Closed joelnitta closed 2 years ago
PS: the Possible precedence issue with control flow operator
warning shows up even with the test data, so I don't think that has anything to do with the above error.
bash-4.2# FEELnc_filter.pl -i transcript_chr38.gtf -a annotation_chr38.gtf -b transcript_biotype=protein_coding > test.gtf
Possible precedence issue with control flow operator at /usr/local/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.
Filtered transcripts will be available in file: 'transcript_chr38.feelncfilter.log'
Parsing file 'transcript_chr38.gtf'...
Parse input file: [----------------------------------------------------------------------------------------------------]
> Filter size (200): 36
> Filter monoexonic (0): 1265
> Filter biexonicsize (25): 15
>> Transcripts left after fitler(s): 2146
Parsing file 'annotation_chr38.gtf'...
Parse input file: [----------------------------------------------------------------------------------------------------]
38
Intersect fileA: [----------------------------------------------------------------------------------------------------]
Hi @joelnitta ,
First, thanks for all the info and the files (it help to debug)!
In fact the "error" is in the file daphnia_genome.gtf
, the biotype are not as expected and instead of protein_coding
, it is mRNA
.
So you just need to replace protein_coding
by mRNA
in the command line and it will work (at least for me yes).
Tell us if you have other issues! Bye, Valentin
Thanks @vwucher for the prompt reply! Can you please let me know the code you used to fix daphnia_genome.gtf
? I have tried changing protein_coding
to mRNA
but I am still getting the same error.
Hi,
I didn't fix the file. I just changed your command line by replacing protein_coding
by mRNA
.
Did you tried that?
Bye
Ah, now I see what you mean! Yes that fixes it, thanks!
(for anybody else who comes across this, it means using -b transcript_biotype=mRNA
in the FEELnc_filter.pl
command)
Hello,
I am trying to run
FEELnc_filter.pl
and I encounter theParser::parseGTF => Data Structure returns an empty hash
error as follows:daphnia_genome.gtf
does containexon
annotations in the 3rd field.I am not sure what the other two possible reasons refer to, or how to check those.
The input files can be downloaded from these dropbox links:
FEELnc v0.2-0 run in docker image
quay.io/biocontainers/feelnc:0.2--pl526_0
I would greatly appreciate it if you can help me troubleshoot this.
Thanks!