perl file not working - Githubissues

junchaoshi / sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs

GNU General Public License v3.0

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perl file not working #10

Closed maxybck closed 3 years ago

maxybck commented 3 years ago

whenever I run the perl script sports.pl I get the same issue. What is going on?

junchaoshi commented 3 years ago

Hi,

It seems Perl cannot get the absolute path of your file test.txt, maybe you can try to input it manually.

maxybck commented 3 years ago

No that is not the issue:

junchaoshi commented 3 years ago

Could you print the head of your test.txt file?

junchaoshi commented 3 years ago

You can try to input a single .fa/.fastq file first to test the script.

maxybck commented 3 years ago

hello, you got me it was user error. I left the /home out of the absolute path. If you don't mind, can you confirm the format of the input files, do they need to be unzipped fastq files?

junchaoshi commented 3 years ago

Yes, the compressed files need to be unpacked.

maxybck commented 3 years ago

also it needs to be called .fastq correct? my files were fastq format but called .fastqsanger and that did not work

junchaoshi commented 3 years ago

Yes, suffix with .fastq/.fq is needed in your case.