Encountered an exception during calling 'std::bad_alloc'

Ankita-1211 commented 1 year ago

Describe the bug [2023-11-11 04:03:11] chrY:22228260 99.9% 19m 42s 1s [2023-11-11 04:04:05] chr5:50000000 100.0% 20m 36s - [2023-11-11 04:12:26] - 100% 28m 57s - [2023-11-11 04:12:34] Starting Call Set Refinement (CSR) filtering [2023-11-11 04:12:36] Removed 390 temporary files [2023-11-11 04:12:41] A program error has occurred: [2023-11-11 04:12:41] [2023-11-11 04:12:41] Encountered an exception during calling 'std::bad_alloc'. This means [2023-11-11 04:12:41] there is a bug and your results are untrustworthy. [2023-11-11 04:12:41] [2023-11-11 04:12:41] To help resolve this error run in debug mode and send the log file to [2023-11-11 04:12:41] https://github.com/luntergroup/octopus/issues. [2023-11-11 04:12:41] ------------------------------------------------------------------------

Version

0.7.4

Command using docker image

Command line to run octopus:

```shell
docker run -v /bp:/bp dancooke/octopus -R /bp/GRCh38.ensembl.181203.fa -I /bp/*.bam --somatic-forest /bp/somatic.v0.7.4.forest.gz --forest /bp/germline.v0.7.4.forest.gz --sequence-error-model PCR-FREE.NOVASEQ --threads 64 -o /bp/lib32rem_fastq_vs_lib32_fastq.GRCh38.variants.vcf.gz  -N lib32_fastq

supermax1234 commented 12 months ago

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 commented 6 months ago

had this too using 0.7.4 docker image

luntergroup / octopus