HKU-BAL / Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
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vcf pileup file not created #228

Closed rongiergaetan closed 1 year ago

rongiergaetan commented 1 year ago

I launch Clair3 like this:

./run_clair3.sh --bam_fn=Bam/consensus_sample_sorted.bam --ref_fn=ref/ref_seq.fasta --threads=8 --platform="ont" --model_path=models/r941_prom_sup_g5014 --output=output/ --include_all_ctgs --chunk_size=2000

The run stop during 1/7 Call variants using pileup model Because he cannot found the file: output/tmp/pileup_output/pileup_SP9D_LR_F2/R2_1.vcf

I join the log file. run_clair3.log

zhengzhenxian commented 1 year ago

@rongiergaetan,

FileNotFoundError: [Errno 2] No such file or directory: '/Clair3/output_clair3/tmp/pileup_output/pileup_SP9D_LR_F2/R2_3.vcf'"

It appears that the output directory /Clair3/output_clair3 is not writable. Please consider using a different output directory that allows for write access.