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$
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$