"Not enough reads to make call" error.

[dottieyu]

Issue: Consistently getting a "not enough reads to make call" error.

I am using the official released HLAProfiler database (downloaded https://github.com/ExpressionAnalysis/HLAProfiler/releases/tag/v1.0.0-db_only).

When I run this predict command: $ perl HLAProfiler.pl predict -fastq1 dataset1/ERR009106_1.fastq -fastq2 dataset1/ERR009106_2.fastq -database_name hla_database -database_dir test/outputs/HLAProfiler-1.0.0-db_only -reference $HOME/local/HLAProfiler/test/outputs/HLAProfiler-1.0.0-db_only/hla_database/data/reference/hla.ref.merged.fa -if -l runlogs/ERR009106.HLAProfiler.log

Log file (ERR009106.HLAProfiler.log) shows typically ~80% alleles classified, ~20% unclassified. In prediction file however, all alleles show "not enough reads to make call".

Do you have advice, suggestions or feedback on how to avoid this issue - maybe some parameters we can try that will increase the likelihood of getting enough reads to make a prediction? Thank you.