docker run -v pwd:pwd -w pwd humanlongevity/hla --sample_id 'SU-DIPG_24' --input_bam_path SU-DIPG-24.bam --output_path myoutput
[31/Jul/2022 11:37:10] INFO - Xie Chao's HLA typing algorithm
[31/Jul/2022 11:37:10] INFO - Sample_id: SU-DIPG_24 Input file: SU-DIPG-24.bam
typer.sh parameters: DELETE=false FULL=false
Extracting reads from S3
Aligning reads to IMGT database
processing FASTQ file
found 5143 reads
processing MSA file
found 26381 HLA exons
processing FASTQ file
matched to 8 HLA exons
16 reads matched to HLA types not in the MSA file
translating matches to MSA
Typing
Error in fread(align.path) : File is empty: hla-SU-DIPG_24/SU-DIPG_24.tsv
Execution halted
Traceback (most recent call last):
File "/opt/bin/run.py", line 64, in
check_call(bin_args)
File "/usr/lib/python2.7/subprocess.py", line 540, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/opt/bin/typer.sh', 'SU-DIPG-24.bam',
'SU-DIPG_24']' returned non-zero exit status 1