Unable to run hisatgenotype with pre-aligned data

[ryanalomair]

Hello! I am trying to run hisatgenotype (installed manually using these instructions: https://daehwankimlab.github.io/hisat-genotype/manual/) using pre-aligned data with the following command:

./hisatgenotype --base hla --locus-list A,B,C,DRB1,DQA1,DQB1 -z . -f -1 ERR009096Aligned.sortedByCoord.out.extracted.1.fq -2 ERR009096Aligned.sortedByCoord.out.extracted.2.fq --in-dir /scratch1/rayyala/HLA_data/d1

Which returns the following:

==========================================
Files found: Omitted extracting reads from ERR009096Aligned.sortedByCoord.out.extracted.1.fq
A B C DRB1 DQA1 DQB1
Error in running HISATgenotype: Incomplete Align Return

The data was aligned using star aligner. Chromosome 6 was extracted from corresponding BAM files to convert back to FASTA format using samtools and bamtofastq. Do you have any thoughts or advice? Thanks!

[marchoeppner]

old thread, and not a developer, but make sure you name-sort the BAM file before you extract the reads back to fastq. Else the fastq files will be out of order and should probably fail the alignment stage.