lima: terminate called after throwing an instance of 'std::length_error'

[Jiayi-Wang-Joey]

Hi, I am running lima on PacBio MAS-seq long-read scRNA-seq data. This is the command I used:

lima /home/jiayiwang/loggedfs_david_penton/data/kinnex/segmented/PB258_3_r0362_bcM0004-segmented.bam data/primer/10x_3kit_primers.fasta /home/jiayiwang/loggedfs_david_penton/result/preprocessing/primer_removal/PB258_3_r0362_bcM0004.fl.5p--3p.bam --no-reports --num-threads 4 --isoseq

This command works for my other samples/bams. However, it returns error for this specific sample:

terminate called after throwing an instance of 'std::length_error'
  what():  cannot create std::vector larger than max_size()
Aborted (core dumped)

I am not sure what this error means. Is the number of reads too large? My bam file is 67GB. I tried --split-bam, however, the error persists. It will be great if you could help me with this.

Thanks very much in advance!

[kristina28]

I am having the same problem with a hifi_read.bam file, with the command lima m84132_250124_184858_s3.hifi_reads.bam old-16S-primers.fasta Kinnex-m84132.asym.demux.bam --split --peek-guess --hifi-preset ASYMMETRIC

My bam file is approximately the same size (63GB) and I'm wondering if the file size is part of the problem since I've been able to process smaller read files successfully.

Has anyone found a resolution for this?

[zihian]

Faced the same issue for large bams, ~64GB for me. I resolved it by assigning more memory, it works with 100GB but I assigned more (>120GB) just to be sure for future analysis.

[Jiayi-Wang-Joey]

Hi Thanks for your suggestions. I solved the issue by simply updating the lima version.