Clair3
Clair3 copied to clipboard
minor bug with conda install `import: command not found`
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