Problems running the Nanopolish example: libcrypto.so.1.0.0:

[NiRuff]

Hi, @zakayuen,

I ran into a problem while samtools_sort after running the following line of your Nanopore example:

snakemake -s Nanopolish nanopolish_results/example_nanopolish-freq-perCG.tsv --cores all

Installation actually seems to have worked fine - I tried both, the .yml file and installation using mamba.

(meteore_nanopolish_env) nicolas@nicolas-Precision-7820-Tower:~/Programs/METEORE$ snakemake -s Nanopolish nanopolish_results/example_nanopolish-freq-perCG.tsv --cores all Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Conda environments: ignored Job counts: count jobs 1 calculate_frequency 1 call_methylation 1 index 1 minimap2 1 samtools_index 1 samtools_sort 1 split_cpgs 7

[Thu Sep 16 10:55:20 2021] rule minimap2: input: data/ecoli_k12_mg1655.fasta, example.fastq output: nanopolish_results/mapped/example.bam log: nanopolish_results/mapped/example.log jobid: 6 wildcards: sample=example threads: 6

[Thu Sep 16 10:55:20 2021] rule index: input: data/example, example.fastq output: example.fastq.index, example.fastq.index.fai, example.fastq.index.gzi, example.fastq.index.readdb jobid: 5 wildcards: sample=example

[readdb] indexing data/example [readdb] num reads: 50, num reads with path to fast5: 50 [Thu Sep 16 10:55:20 2021] Finished job 5. 1 of 7 steps (14%) done [Thu Sep 16 10:55:21 2021] Finished job 6. 2 of 7 steps (29%) done

[Thu Sep 16 10:55:21 2021] rule samtools_sort: input: nanopolish_results/mapped/example.bam output: nanopolish_results/mapped/example.sorted.bam jobid: 3 wildcards: sample=example

samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory [Thu Sep 16 10:55:21 2021] Error in rule samtools_sort: jobid: 3 output: nanopolish_results/mapped/example.sorted.bam shell: samtools sort -o nanopolish_results/mapped/example.sorted.bam nanopolish_results/mapped/example.bam (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /home/nicolas/Programs/METEORE/.snakemake/log/2021-09-16T105520.230639.snakemake.log

Best, Nicolas

[NiRuff]

Now trying mamba installation another time, I saw an error occurrin there:

Encountered problems while solving:

• nothing provides openmp needed by nanopolish-0.10.1-h78a5b34_0

However, when using the .yml installation, no error occurs but there I run into the above given problem.

Best, Nicolas

[zakayuen]

Hi Nicolas,

It seems like it is a conda issue.

Can you please try reinstall samtools in your Nanopilish environment?

conda install -c bioconda samtools=1.9 --force-reinstall

Then rerun the snakemake pipeline again.

Let me know if it solves the issue.

Zaka