Issue with Reference Building Process in IRFinder

[inagaki-s]

Dear IRFinder team,

I am currently encountering an issue with the reference building process using IRFinder. Despite following the instructions closely and ensuring all dependencies are correctly installed, I am facing errors during the reference preparation phase.

Environment:

Perl version: 5.32.0 (x86_64-linux)
IRFinder version: (Please include the version you are using)
Bedtools version: 2.30.0
STAR version: 2.7.11a
Command used:

bash
Copy code
bin/IRFinder -m BuildRefFromSTARRef -r REF/Human-GRCh38-release111
-f /mnt/c/Ubuntu/reference_111_human/Homo_sapiens.GRCh38.dna.primary_assembly.fa
-g /mnt/c/Ubuntu/reference_111_human/Homo_sapiens.GRCh38.111.gtf
-e REF/extra-input-files/RNA.SpikeIn.ERCC.fasta.gz
-b REF/extra-input-files/Human_hg38_nonPolyA_ROI.bed
-x /mnt/c/Ubuntu/STAR_index_111_human
Errors encountered:

Error: exclude.directional.bed is empty.
Error: introns.unique.bed is empty.
Error: ref-cover.bed is empty.
Error: ref-read-continues.ref is empty.
Error: ref-sj.ref is empty.
Error: IRFinder reference building FAILED.
Additionally, I observed an error related to a Perl script during the reference preparation phase: sort: unknown subpragma '_mergesort' at /mnt/c/Ubuntu/IRFinder/IRFinder-1.3.0/bin/util/gtf2bed-custom.pl line 33.

I have verified that both Bedtools and STAR are properly installed and accessible in my PATH. My system has sufficient memory and disk space available for the process. I am wondering if there might be an issue with the compatibility of the input files or a specific requirement for the Perl environment that I might have overlooked.

Could you please provide guidance on how to resolve these errors and successfully complete the reference building process? Any suggestions or insights into what might be causing these issues would be greatly appreciated.

Thank you for your time and assistance.

[dg520]

@inagaki-s Can you try to comment out the line starting with use if $]<5.028 and retry the command? That is supposed to be Line 29 instead of Line 33 though, according to the latest version.

Let me know if this works for you.

[inagaki-s]

Thank you very much. You have helped me to solve the problem.