Encountered an exception during calling 'std::bad_alloc' about octopus

[supermax1234]

Hello,
I also have the same bug, here are the details

debug.log

[...]
[2023-11-20 08:48:18] Writing completed task chrY:57187917-57188038 that finished in 0ms
[2023-11-20 08:48:18] Writing completed task chrY:57189391-57189549 that finished in 0ms
[2023-11-20 08:48:18] Writing completed task chrY:57189958-57190090 that finished in 0ms
[2023-11-20 08:48:18] Writing completed task chrY:57190186-57190385 that finished in 0ms
[2023-11-20 08:48:18] Writing completed task chrY:57190929-57191095 that finished in 0ms
[2023-11-20 08:48:18] Writing completed task chrY:57191787-57192009 that finished in 0ms
[2023-11-20 08:48:18] Writing completed task chrY:57192592-57192718 that finished in 0ms
[2023-11-20 08:48:18] Writing completed task chrY:57194032-57194137 that finished in 0ms
[2023-11-20 08:48:18] Writing completed task chrY:57196325-57196939 that finished in 0ms
[2023-11-20 08:48:18] - 100% 1d 2h -
[2023-11-20 08:48:18] Merging 24 temporary VCF files
[2023-11-20 08:48:22] Starting Call Set Refinement (CSR) filtering
[2023-11-20 08:48:23] Encountered an error whilst filtering, attempting to cleanup
[2023-11-20 08:48:23] Removed 50 temporary files
[2023-11-20 08:48:23] A program error has occurred:
[2023-11-20 08:48:23]
[2023-11-20 08:48:23] Encountered an exception during calling 'std::bad_alloc'. This means
[2023-11-20 08:48:23] there is a bug and your results are untrustworthy.
[2023-11-20 08:48:23]
[2023-11-20 08:48:23] To help resolve this error run in debug mode and send the log file to
[2023-11-20 08:48:23] https://github.com/luntergroup/octopus/issues.
[2023-11-20 08:48:23] ------------------------------------------------------------------------

command

REFERENCE=genome.fa
BED=Twist_Comprehensive_Exome_Covered_Targets_hg38.bed
UMI_CONFIG=resources/configs/UMI.config
GERMLINE_FOREST=resources/forests/germline.v0.7.4.forest.gz
SOMATIC_FOREST=resources/forests/somatic.v0.7.4.forest.gz
INPUT_NORMAL=S1_normal.bam
INPUT_TUMOR=S1_tumor.bam
NORMAL="normal"
OUTPUT=out.vcf

singularity
exec
--bind /project
octopus_latest.sif
octopus
--reference $REFERENCE
--reads $INPUT_NORMAL $INPUT_TUMOR
--output $OUTPUT
--normal-sample $NORMAL
--regions-file $BED
--config $UMI_CONFIG
--forest-model $GERMLINE_FOREST
--somatic-forest-model $SOMATIC_FOREST
--debug debug.log
--threads 4

version

Singularity> octopus --version
octopus version 0.7.4
Target: x86_64 Linux 5.10.25-linuxkit
SIMD extension: AVX2
Compiler: GNU 11.1.0
Boost: 1_76

---

thanks for the support!

Best,

Max

[tzvi909]

had this too using 0.7.4 docker image