Error in Nanopolish Snakemake

Hi,

While trying to run the Nanopolish snakemake with the example data I get the following error:

RuleException:
WorkflowError in line 25 of /METEORE/Nanopolish:
HTTPError: HTTP Error 404: Not Found
File "/METEORE/Nanopolish", line 25, in __rule_minimap2
File "/services/tools/anaconda3/4.4.0/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

The problem is with the wrapper: "0.66.0/bio/minimap2/aligner"

I am using the 0.14.0. version of Nanopolish.

How could I solve this?

Thank you in advance

[zakayuen]

Hi,

Have you added minimap2 to your conda environment? Check if it is installed:

conda list | grep minimap2

If minimap2 is not installed yet, please add this to the environment:

mamba install -c bioconda minimap2

Then rerun the snakemake:

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

You should be able to generate the output with the example data.

p.s. I have updated the wrapper code in the snakemake file Nanopolish

Zaka

[zakayuen]

v0.66 is changes to v1.5.0/bio/minimap2/aligner

Does it work for you now?

[Bessyyi]

v0.66 is changes to v1.5.0/bio/minimap2/aligner

Does it work for you now?
Hi,
I try to use v1.5.0/bio/minimap2/aligner but while trying to run the Nanopolish snakemake with the example data I get the following error:
RuleException:
WorkflowError in line 25 of /home/ywj/METEORE-master/Nanopolish:
Unable to locate wrapper script for wrapper v1.5.0/bio/minimap2/aligner. This can be a network issue or a mistake in the wrapper URL.
File "/home/ywj/METEORE-master/Nanopolish", line 25, in __rule_minimap2
File "/home/ywj/yzy/miniconda3/envs/meteore_nanopolish_env/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Shutting down, this might take some time.

[zakayuen]

Hi @Bessyyi

What are the current versions of minimap2 and samtools in the environment?
Check the versions:

conda list minimap2
conda list samtools

The Nanopolish pipeline was tested with minimap2 v2.24 and samtools v1.15

Cheers,
Zaka

The problem is that it is impossible to find the folder in which the aligner is found. Could you share the total path so we can try to find it?

[zakayuen]

Snakemake will automatically download the wrapper from the Snakemake Wrapper Repository. The wrapper directive can point to full URLs, including URLs to local files with absolute paths file:// or relative paths file: for development purposes. See more info here: https://snakemake.readthedocs.io/en/v7.7.0/snakefiles/modularization.html

[jayradke]

similar issue...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 48
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job count min threads max threads

---

calculate_frequency 1 1 1
call_methylation 1 1 1
index 1 1 1
minimap2 1 6 6
samtools_index 1 1 1
samtools_sort 1 1 1
split_cpgs 1 1 1
total 7 1 6

Select jobs to execute...

[Sat Dec 3 16:21:41 2022]
rule minimap2:
input: data/ecoli_k12_mg1655.fasta, example.fastq
output: nanopolish_results/mapped/example.bam
log: nanopolish_results/mapped/example.log
jobid: 4
reason: Missing output files: nanopolish_results/mapped/example.bam
wildcards: sample=example
threads: 6
resources: tmpdir=/tmp

[Sat Dec 3 16:21:41 2022]
rule index:
input: data/example, example.fastq
output: example.fastq.index, example.fastq.index.fai, example.fastq.index.gzi, example.fastq.index.readdb
jobid: 6
reason: Missing output files: example.fastq.index, example.fastq.index.fai, example.fastq.index.gzi, example.fastq.index.readdb
wildcards: sample=example
resources: tmpdir=/tmp

/usr/bin/bash: line 1: nanopolish: command not found
[Sat Dec 3 16:21:41 2022]
Error in rule index:
jobid: 6
input: data/example, example.fastq
output: example.fastq.index, example.fastq.index.fai, example.fastq.index.gzi, example.fastq.index.readdb
shell:
nanopolish index -d data/example example.fastq
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Traceback (most recent call last):
File "/home/jayradke/METEORE/.snakemake/scripts/tmp16fgccly.wrapper.py", line 53, in
shell(
File "/home/jayradke/miniconda3/envs/meteore_nanopolish_env/lib/python3.9/site-packages/snakemake/shell.py", line 296, in new
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail; (minimap2 -t 6 -a -x map-ont -a data/ecoli_k12_mg1655.fasta example.fastq | samtools view -h --output-fmt BAM - > nanopolish_results/mapped/example.bam) 2> nanopolish_results/mapped/example.log' returned non-zero exit status 127.
[Sat Dec 3 16:21:43 2022]
Error in rule minimap2:
jobid: 4
input: data/ecoli_k12_mg1655.fasta, example.fastq
output: nanopolish_results/mapped/example.bam
log: nanopolish_results/mapped/example.log (check log file(s) for error message)
conda-env: /home/jayradke/METEORE/.snakemake/conda/7ce527443c989fafe22c477840513c71_

RuleException:
CalledProcessError in line 25 of /home/jayradke/METEORE/Nanopolish:
Command 'set -euo pipefail; /home/jayradke/miniconda3/envs/meteore_nanopolish_env/bin/python3.9 /home/jayradke/METEORE/.snakemake/scripts/tmp16fgccly.wrapper.py' returned non-zero exit status 1.
File "/home/jayradke/METEORE/Nanopolish", line 25, in __rule_minimap2
File "/home/jayradke/miniconda3/envs/meteore_nanopolish_env/lib/python3.9/concurrent/futures/thread.py", line 58, in run
Removing output files of failed job minimap2 since they might be corrupted:
nanopolish_results/mapped/example.bam
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2022-12-03T162141.697612.snakemake.log