Error in rule snippy_core:

[luis-laurindo]

Hi, Idolawoye. Please help. I am having a hard time running BAGEP.

Log

(bagep) laurindo@LAPTOP-M857EF9P:~/BAGEP$ snakemake --cores 6 --config ref=vc_reference.fasta
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 6
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads

---

abricate 1 1 1
all 1 1 1
move_files 1 1 1
snippy_core 1 1 1
tree 1 1 1
vcf_viewer 1 1 1
total 6 1 1

Select jobs to execute...

[Thu Jan 4 18:00:07 2024]
Job 2: Aligning core and whole genomes into a multi fasta file

This is snippy-core 4.6.0
Obtained from http://github.com/tseemann/snippy
Enabling bundled tools for linux
Found any2fasta - /home/laurindo/miniconda3/envs/bagep/bin/any2fasta
Found samtools - /home/laurindo/miniconda3/envs/bagep/bin/samtools
Found minimap2 - /home/laurindo/miniconda3/envs/bagep/bin/minimap2
Found bedtools - /home/laurindo/miniconda3/envs/bagep/bin/bedtools
Found snp-sites - /home/laurindo/miniconda3/envs/bagep/bin/snp-sites
Saving reference FASTA: core.ref.fa
This is any2fasta 0.4.2
Opening 'vc_reference.fasta'
Detected FASTA format
Read 67228 lines from 'vc_reference.fasta'
Wrote 2 sequences from FASTA file.
Processed 1 files.
Done.
Loaded 2 sequences totalling 4033501 bp.
Will mask 0 regions totalling 0 bp ~ 0.00%
Opening: core.tab
Opening: core.vcf
Processing contig: AE003852
Processing contig: AE003853
Generating core.full.aln
Creating TSV file: core.txt
Running: snp-sites -c -o core.aln core.full.aln
Warning: No SNPs were detected so there is nothing to output.
ERROR: Could not run: snp-sites -c -o core.aln core.full.aln
[Thu Jan 4 18:00:09 2024]
Error in rule snippy_core:
jobid: 0
output: core.aln, core.vcf, core.full.aln

Traceback (most recent call last):
File "/home/laurindo/miniconda3/envs/bagep/lib/python3.6/site-packages/snakemake/executors/init.py", line 593, in _callback
raise ex
File "/home/laurindo/miniconda3/envs/bagep/lib/python3.6/concurrent/futures/thread.py", line 56, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/laurindo/miniconda3/envs/bagep/lib/python3.6/site-packages/snakemake/executors/init.py", line 579, in cached_or_run
run_func(*args)
File "/home/laurindo/miniconda3/envs/bagep/lib/python3.6/site-packages/snakemake/executors/init.py", line 2461, in run_wrapper
raise ex
File "/home/laurindo/miniconda3/envs/bagep/lib/python3.6/site-packages/snakemake/executors/init.py", line 2442, in run_wrapper
runtime_sourcecache_path,
File "/home/laurindo/BAGEP/Snakefile", line 171, in __rule_snippy_core
File "/home/laurindo/miniconda3/envs/bagep/lib/python3.6/site-packages/snakemake/shell.py", line 287, in new
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'set -euo pipefail; snippy-core --ref vc_reference.fasta --prefix core' returned non-zero exit status 2.
Exiting because a job execution failed. Look above for error message
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/laurindo/BAGEP/.snakemake/log/2024-01-04T180007.501282.snakemake.log
(bagep) laurindo@LAPTOP-M857EF9P:~/BAGEP$