uint16 problem

[mromanov2001]

Hello!
I executed this command
optitype run -i sample1.bam --rna -v -o results/
and ran into this problem

OptiType 1.5.0
Input files: ['sample1.bam']
Sequence type: rna
Output directory: results/
Mapper: razers3
Solver: glpk

0:00:00.76 Generating binary hit matrix.
0:00:00.76 Loading Tesla4_chr6.bam started. Number of HLA reads loaded (updated every thousand):
Error: Python integer 88866 out of bounds for uint16

How can I fix it?

[MaybeTommorow]

@mromanov2001

Hi, I got similar issue when I input wes-mapped bam file to pipeline.
My understand is that the optiType's BAM mode expects a BAM that has already been aligned to HLA reference sequences (produced internally by razers3/yara). Passing a standard whole-genome BAM is incorrect — OptiType would try to load all genome-wide mapped reads, producing meaningless results and consuming excessive memory/runtime.

However, if the input file is in the fastq format, everything will work as expected.