Error in Nanopolish Snakemake

[ghost]

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

[ghost]

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