Process hla_types_out (Printing HLA types to a csv file) terminated with an error exit status (1)

[palanikumarraaj]

Dear Nanjala Ruth,

I have followed the instructions mentioned for the usage of your nextflow pipeline with singularity for my NGS HLA data and tried both single and paired end method as explained. Both NGS data, I have faced some issue. But, let me highlight for single end alone for now.

Command used:
nextflow run nanjalaruth/HLA-typing -profile singularity --input "S2500910_L01_277_R1.fastq.gz" --reference_genome "/Database/hg19/ref_megabolt/hg19.fa" --hla_ref "/HLA-testing/other/org/HLA-typing/hla_all_v2.fasta" --hla_txt_file "/HLA-testing/other/org/HLA-typing/Allelelist_v2.txt" -r main --single_end

Error:
ERROR ~ Error executing process > 'hla_types_out (Printing HLA types to a csv file)'

Caused by:
Process hla_types_out (Printing HLA types to a csv file) terminated with an error exit status (1)

Command error:
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
readline() on closed filehandle IN at /usr/local/bin/parse_result.pl line 11.

Version used:
nextflow version 23.10.1.5891
apptainer version 1.2.5

Using: nextflow pull nanjalaruth/HLA-typing

Please, update any insights from your side.
Thank you.