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bacpop / ggCaller

Bifrost graph gene caller.
MIT License
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ggcaller terminate called after throwing an instance of 'std::out_of_range' #35

Closed afrouin closed 1 month ago

afrouin commented 2 months ago

Hi Sam and all,

So i tried to run ggcaller (version 1.3.6) on my institute SLURM cluster and got the following error message:

Building coloured compacted DBG... Generating graph stop codon index... Mapping contigs to graph... terminate called after throwing an instance of 'std::out_of_range' what(): vector::_M_range_check: __n (which is 18446744073709551615) >= this->size() (which is 431399) /local/scratch/tmp/tmpnm3wpbd2: line 3: 2260531 Aborted ggcaller --refs scratch/genomes/input_strains.txt --annotation ultrasensitive --aligner def --alignment pan --save --out scratch/ggc_ScreenCryo --threads 16 --quiet ERROR conda.cli.main_run:execute(125): conda run ggcaller --refs scratch/genomes/input_strains.txt --annotation ultrasensitive --aligner def --alignment pan --save --out scratch/ggc_ScreenCryo --threads 16 --quiet failed. (See above for error)

I don't think it's a memory problem: it crashed using only 8 of the 500+G allocated ... Any idea how to fix this ?

Thanks a lot !

samhorsfield96 commented 2 months ago

Hi, would you be able to provide the input_strains.txt file, please? Also how did you install ggCaller?

afrouin commented 2 months ago

Hi Sam, thank you for your answer.

Please find attached the input_strains.txt file.

input_strains.txt

Also, i installed ggCaller using apptainer (recipe is also attached).

ggCaller-1-3-6.txt

Thanks again for your help

samhorsfield96 commented 1 month ago

Hi, I have not been able to reproduce the error with my own datasets, however, I have tried a potential fix in the branch issue35. If you can, please install using this branch from source and retry using the same command and dataset.

afrouin commented 1 month ago

Hi Sam, it worked! Thank you very much for your responsiveness and have a nice day!