I'm trying to run alignment mode with my .fq files using the following command:
./HLAminer.pl -h /u/scratch/user_hla_files/scrnaseq/SRRxyz.fq
I get the following error:
Running ./HLAminer.pl [v1.4]
Derivation of HLA class I and II predictions from shotgun sequence datasets
-b NA
-r NA
-c NA
-a NA
-e 0
-h /u/scratch/user_hla_files/scrnaseq/SRRxyz.fq
-p ../database/hla_nom_p.txt
-z 200
-i 99
-q 30
-s 1000
-n 0
Reading p-nomenclature file ../database/hla_nom_p.txt...
Reading HLA reference sequence file /u/scratch/user_hla_files/scrnaseq/SRRxyz.fq...
Reading HLA reference sequence file NA...
Can't open -h NA for reading -- fatal.
I manually viewed my .fq files and they seemed fine.
Hi,
I'm trying to run alignment mode with my .fq files using the following command: ./HLAminer.pl -h /u/scratch/user_hla_files/scrnaseq/SRRxyz.fq
I get the following error: Running ./HLAminer.pl [v1.4] Derivation of HLA class I and II predictions from shotgun sequence datasets -b NA -r NA -c NA -a NA -e 0 -h /u/scratch/user_hla_files/scrnaseq/SRRxyz.fq -p ../database/hla_nom_p.txt -z 200 -i 99 -q 30 -s 1000 -n 0 Reading p-nomenclature file ../database/hla_nom_p.txt... Reading HLA reference sequence file /u/scratch/user_hla_files/scrnaseq/SRRxyz.fq... Reading HLA reference sequence file NA... Can't open -h NA for reading -- fatal.
I manually viewed my .fq files and they seemed fine.
Can you please help?