Blast container omitting penalty flag in command execution.

Jobs are failing because the penalty flag is being omitted. It is sent into the blast server by the mblast service, but the produced command is does not appear to include it.

Input:

{
  "tool":"blastn",
  "-outfmt":{"type":15},
  "-max_target_seqs":100,
  "-db":"//db/FungiDB/build-56/AfumigatusA1163/blast/AfumigatusA1163Genome",
  "-soft_masking":true,
  "-task":"blastn",
  "-word_size":11,
  "-gapopen":12,
  "-gapextend":8,
  "-penalty":-5,
  "-reward":4,
  "-dust":"yes"
}

Output:

blastn -outfmt=11 -max_target_seqs=100 -out=report.asn1 -query=query.txt -db=//db/PlasmoDB/build-57/Pfalciparum3D7/blast/Pfalciparum3D7AnnotatedTranscripts -soft_masking=true -task=blastn -reward=4 -dust=yes

Exit code 3

VEuPathDB / service-multi-blast

Blast container omitting penalty flag in command execution. #126