Partial message:

./bin/hlahd.sh: line 121: /mountpoint/hla-hd/hlahd.1.7.0/bin/drop_intron_map: Permission denied Warning: Could not open read file "estimation/ALL192/mapfile/ALL192.exon.over.R1.fastq" for reading; skipping... Error: No input read files were valid

I've followed the demo attached on this link: https://w3.genome.med.kyoto-u.ac.jp/HLA-HD/

My script:

bash ./bin/hlahd.sh -t 2 -m 100 -f freq_data -c 0.95 data/$FQ.R1.subseq2.fq data/$FQ.R2.subseq2.fq HLA_gene.split.txt dictionary/ ALL192 estimation

It's really similar to that reported in the readme.md file; the tool generates ALL192.exon.over.R1.fastq file and others in the directory, but they are 0 kbytes files.

Is there someone who can help me to resolve? Doing chmod +x doesn't work, unfortunately.