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HadrienG / InSilicoSeq

:rocket: A sequencing simulator
https://insilicoseq.readthedocs.io
MIT License
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'Seq' object has no attribute 'tomutable' #232

Closed Sanrrone closed 1 year ago

Sanrrone commented 1 year ago

Dears, I'm trying to generate reads from an multifasta (60G), I don't know if the size of the genomes trigger the error but the software doesn't ends. (Installation via conda). iss generate --cpus 16 --n_reads 5000000 --seed 1 --model NovaSeq --output test_1.fastq --draft humgut.fna --debug --compress

DEBUG:iss.app:iss version 1.5.3
DEBUG:iss.app:Using verbose logger
INFO:iss.app:Starting iss generate
INFO:iss.app:Using kde ErrorModel
INFO:iss.app:Setting random seed to 1
DEBUG:iss.error_models.kde.KDErrorModel:Loaded ErrorProfile: /scratch/project_2007362/software/mambaforge/lib/python3.10/site-packages/iss/profiles/NovaSeq
INFO:iss.util:Stitching input files together
INFO:iss.app:Using lognormal abundance distribution
INFO:iss.app:Using 16 cpus for read generation
INFO:iss.app:Generating 5000000 reads
INFO:iss.app:Generating reads for record: HumGut_17012_1
DEBUG:iss.app:'Seq' object has no attribute 'tomutable'

what can I do? regards

nvaulin commented 1 year ago

There is no tomutable function in biopython.Seq for now, so the iss is crashing. To make it work use a separate environment with the older biopython version installed (for instance, biopython==1.80)

Sanrrone commented 1 year ago

it works now, thank you