$ annotation.pl test/
Can't open 'test/.fa': No such file or directory at /maps/projects/scop/apps/sports1.1-master/source/annotation.pl line 55.
$ annotation.pl test/1_0262_X1_18_S18_R1_001_trimmed/
Can't open 'test/1_0262_X1_18_S18_R1_001_trimmed/.fa': No such file or directory at /maps/projects/scop/apps/sports1.1-master/source/annotation.pl line 55.
$ annotation.pl test/1_0262_X1_18_S18_R1_001_trimmed/0262_X1_18_S18_R1_001_trimmed_fa/
Can't open 'test/1_0262_X1_18_S18_R1_001_trimmed/0262_X1_18_S18_R1_001_trimmed_fa/.fa': No such file or directory at /maps/projects/scop/apps/sports1.1-master/source/annotation.pl line 55.
$ annotation.pl test/1_0262_X1_18_S18_R1_001_trimmed/0262_X1_18_S18_R1_001_trimmed_fa/0262_X1_18_S18_R1_001_trimmed_match_genome
readline() on closed filehandle $file_handle{...} at /maps/projects/scop/apps/sports1.1-master/source/annotation.pl line 120.
And the output folder looks like
$ ll test/
total 144
1_0262_X1_18_S18_R1_001_trimmed
processing_report
run_this.sh
sh_file
Hi Sports team!
Thanks for making this pipeline and I am trying to run the annotation.pl but faced the error with the incorrect file path.
The error is below
And the output folder looks like
Thanks for your help!