Closed quocviet0908 closed 1 year ago
cjw85
commented
1 year ago A quick Google search led me to:
https://github.com/bioconda/bioconda-recipes/issues/34190
This suggests that your channel order in your conda setup is not correct. You should review the bioconda usage documentation.
quocviet0908
commented
1 year ago A quick Google search led me to:
bioconda/bioconda-recipes#34190
This suggests that your channel order in your conda setup is not correct. You should review the bioconda usage documentation.
Brilliant!!! I could not figure out that channel priority was the problem. Changing channel restriction and conda-forge priority solved the problem flawlessly. Thank you very much @cjw85,
Hi everyone.
I'm trying to use medaka to polish my draft genome from the long-read assembly, particularly Flye. However I keep struggling with installing and running medaka on both my virtual machine and dedicated PC with Ubuntu 20.04.
I tried conda, mamba, or virtualenv but no luck so far.
Medaka 1.8.0 installation with conda often ends up freezing or silent kill unless installing with mamba, 1.7.2 or the previous version can be installed fine, but can't run as expected. Every time I try to run medaka_consensus it always ends up with the bcftools problem.
This is the command I use to polish my genome and the output:
medaka_consensus -t 2 -m r941_prom_variant_g360 -i bacillus_amylo.fastq -d /home/cbb/Work/3rd_party/Bacillus_amyloquefaciens/raw_reads_ONT/flye_out_20230602/assembly.fasta -o medaka_20230605 Checking program versions This is medaka 1.7.2 bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory Program Version Required Pass
bcftools Not found 1.11 False
bgzip 1.16 1.11 True
minimap2 2.26 2.11 True
samtools 1.16.1 1.11 True
tabix 1.16 1.11 True
Environment (if you do not have a GPU, write No GPU):
Could you please help me make it run? Thank you for any help and suggestion.