Error in dcast.data.table

I have a bam file generated using BWA-mem against GRCh37. I have changed one line in typer.sh : https://github.com/humanlongevity/HLA/blob/master/bin/typer.sh#L34 from chr6:29886751-33090696 to 6:20000000-40000000, rebuilt Image and got the following error:

typer.sh parameters: DELETE=false FULL=false
Extracting reads from S3
Aligning reads to IMGT database
processing FASTQ file
    found 1088 reads
processing MSA file
    found 26381 HLA exons
processing FASTQ file
    matched to 445 HLA exons
    2 reads matched to HLA types not in the MSA file
translating matches to MSA
Typing
[1] 1434
[1] 1434
[1] 231
[1] 0
[1] 1050
[1] 729
[1] 729
[1] 0
dcast
Error in dcast.data.table(core, q ~ type, value.var = "specific", fun.aggregate = max,  : 
  Can not cast an empty data.table
Calls: dcast -> dcast.data.table
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', 'SRR070472/SRR070472.bam', 'SRR070472']' returned non-zero exit status 1

Seems like the algorithm is complaining about zeros, but no idea how to fix it...

humanlongevity / HLA

Error in dcast.data.table #26