intermediate alignment issue

[sulevk]

Dear all,

When trying to run arcasHLA from the intermediate alignment file, I am getting very persistent errors:

./arcasHLA genotype /path/my.alignment.p -o /my_hlaGT

"Traceback (most recent call last):
File "/Users/sulev/Terminalis/arcasHLA/scripts/genotype.py", line 716, in
alignment_info = load_alignment(args.file[0], commithash)
File "/Users/sulev/Terminalis/arcasHLA/scripts/align.py", line 337, in load_alignment
align_stats, gene_stats, num, avg, std) = alignment_info
ValueError: not enough values to unpack (expected 9, got 6)"

The previous run from bam files with extract followed by genotype worked without a glitch. And it works when I feed in sample.extracted.1.fq.gz, sample.extracted.2.fq.gz, not from the my.alignment.p.

Any help would be much appreciated.

Best regards
Sulev