format_custom.pl cannot open custom tsv file
01Andrea01 opened this issue · comments
I built my own tsv file from selected taxa in BOLD (see attached) and I'm trying to make a reference database.
perl format_custom.pl -custom ./home/andrea/mkCOInr/terrestrial_arthropods/Diplura.tsv -taxonomy /home/andrea/mkCOInr/COInr/taxonomy.tsv -outdir /home/andrea/mkCOInr/terrestrial_arthropods
I get the error message
Cannot open ./home/andrea/mkCOInr/terrestrial_arthropods/Diplura.tsv
and this is the log:
2022-07-19-12-20-53
PARAMETERS:
check_seqid_format: 1
custom: ./home/andrea/mkCOInr/terrestrial_arthropods/Diplura.tsv
max_length: 2000
max_n: 5
min_length: 100
outdir: /home/andrea/mkCOInr/terrestrial_arthropods
taxonomy: /home/andrea/mkCOInr/COInr/taxonomy.tsv
Read input file
what am I doing wrong? The tsv file seems correctly formatted to me
Hi Andrea,
The dot before the first slash in the following path represents your current working directory.
./home/andrea/mkCOInr/terrestrial_arthropods/Diplura.tsv
Just delete the dot:
/home/andrea/mkCOInr/terrestrial_arthropods/Diplura.tsv
Cheers,
Emese
Hi Emese,
Why am I so stupid? A simple typo. I went checking everything from the file format to the script. Just a stupid typo.
Sorry for the hassle and thank you for the kind answer.
Cheers,
Andrea
No problem!