I think there is an error when I run xHLA on some the bam-file with the alignment of target reads. It is some kind of test data in my case, that is used in a big pipeline with many tools. I suppose that region of interest is absent in my test data, but I think the error should be more human-readable.
[27/Jul/2021 23:37:42] INFO - Sample_id: SRR6000626 Input file: /dCCkYn/output/inputs/SRR6000626_alignment.bam
typer.sh parameters: DELETE=true FULL=false
Extracting reads from S3
Aligning reads to IMGT database
processing FASTQ file
found 245 reads
processing MSA file
found 76507 HLA exons
processing FASTQ file
matched to 2312 HLA exons
0 reads matched to HLA types not in the MSA file
translating matches to MSA
Typing
[1] "nrow(all) 2769"
[1] "nrow(all) 2769"
[1] "nrow(all) 1450"
[1] "nrow(all) 1450"
[1] "length(unique(all[,q])) 3"
[1] "n.core.reads 3"
[1] "nrow(all) 1343"
[1] "nrow(all) 1343"
[1] "nrow(non.core) 0"
[1] "nrow(core) 1343"
dcast
done dcast
weight
done weight
set to 1
done set to 1
dcast2
Error in dcast.data.table(non.core, q ~ type, value.var = "specific", :
Can not cast an empty data.table
Calls: dcast -> dcast.data.table
Execution halted
Traceback (most recent call last):
File "/soft/XHLA-34221ea2bb3e09177e237b33ba946404214cc270/bin/run.py", line 64, in <module>
check_call(bin_args)
File "/usr/lib/python3.7/subprocess.py", line 363, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/soft/XHLA-34221ea2bb3e09177e237b33ba946404214cc270/bin/typer.sh', '/dCCkYn/output/inputs/SRR6000626_alignment.bam', 'SRR6000626', 'delete']' returned non-zero exit status 1.
Hello! Thank you for this great tool!
I think there is an error when I run xHLA on some the bam-file with the alignment of target reads. It is some kind of test data in my case, that is used in a big pipeline with many tools. I suppose that region of interest is absent in my test data, but I think the error should be more human-readable.