After running for several hours demuxlet terminates with the following error:
NOTICE [2022/06/10 06:06:32] - Finished processing 619907 droplets total
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
/home/sgea/sge2/ge2011.11/slab06/spool/w03/job_scripts/34557: line 13: 26789 Aborted (core dumped)
This has happened with several different samples.
Options used:
The following parameters are available. Ones with "[]" are in effect:
Options for input SAM/BAM/CRAM : --sam [ATAC_10/outs/possorted_bam.bam],
--tag-group [CB], --tag-UMI [UB]
Options for input VCF/BCF : --vcf [combined.posG99.reheader.vcf.gz],
--field [GP], --geno-error [0.01],
--min-mac [1], --min-callrate [0.50], --sm,
--sm-list
Available Options
The following parameters are available. Ones with "[]" are in effect:
Options for input SAM/BAM/CRAM : --sam [ATAC_10/outs/possorted_bam.bam],
--tag-group [CB], --tag-UMI [UB]
Options for input VCF/BCF : --vcf [combined.posG99.reheader.vcf.gz],
--field [GP], --geno-error [0.01],
--min-mac [1], --min-callrate [0.50], --sm,
--sm-list
Output Options : --out [ATAC_10_demuxlet], --alpha,
--write-pair, --doublet-prior [0.50],
--sam-verbose [1000000],
--vcf-verbose [10000]
Read filtering Options : --cap-BQ [40], --min-BQ [13],
--min-MQ [20], --min-TD,
--excl-flag [3844]
Cell/droplet filtering options : --group-list, --min-total, --min-uniq,
--min-snp
After running for several hours demuxlet terminates with the following error:
NOTICE [2022/06/10 06:06:32] - Finished processing 619907 droplets total terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc /home/sgea/sge2/ge2011.11/slab06/spool/w03/job_scripts/34557: line 13: 26789 Aborted (core dumped)
This has happened with several different samples.
Options used:
The following parameters are available. Ones with "[]" are in effect: Options for input SAM/BAM/CRAM : --sam [ATAC_10/outs/possorted_bam.bam], --tag-group [CB], --tag-UMI [UB] Options for input VCF/BCF : --vcf [combined.posG99.reheader.vcf.gz], --field [GP], --geno-error [0.01], --min-mac [1], --min-callrate [0.50], --sm, --sm-list
Available Options
The following parameters are available. Ones with "[]" are in effect: Options for input SAM/BAM/CRAM : --sam [ATAC_10/outs/possorted_bam.bam], --tag-group [CB], --tag-UMI [UB] Options for input VCF/BCF : --vcf [combined.posG99.reheader.vcf.gz], --field [GP], --geno-error [0.01], --min-mac [1], --min-callrate [0.50], --sm, --sm-list Output Options : --out [ATAC_10_demuxlet], --alpha, --write-pair, --doublet-prior [0.50], --sam-verbose [1000000], --vcf-verbose [10000] Read filtering Options : --cap-BQ [40], --min-BQ [13], --min-MQ [20], --min-TD, --excl-flag [3844] Cell/droplet filtering options : --group-list, --min-total, --min-uniq, --min-snp