Error when using Dockerized PHLAT

[rbowenj]

Hi,

I'm trying to use sub-tools from the ProTECT pipeline individually, using the Dockerized versions owned by aarjunrao. In particular, I'm trying to use PHLAT for HLA typing via the aarjunrao/phlat Docker image, but I get the following error:

..... Running PHLAT .......
Traceback (most recent call last):
  File "/home/phlat-1.0/dist/PHLAT.py", line 64, in <module>
    go(tag,outdir,phlatdir)
  File "/home/yubai/programs/phlat-1.0/dist/utilities.py", line 79, in go
  File "/home/yubai/programs/phlat-1.0/dist/extensions.py", line 617, in __init__
  File "/home/yubai/programs/phlat-1.0/dist/extensions.py", line 645, in setMaster
IndexError: list index out of range

The following command was used to run PHLAT (using a volume sourced from a local directory ~/PHLAT) on the example fastqs provided with the phlat-1.0 release:

docker run -v ~/PHLAT:/opt/PHLAT aarjunrao/phlat -1 /home/phlat-1.0/example/example_1.fastq.gz -2 /home/phlat-1.0/example/example_2.fastq.gz -index /opt/PHLAT/phlat-1.0/index4phlat -b2url /home/bowtie2-2.2.3/bowtie2 -tag test -e /home/phlat-1.0 -o /opt/PHLAT/results

Do you have any idea what's causing this and how I can fix it? As far as I can tell, this usage matches that implemented in the ProTECT phlat.py file.

Any help is much appreciated!
Thanks