IndexError: list index out of range

[sim3023]

Could someone please help with the error? snakemake --snakefile /home/snp/odp/scripts/odp -c1 Building DAG of jobs... InputFunctionException in rule hmm_1_against_prots in file /home/snp/odp/scripts/odp, line 2133: Error: IndexError: list index out of range Wildcards: coloredby=BCnS_LGs sample=mab Traceback: File "/home/snp/odp/scripts/odp", line 2161, in

snakemake --version is 7.32.4

config_file ignore_autobreaks: True # Skip steps to find breaks in synteny blocks diamond_or_blastp: "blastp" # "diamond" or "blastp" duplicate_proteins: "pass" # currently only "fail" or "pass". plot_LGs: True # Plot the ALGs based on the installed databases plot_sp_sp: True # Plot the synteny between two species, if False just generates .rbh files

species: mabref: proteins: /home/snp/odp/scripts/ref.faa chrom: /home/snp/odp/scripts/ref.chrom genome: /home/snp/odp/scripts/ref.fna minscafsize: 10 # Only plots scaffolds that are 10 bp or longer mab: proteins: /home/snp/odp/scripts/1046.faa chrom: /home/snp/odp/scripts/1046.chrom genome: /home/snp/odp/scripts/1046.fna minscafsize: 10 # Only plots scaffolds that are 10 bp or larger

Also, I am providing bacterial genomes as input. Can that be the reason for this error?

[conchoecia]

Hi @sim3023 - at the moment this software is designed with genomes with multiple chromosomes in mind, and I have done no testing on prokaryotic genome assemblies. I'm not sure why this is breaking, as the error message is encountering something for which I haven't set up an error:

InputFunctionException in rule hmm_1_against_prots in file /home/snp/odp/scripts/odp, line 2133:
Error:
IndexError: list index out of range

If you send me an email with a way to download your dataset, plus the config file, I could do some tests to try to provide the user with an error message about why it is breaking.

[MANaranjo]

Greetings,

Was this issue ever solved? I'm having the exact same error (with Metazoan genomes).