Sage this.mRefContext is null error

[RP-Silk]

Description of the bug

When trying to run oncoanalyser in offline mode, the pipeline runs fine until the SAGE_CALLING somatic and germline processes. At this point I get a this.mRefContext is null error. I have provided all reference data in a separate local config file, but Sage seems to be complaining that it doesn't have access to the reference material it needs? Do I need to point sage to the right reference files when running in offline mode so that it doesn't try to download it itself? Unfortunately, it's quite difficult to share log files as the research environment I am working on is very strict for exporting data.

Command used and terminal output

`nextflow run main.nf \
    --input params.csv \
    --outdir results \
    --genome GRCh38_hmf \
    --mode wgts \
    -c refdata.local.config \
    -c hpc.config \
    -resume`

Relevant files

Command error: INFO: Mounting image with FUSE. /usr/local/bin/sage: line 6: warning: setlocale: LC ALL: cannot change locale (en_US.UTF-8): No such file or directory java. lang.NullPointerException: Cannot invoke "com.hartwig.hmftools. sage. candidate.RefContext.processAltRead(String, St ring, int, int, com.hartwig.hmftools.sage.common.ReadContext)" because "this.mRefContext" is null at com.hartwig.hmftools.sage.candidate.AltRead.updateRefContext(AltRead.java:73) at com.hartwig.hmftools.sage.candidate.RefContextConsumer.processRead(RefContextConsumer.java: 188) at com.hartwig.hmftools.sage.evidence.CandidateEvidence.lambda$readBam$1(CandidateEvidence.java:52) at com.hartwig.hmftools.common.samtools.BamSlicer.slice(BamSlicer.java:72) at com.hartwig.hmftools.sage.common.SamSlicer.slice(SamSlicer.java:28) at com.hartwig.hmftools.sage.evidence.CandidateEvidence.readBam(CandidateEvidence.java:72) at com.hartwig.hmftools.sage.evidence.CandidateEvidence. readBam(CandidateEvidence.java:60) at com.hartwig.hmftools.sage.pipeline.CandidateStage.findCandidates(CandidateStage.java:59) at com.hartwig.hmftools.sage.pipeline.RegionTask. run(RegionTask.java:97) at com.hartwig.hmftools.sage.pipeline.RegionThread. run(RegionThread.java: 98)

System information

Nextflow version: 24.10.4
Hardware: HPC
Executor: LSF
Container engine: Singularity
OS: Linux
nf-core/oncoanalyser version: master

[scwatts]

Hi @RP-Silk, can you please post your configuration files, samplesheet, and the params.csv file?