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HKU-BAL / Clair3

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
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minor bug with conda install `import: command not found` #327

Closed gbouras13 closed 1 week ago

gbouras13 commented 3 months ago

Hi developers,

Thanks for the great tool - very fast and accurate!

I installed clair3 via option 3 Bioconda. Linux system with GPU available Ubuntu 20.04

I ran Clair3 as follows:

run_clair3.sh \
    --bam_fn="$aln" \
    --ref_fn="$ref" \
    --threads=24 \
    --platform="ont" \
    --model_path="$model_path" \
    --output="$outdir" \
    --sample_name="$sample" \
    --include_all_ctgs \
    --haploid_precise \
    --no_phasing_for_fa \
    --enable_long_indel

with relevant correct variables. There was an error:

/home/user/miniforge3/envs/clair3/bin/clair3.py: line 1: import: command not found
from: can't read /var/mail/importlib
from: can't read /var/mail/shared.param_p

Solved by adding a shebang:

#!/usr/bin/env python3 to the file /home/user/miniforge3/envs/clair3/bin/clair3.py

George

zhengzhenxian commented 3 months ago

Thank you, George! Will add in our next release.

aquaskyline commented 1 week ago

Fixed in v1.0.10