Empty files generated when attempting building a HLA graph reference.

[field654]

Dear Hisat group,

Thank you so much for posting such awesome algorithm. We are currently comparing all available algorithms for HLA typing.

We didn't find a official tutorial for HLA reference construction that's in detail. Let me know please if there's one that I missed.

I have however, followed the link that I occationally found.
https://hackmd.io/@linnil1/rkraXkHxF

I was able to install Hisat2, as well as downloading the uptodate HLA database.

mkdir hisat_index
cd hisat_index
wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat-genotype/data/genotype_genome_20180128.tar.gz
tar xvzf genotype_genome_20180128.tar.gz

wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/grch38.tar.gz
tar xvzf grch38.tar.gz
rm grch38.tar.gz
hisat2-inspect grch38/genome > genome.fa
samtools faidx genome.fa
cd ..

mkdir -p hisat_index/hisatgenotype_db/HLA/
cd hisat_index/hisatgenotype_db/HLA/
wget -nd -mL ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/fasta/* -P fasta
wget -nd -mL ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/msf/* -P msf
wget ftp://ftp.ebi.ac.uk/pub/databases/ipd/imgt/hla/hla.dat
cd ../../..

Above are the exact code I used to acquire the database for genome and HLA Loci.
I have attempted to make a genotyping of my own data.

hisat_index="./hisat_index"
hisatgenotype --base hla
--threads 30
--keep-alignment -v --keep-extract
-z ${hisat_index}
-1 ${sample_name}.R1.fq.gz
-2 ${sample_name}.R2.fq.gz
--out-dir ./tmp_hisat

I have run the above code substituting into my own data. I have seen the exact log that was posted. However, I saw no result generated.

Also, I'd like to check if the index and or reference were successfully built. I looked into the "hisat_index" folder. A number of files were generated with names of "hla_backbone.fa", "hla_sequences.fa", "hla.snp", etc. They are however all empty.

I do not have the proficiency to check the coding. I look forward to receiving your reply.

All the best.
Field Tian