Open alexvpickering opened 4 years ago
here is the full output:
[12/Jun/2020 16:16:54] INFO - Xie Chao's HLA typing algorithm [12/Jun/2020 16:16:54] INFO - Sample_id: 09KTG_TGACCA Input file: ./results/mapped_reads/09KTG_TGACCA.bam typer.sh parameters: DELETE=false FULL=false Extracting reads from S3 Aligning reads to IMGT database processing FASTQ file found 916 reads processing MSA file found 26381 HLA exons processing FASTQ file matched to 9482 HLA exons 203 reads matched to HLA types not in the MSA file translating matches to MSA Typing [1] 13918 [1] 13918 [1] 142 [1] 55 [1] 10218 [1] 5065 [1] 1568 [1] 3497 dcast done dcast weight done weight set to 1 done set to 1 dcast2 done dcast2 lpsolve done lpsolve [1] "DPB1*04:01" "DQB1*06:02" pulling non-core exons in Warning message: In mclapply(solution, function(s) { : all scheduled cores encountered errors in user code Error in more$solution : $ operator is invalid for atomic vectors Calls: unique Execution halted Traceback (most recent call last): File "/opt/bin/run.py", line 64, in <module> 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', './results/mapped_reads/09KTG_TGACCA.bam', '09KTG_TGACCA']' returned non-zero exit status 1
I'm having the same issue for one of my WES sample. All other samples in my cohort ran well. Any updates?
here is the full output: