Is there a way to change labels for the figures?

[rebeelouise]

I tried changing the names of my fasta files and now the scripts crashing.
It gets up to local trees and catchment trees, and the metadata is merged fine.
input csv and fasta names match but scripts fail at the point where it makes the figures - which I already have but with bad labels and it looks messy!

So is there a way to 1. have in the input.csv a column for figure labels as well as a name column to match the fasta? As this woked fine before I changed my fasta IDs and input csv - adding another column would be easy?

Or 2. What do these errors mean..?

Error in rule extract_taxa:
    jobid: 15
    output: /tmp/tmp3fhoywgs/local_trees_seqs/localsubtree_2_taxon_names.txt
    shell:
        clusterfunk get_taxa -i /home/hlrpenri/results/articPM/consensus/pangolin/llama/please_work/local_trees/localsubtree_2.tree --in-format newick -o /tmp/tmp3fhoywgs/local_trees_seqs/localsubtree_2_taxon_names.txt --out-format newick
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Error in rule extract_taxa:
    jobid: 16
    output: /tmp/tmp3fhoywgs/local_trees_seqs/localsubtree_3_taxon_names.txt
    shell:
        clusterfunk get_taxa -i /home/hlrpenri/results/articPM/consensus/pangolin/llama/please_work/local_trees/localsubtree_3.tree --in-format newick -o /tmp/tmp3fhoywgs/local_trees_seqs/localsubtree_3_taxon_names.txt --out-format newick
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Error in rule find_snps:
    jobid: 0
    output: /home/hlrpenri/results/articPM/consensus/pangolin/llama/please_work/figures/genome_graph.png, /home/hlrpenri/results/articPM/consensus/pangolin/llama/please_work/snp_reports/snp_reports.txt

RuleException:
CalledProcessError in line 266 of /home/hlrpenri/miniconda2/envs/llama/lib/python3.6/site-packages/llama-0.1-py3.6.egg/llama/scripts/assess_putative_lineage.smk:
Command 'set -euo pipefail;  snakemake --nolock --snakefile /home/hlrpenri/miniconda2/envs/llama/lib/python3.6/site-packages/llama-0.1-py3.6.egg/llama/scripts/find_snps.smk --forceall  --quiet --directory /tmp/tmp3fhoywgs --config catchment_str=localsubtree_2,localsubtree_3,localsubtree_5,localsubtree_1,localsubtree_4 outdir=/home/hlrpenri/results/articPM/consensus/pangolin/llama/please_work tempdir=/tmp/tmp3fhoywgs outgroup_fasta=/home/hlrpenri/miniconda2/envs/llama/lib/python3.6/site-packages/llama-0.1-py3.6.egg/llama/data/reference.fasta aligned_query_seqs=/tmp/tmp3fhoywgs/post_qc_query.aligned.fasta seqs=/home/hlrpenri/results/articPM/consensus/pangolin/llama/../data_directory/alignment.fasta threshold=1 --cores 100' returned non-zero exit status 1.
  File "/home/hlrpenri/miniconda2/envs/llama/lib/python3.6/site-packages/llama-0.1-py3.6.egg/llama/scripts/assess_putative_lineage.smk", line 266, in __rule_find_snps
  File "/home/hlrpenri/miniconda2/envs/llama/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Exiting because a job execution failed. Look above for error message
Exiting because a job execution failed. Look above for error message

and how do I fix it...

Thank you!