azurillandfriend
commented
1 month ago appending to comment. The file "/home/dyern/lstm_scratch/rna-seq-pop/.snakemake/conda/b9a84f51ae3c40ad84a2205742a549eb/lib/R/library/rhdf5/libs/rhdf5.so" does exist and has size 3959800
The test dataset was run as per the instructions in the tutorial by running the command:
snakemake --cores 4 --directory .test/ --use-conda --configfile .test/config/config_paired_end.yaml
The DAG indicated a total of 21 jobs to be run.
The first error was "Error in rule DifferentialIsoformExpression". This appears to be because sleuth package is not loading in R The full error file (logs/DifferentialIsoformExpression.log) is pasted below:
── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ── ✔ ggplot2 3.3.6 ✔ purrr 0.3.4 ✔ tibble 3.1.8 ✔ dplyr 1.0.10 ✔ tidyr 1.2.1 ✔ stringr 1.4.1 ✔ readr 2.1.2 ✔ forcats 0.5.2 ── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Error: package or namespace load failed for ‘sleuth’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/dyern/lstm_scratch/rna-seq-pop/.snakemake/conda/b9a84f51ae3c40ad84a2205742a549eb/lib/R/library/rhdf5/libs/rhdf5.so': libcrypto.so.1.1: cannot open shared object file: No such file or directory Execution halted (py90) dyern@neptune2:~/lstm_scratch/rna-seq-pop$ less logs/DifferentialIsoformExpression.log ── Attaching packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse 1.3.1 ── ✔ ggplot2 3.3.6 ✔ purrr 0.3.4 ✔ tibble 3.1.8 ✔ dplyr 1.0.10 ✔ tidyr 1.2.1 ✔ stringr 1.4.1 ✔ readr 2.1.2 ✔ forcats 0.5.2 ── Conflicts ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() Error: package or namespace load failed for ‘sleuth’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/dyern/lstm_scratch/rna-seq-pop/.snakemake/conda/b9a84f51ae3c40ad84a2205742a549eb/lib/R/library/rhdf5/libs/rhdf5.so': libcrypto.so.1.1: cannot open shared object file: No such file or directory Execution halted