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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 : Why does this happen Any help to overcome this is appreciated!
Best
The text was updated successfully, but these errors were encountered:
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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](https://private-user-images.githubusercontent.com/145557567/346270195-71ba7c9f-674e-4eeb-8d13-526417ea7b7b.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjEzMDUzNzEsIm5iZiI6MTcyMTMwNTA3MSwicGF0aCI6Ii8xNDU1NTc1NjcvMzQ2MjcwMTk1LTcxYmE3YzlmLTY3NGUtNGVlYi04ZDEzLTUyNjQxN2VhN2I3Yi5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNzE4JTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDcxOFQxMjE3NTFaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT03MTk4N2Y2Nzc1OWQyZmYyOGQ1MGJlNjhjZTIxOWM2MDQ5NWIwZmU1NjI0Y2RhZTgzNGQ5ZDVkOWI1OTYzYTYxJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.WhtFwUcq8QhBHm9hq9PnTiSCTZgHKlA8XVz-IxK4QPE)
Why does this happen
Any help to overcome this is appreciated!
Best
The text was updated successfully, but these errors were encountered: