Problem in running annotation.pl

[ShanshanHe-44]

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

 $ sports.pl -i 1_trim_out/1_0262_X1_18_S18_R1_001_trimmed.fastq -p 20 -k -z -M 2 
  -g /home/wkq953/scop/SCOP_2024_0262/pipeline-out/foo/bar/Homo_sapiens/genome/hg38/genome 
  -m /home/wkq953/scop/SCOP_2024_0262/pipeline-out/foo/bar/Homo_sapiens/miRBase/21/miRBase_21-hsa 
  -o /home/wkq953/scop/SCOP_2024_0262/pipeline-out/test/  

  $ 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

Thanks for your help!

[junchaoshi]

Hi Shanshan,

The input for the annotation.pl script should be , not the address you defined. Please also double-check the address of your reference database.