, view it on GitHub <#180 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAN7CHVA74XJGST7KO2SJP3W63VPDANCNFSM6AAAAAAWOXEN5M> . You are receiving this because you commented.Message ID: ***@***.***>

[yaskermezli]

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

Thanks Denis!

[dputhier]

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