Source of "hla.locus" File?

[cwarden45]

Hi,

I am trying to test running hisat-genotype with some of my Illumina Whole Genome Seuquencing data.

I slightly modified the setup script (described here), and I am currently using the following command:

R1=../CharlesWarden-NG1J8B7TDM-30x-WGS-Sequencing_com-10-13-21.1.fq.gz
R2=../CharlesWarden-NG1J8B7TDM-30x-WGS-Sequencing_com-10-13-21.2.fq.gz
THREADS=4
OUTDIR=Sequencing.com_HISAT-genotype

export PATH=/opt/samtools:/opt/hisat2-2.2.1:$PATH
export PYTHONPATH="$PYTHONPATH:/opt/hisat-genotype/hisatgenotype_modules"

python3 /opt/hisat-genotype/hisatgenotype --base hla --locus-list A,B,C,DRB1,DQA1,DQB1 -1 $R1 -2 $R2 -p $THREADS --out-dir $OUTDIR

However, I am receiving an error message related to PermissionError: [Errno 13] Permission denied: '/opt/hisat-genotype/indicies/hla.locus'. I have attached the full log output:

2023-08-05_hisat-genotype.log

I found two other tickets that I believe mention this file. For #11, I think the creation of the files is different than expected, and I am not if that means that I am misunderstanding something about how the program is being run.

For #15, it looks like this file should exist in the same folder as the _genotypegenome reference sequence.

I have downloaded some HLA files, but they are located within /opt/hisat-genotype/indicies/hisatgenotype_db/HLA (on my file system). There is also not a hla.locus file on that location.

Instead, these are the contents that I have with my installation:

-rwxrwxrwx 1 root root 3.0G Aug  3 00:48 genome.fa
-rwxrwxrwx 1 root root 6.3K Aug  3 00:48 genome.fa.fai
-rwxrwxrwx 1 nnnn nnnn 2.0G Jan 28  2018 genotype_genome.1.ht2
-rwxrwxrwx 1 nnnn nnnn 794M Jan 28  2018 genotype_genome.2.ht2
-rwxrwxrwx 1 nnnn nnnn  12K Jan 28  2018 genotype_genome.3.ht2
-rwxrwxrwx 1 nnnn nnnn 703M Jan 28  2018 genotype_genome.4.ht2
-rwxrwxrwx 1 nnnn nnnn 2.1G Jan 28  2018 genotype_genome.5.ht2
-rwxrwxrwx 1 nnnn nnnn 751M Jan 28  2018 genotype_genome.6.ht2
-rwxrwxrwx 1 nnnn nnnn 488M Jan 28  2018 genotype_genome.7.ht2
-rwxrwxrwx 1 nnnn nnnn 152M Jan 28  2018 genotype_genome.8.ht2
-rwxrwxrwx 1 nnnn nnnn 225K Jan 28  2018 genotype_genome.allele
-rwxrwxrwx 1 nnnn nnnn    0 Jan 28  2018 genotype_genome.clnsig
-rwxrwxrwx 1 nnnn nnnn 5.6K Jan 28  2018 genotype_genome.coord
-rwxrwxrwx 1 nnnn nnnn 3.0G Jan 28  2018 genotype_genome.fa
-rwxrwxrwx 1 nnnn nnnn 6.3K Jan 28  2018 genotype_genome.fa.fai
-rwxrwxrwx 1 nnnn nnnn 555M Jan 28  2018 genotype_genome.haplotype
-rwxrwxrwx 1 nnnn nnnn 441M Jan 28  2018 genotype_genome.index.snp
-rwxrwxrwx 1 nnnn nnnn 4.1M Jan 28  2018 genotype_genome.link
-rwxrwxrwx 1 nnnn nnnn 4.7K Jan 28  2018 genotype_genome.locus
-rwxrwxrwx 1 nnnn nnnn 189K Jan 28  2018 genotype_genome.partial
-rwxrwxrwx 1 nnnn nnnn 441M Jan 28  2018 genotype_genome.snp
drwxrwsrwx 2 nnnn nnnn 4.0K Mar 17  2016 grch38
drwxrwxrwx 6 root root 4.0K Aug  3 00:48 hisatgenotype_db

So, these are my questions:

1) If this is an additional reference file that should be prepared before running the method, can you please provide me instructions on how to create this file (and I can potentially change the access to the file once created)?

2) If this is supposed to be an output file, then is there a reason why it is not being created within what I specify with --out-dir $OUTDIR? The Sequencing.com_HISAT-genotype folder is being created, and I don't want to create output files for a particular sample within /opt.

I see that there is a genotype_genome.locus file, which could be more consistent with 1). However, I have not used this particular method before.

Thank you very much!

Sincerely, Charles

[cwarden45]

I believe that I found the issue is that I should install HISAT-genotype within my home directory (or another location where permissions will not be an issue).

While the location was not exactly the same, I believe that is consistent with the installation instructions here.

This is the revised command that ran without error (and was consistent with my results with other methods):

export PATH=/opt/samtools:/opt/hisat2-2.2.1:$PATH
export PYTHONPATH="$PYTHONPATH:/home/cwarden/Ref/hisat-genotype/hisatgenotype_modules"

python3 /home/cwarden/Ref/hisat-genotype/hisatgenotype --base hla --locus-list A,B,C,DRB1,DQA1,DQB1 -1 $R1 -2 $R2 -p $THREADS --out-dir $OUTDIR