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[ERROR] Model path not found #319

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Wshengquan opened this issue Jul 6, 2024 · 0 comments
Open

[ERROR] Model path not found #319

Wshengquan opened this issue Jul 6, 2024 · 0 comments
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community support needed Questions that are not directly related to development and can receive helps from the user community

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@Wshengquan
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Hi,
I have used Rerio to download the models for R10.4.1 data 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 :
1720265139733
Why does this happen
Any help to overcome this is appreciated!

Best

@aquaskyline aquaskyline added the community support needed Questions that are not directly related to development and can receive helps from the user community label Jul 6, 2024
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