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vanheeringen-lab / seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
https://vanheeringen-lab.github.io/seq2science
MIT License
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BUG: Authentication plugin 'mysql_native_password' cannot be loaded #1027

Open Leif78 opened 2 months ago

Leif78 commented 2 months ago

I try to run the RNA-seq pipeline, but got this message:

Seq2science has trouble querying the assembly providers. Try again in a bit.
To see the error stack trace run seq2science with --debug.

Rerun with debug last output:

2059 (HY000): Authentication plugin 'mysql_native_password' cannot be loaded: /usr/lib/mysql/plugin/mysql_native_password.so: cannot open shared object file: No such file or directory

Do we need to update mysql?

Best regards Leif

Maarten-vd-Sande commented 2 months ago

Hi Leif,

I missed your comment. I think it's related to genomepy which checks for the assemblies: https://github.com/vanheeringen-lab/seq2science/issues/1027.

If you downgrade mysql it should work again:

conda activate seq2science
mamba install mysql-connector-python=8.4.0
seq2science run ...
Leif78 commented 2 months ago

thanks for answer. The rna-seq pipeline start now, but it halt at job 20, it has been working now for four days without any progress. However, the system monitor report CPU activity and use of 27 GB RAM. I think there is a problem with activating the conda environment.

[Thu Sep 19 03:48:02 2024] rule star_index: input: /home/leif/Dokumenter/my_project/genomes/danRer11/danRer11.fa, /home/leif/Dokumenter/my_project/genomes/danRer11/danRer11.fa.sizes, /home/leif/Dokumenter/my_project/genomes/danRer11/danRer11.annotation.gtf output: /home/leif/Dokumenter/my_project/genomes/danRer11/index/star log: /home/leif/Dokumenter/my_project/results/log/star_index/danRer11.log jobid: 6 benchmark: /home/leif/Dokumenter/my_project/results/benchmark/star_index/danRer11.benchmark.txt wildcards: assembly=danRer11 priority: 10 threads: 2 resources: tmpdir=/tmp, mem_gb=31

Activating conda environment: ../../miniconda3/envs/seq2science/lib/python3.10/site-packages/seq2science/.snakemake/d4ddee16ca386a100fdc27dab1fe8127_

Best regards, Leif

Maarten-vd-Sande commented 2 months ago

Can you post the content of:

/home/leif/Dokumenter/my_project/results/log/star_index/danRer11.log
Maarten-vd-Sande commented 2 months ago

btw, star is quite memory instensive. It might just be that your computer does not have enough memory to run star. You can try changing star to hisat2 as aligner in your config.yaml