Open hafizmtalha opened 2 years ago
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
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