Empty outputs w/ no warnings or errors

[helixscript]

Hi hista-genotype folks,

Our group is very interested in your software to determine the haplotypes of patient samples. We sequenced the HLA-A and HLA-B loci. When we run your software it typically runs for a couple of minutes then ends with empty report files (below). Any suggestions would be very much appreciated.

Best, John

%> hisatgenotype -1 227OP20200422.R1.fastq.gz -2 227OP20200422.R2.fastq.gz -v -p 25 --out-dir out 1: Extracting reads from 227OP20200422.R1.fastq.gz running hisat2 -x /home/everett/hisatgenotype/indicies/genotype_genome --no-spliced-alignment -X 1000 -1 ./227OP20200422.R1.fastq.gz -2 ./227OP20200422.R2.fastq.gz

     1A1 2A6 3A4 19A1 2A13 26A1 3A43 4A22 2B6 2C8 2C9 2C19 2D6 2F1 4F2 2J2 2R1 2S1 2W1
     A B C DMA DMB DOA DOB DPA1 DPB1 DPB2 DQA1 DQB1 DRA DRB1 E F G H HFE K L MICA MICB TAP1 TAP2 V

%> ls -alh out/ -rw-rw-r-- 1 everett everett 0 Nov 25 11:29 assembly_graph-cyp.227OP20200422_R1_fastq_gz-cyp-extracted-1_fq.report -rw-rw-r-- 1 everett everett 0 Nov 25 11:29 assembly_graph-hla.227OP20200422_R1_fastq_gz-hla-extracted-1_fq.report

[chbe-helix]

Hi everettJK,

Sorry for the late reply to your issue. Since you sequenced the HLA-A and B loci exclusively, my first suggestion would be to use the following command:

hisatgenotype --base hla --locus-list A,B -1 227OP20200422.R1.fastq.gz -2 227OP20200422.R2.fastq.gz -v -p 25 --out-dir out

This should narrow the program to only typing HLA-A and HLA-B. Let me know how this works for you.

Thanks, Chris