octopus: An unclassified error has occurred: Map::at

Describe the bug I am trying to joint genotype two files for a test (they are both ~1x). I get the following output:

[2019-12-11 16:30:10] <INFO> ------------------------------------------------------------------------
[2019-12-11 16:30:10] <INFO> octopus v0.6.3-beta (release/0.6.3-beta 8b0e2968)
[2019-12-11 16:30:10] <INFO> Copyright (c) 2015-2019 University of Oxford
[2019-12-11 16:30:10] <INFO> ------------------------------------------------------------------------
[2019-12-11 16:30:12] <EROR> An unclassified error has occurred:
[2019-12-11 16:30:12] <EROR> 
[2019-12-11 16:30:12] <EROR>     Map::at.
[2019-12-11 16:30:12] <EROR> 
[2019-12-11 16:30:12] <EROR> To help resolve this error submit an error report.
[2019-12-11 16:30:12] <INFO> ------------------------------------------------------------------------

Version

$ octopus --version
octopus version 0.6.3-beta (release/0.6.3-beta 8b0e2968)
Target: x86_64 Linux 5.0.0-1023-azure
Compiler: GNU 8.3.0
Boost: 1_71

Command Command line to run octopus:

#!/bin/bash -ue
octopus \
  -R Homo_sapiens_assembly38.fasta \
  -I 0_NA12878.bam 1_NA12878.bam \
  -c 0_NA12878.bcf 1_NA12878.bcf \
  -o cohort.bcf \
  -g off \
  -a off \
  --repeat-candidate-generator off \
  --sequence-error-model PCR-FREE.NOVASEQ \
  --forest ~/octopus/resources/forests/germline.v0.6.3-beta.forest \
  --threads 10 \
  --debug

About this issue

  • Original URL
  • State: closed
  • Created 5 years ago
  • Comments: 16 (7 by maintainers)

Most upvoted comments

It builds, I just wanted to run with the forest. It’ll take about an hour to reprocess the data with the changed command. I will let you know what happens.