problem with running IR finder

[adi8897]

im tryng to run my analysis in IRfinder.
i have 1- files I created a file with the pathes like this: (txt files with the pathes to the bam file).
/sci/labs/maayan.salton/adi8897/intron_retention_project/astonian_family_data/21_12/output_HK-1-1_Aligned.out.bam
/sci/labs/maayan.salton/adi8897/intron_retention_project/astonian_family_data/21_12/output_HK-1-2_Aligned.out.bam
/sci/labs/maayan.salton/adi8897/intron_retention_project/astonian_family_data/21_12/output_HK-1-3_Aligned.out.bam
/sci/labs/maayan.salton/adi8897/intron_retention_project/Israel_family/gz_files/21_12/output_1024-1_Aligned.out.bam
/sci/labs/maayan.salton/adi8897/intron_retention_project/Israel_family/gz_files/21_12/output_1024-2_Aligned.out.bam
/sci/labs/maayan.salton/adi8897/intron_retention_project/Israel_family/gz_files/21_12/output_1024-3_Aligned.out.bam
/sci/labs/maayan.salton/adi8897/master_project/WBP4/processed_data/SRR9600556_Aligned.out.bam
/sci/labs/maayan.salton/adi8897/master_project/WBP4/processed_data/SRR9600557_Aligned.out.bam
/sci/labs/maayan.salton/adi8897/master_project/WBP4/processed_data/SRR9600558_Aligned.out.bam
/sci/labs/maayan.salton/adi8897/master_project/WBP4/processed_data/SRR9600559_Aligned.out.bam

now I'm trying to run but I'm always getting an error and I'm not understanding the problem
this is the command I ran:
./irfinder -m BAM -r /sci/labs/maayan.salton/adi8897/intron_retention_project/refrence/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa -d /sci/labs/maayan.salton/adi8897/master_project/WBP4/IR_finder/output -b /sci/labs/maayan.salton/adi8897/master_project/WBP4/IR_finder/filePaths.txt

this is the error:
<16|0>adi8897@moriah-gw-02:~/adi8897/IR_finder_venv/IRFinder-1.3.0/src/irfinder% cat slurm-20947187.out
Usage: gzip -cd < input.bam | IRFinder output-directory ref-coverage.bed ref-SJ.ref ref-spans-point.ref ROI-named.bed(or NULL) out.bam(or NULL)

please I would like some help

[dg520]

@adi8897 There are many issues in your command, Please check the following very carefully:

1. After git clone the IRFinder package, you should call IRFinder that is located inside bin folder. Note: the spelling is "IRFinder" instead of "irfinder". Did you use "irfinder" under bin/util folder? If so, you are using the wrong execution file.
2. -r option expects a folder that contains IRFinder reference, not a FASTA file. You need to build this IRFinder reference yourself. As you have already aligned your RNASeq using STAR, I would recommend you follow the steps here,
3. -b is not an option for IR quantification. It is an option for building the IRFinder reference mentioned in 3).
4. IRFinder doesn't support batch processing. Instead of providing a file listing all the BAM files, you need to quantify IR on each BAM file one by one. Note: each call should be provided a unique output folder via -d option. DO NOT use the same output folder for different calls.