[ERROR] No pileup model found in provided model path and model prefix

[jsromanowski]

Hello,

I followed installation instructions using conda and ran the follow clair3 command in bash to call variants in nanopore sequencing data:

$ run_clair3.sh --bam_fn=1026NJ4_NHEJ_FLsorted.bam --ref_fn=NHEJAssayABshortref.fas --output=/mnt/c/users/josep/Downloads/ROMANOWSKI_CUSTOM_253/NHEJassay_IGV_files --threads=16 --platform=ont --model_path=/home/joeromanowski/miniconda3/envs/clair3/bin/models/

To which I received the following output:

[INFO] CLAIR3 VERSION: v1.0.5 [INFO] BAM FILE PATH: /mnt/c/users/josep/Downloads/ROMANOWSKI_CUSTOM_253/NHEJassay_IGV_files/1026NJ4_NHEJ_FLsorted.bam [INFO] REFERENCE FILE PATH: /mnt/c/users/josep/Downloads/ROMANOWSKI_CUSTOM_253/NHEJassay_IGV_files/NHEJAssayABshortref.fas [INFO] MODEL PATH: /home/joeromanowski/miniconda3/envs/clair3/bin/models [INFO] OUTPUT FOLDER: /mnt/c/users/josep/Downloads/ROMANOWSKI_CUSTOM_253/NHEJassay_IGV_files [INFO] PLATFORM: ont [INFO] THREADS: 16 [INFO] BED FILE PATH: EMPTY [INFO] VCF FILE PATH: EMPTY [INFO] CONTIGS: EMPTY [INFO] CONDA PREFIX: /home/joeromanowski/miniconda3/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

[ERROR] No pileup model found in provided model path and model prefix /home/joeromanowski/miniconda3/envs/clair3/bin/models/pileup

real 0m0.065s user 0m0.011s sys 0m0.004s

Any help to overcome this is appreciated!

Best,

Joe

[zhengzhenxian]

Hi, @jsromanowski

The pileup and full-alignment models are not found in /home/joeromanowski/miniconda3/envs/clair3/bin/models/, please check the model path.

[jsromanowski]

Thank you for the quick reply. Apologies if this is a simple question (but since I am very new to conda/python) how exactly would I do that? And further, if it is not included in the model path how would I add it?

-Joe

[zhengzhenxian]

Here is the instruction to download models. You can also try the following command to download the models:

mkdir models
wget http://www.bio8.cs.hku.hk/clair3/clair3_models/clair3_models.tar.gz 
tar -zxvf clair3_models.tar.gz -C ./models

And then select the appropriate models using the --model_path command such as: --model_path=./models/r941_prom_sup_g5014.

If you require the latest ONT-provided model, please visit Rerio to download the models.