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nanoporetech / rerio

Research release basecalling models and configurations
https://nanoporetech.com/
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[ERROR] Model path not found #65

Closed Wshengquan closed 2 months ago

Wshengquan commented 3 months ago

Hi， I have used Rerio to download the models for R10.4.1 data when I want to call variants by Clair3 and I run : run_clair3.sh --bam_fn=../LR1D.sort.bam --ref_fn=/share/home/yzwl_hanxs/basecalling/referenceGene/Sus_scrofa.Sscrofa11.1.dna_sm.toplevel.fa --threads=4 --platform='ont' --model_path='/share/home/yzwl_hanxs/app/rerio/clair3_models/r1041_e82_400bps_sup_g615_model' --output=/share/home/yzwl_hanxs/company-third/LR1D/bam/SNP And then the error was reported： [INFO] CLAIR3 VERSION: v1.0.8 [INFO] BAM FILE PATH: /share/home/yzwl_hanxs/company-third/LR1D/bam/SNP/../LR1D.sort.bam [INFO] REFERENCE FILE PATH: /share/home/yzwl_hanxs/basecalling/referenceGene/Sus_scrofa.Sscrofa11.1.dna_sm.toplevel.fa [INFO] MODEL PATH: /share/home/yzwl_hanxs/app/rerio/clair3_models/r1041_e82_400bps_sup_g615_model [INFO] OUTPUT FOLDER: /share/home/yzwl_hanxs/company-third/LR1D/bam/SNP [INFO] PLATFORM: ont [INFO] THREADS: 4 [INFO] BED FILE PATH: EMPTY [INFO] VCF FILE PATH: EMPTY [INFO] CONTIGS: EMPTY [INFO] CONDA PREFIX: /share/home/yzwl_hanxs/anaconda3/envs/clair3 [INFO] SAMTOOLS PATH: samtools [INFO] PYTHON PATH: python3 [INFO] PYPY PATH: pypy3 [INFO] PARALLEL PATH: parallel [INFO] WHATSHAP PATH: whatshap [INFO] LONGPHASE PATH: EMPTY [INFO] CHUNK SIZE: 5000000 [INFO] FULL ALIGN PROPORTION: 0.7 [INFO] FULL ALIGN REFERENCE PROPORTION: 0.1 [INFO] PHASING PROPORTION: 0.7 [INFO] MINIMUM MQ: 5 [INFO] MINIMUM COVERAGE: 2 [INFO] SNP AF THRESHOLD: 0.08 [INFO] INDEL AF THRESHOLD: 0.15 [INFO] BASE ERROR IN GVCF: 0.001 [INFO] GQ BIN SIZE IN GVCF: 5 [INFO] ENABLE FILEUP ONLY CALLING: False [INFO] ENABLE FAST MODE CALLING: False [INFO] ENABLE CALLING SNP CANDIDATES ONLY: False [INFO] ENABLE PRINTING REFERENCE CALLS: False [INFO] ENABLE OUTPUT GVCF: False [INFO] ENABLE HAPLOID PRECISE MODE: False [INFO] ENABLE HAPLOID SENSITIVE MODE: False [INFO] ENABLE INCLUDE ALL CTGS CALLING: False [INFO] ENABLE NO PHASING FOR FULL ALIGNMENT: False [INFO] ENABLE REMOVING INTERMEDIATE FILES: False [INFO] ENABLE LONGPHASE FOR INTERMEDIATE VCF PHASING: False [INFO] ENABLE PHASING FINAL VCF OUTPUT USING WHATSHAP: False [INFO] ENABLE PHASING FINAL VCF OUTPUT USING LONGPHASE: False [INFO] ENABLE HAPLOTAGGING FINAL BAM: False [INFO] ENABLE LONG INDEL CALLING: False [INFO] ENABLE C_IMPLEMENT: True

ESC[31m[ERROR] Model path not foundESC[0m

and then I checked this : 1720268229006

Why does this happen Any help to overcome this is appreciated!

Best

davidnewman02 commented 3 months ago

The error from Clair3 looks like the model can not be found and/or hasn't been downloaded correctly.

It looks like you are trying to use the r1041_e82_400bps_sup_g615_model. Is this the model you intended to use? Did this model download correctly? What is the content of the folder: /share/home/yzwl_hanxs/app/rerio/clair3_models/r1041_e82_400bps_sup_g615_model ?

From your screenshot it seems like the only clair3 models you have downloaded are the v430 and v500 (highlighted in green)? Depending on what model you have used in basecalling these are the models we would recommend rather than the outdated g615 model.

If you are still having trouble, could you please include the commands used to download the model from Rerio.

Wshengquan commented 2 months ago

Thank you very much for your reply. It should be caused by the incomplete download of my model. I have solved it. Thanks again for your reply