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conchoecia / odp

oxford dot plots
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IndexError: list index out of range #39

Closed amesclir closed 9 months ago

amesclir commented 1 year ago

I have found the next error when using odp. It seems to be something related with Wildcards and the number of colors.

snakemake --snakefile ./scripts/odp -c4 Building DAG of jobs... InputFunctionException in rule hmm_against_prots in file /home/amesclir/local/bin/odp/scripts/odp, line 1824: Error: IndexError: list index out of range Wildcards: coloredby=BCnS_LGs sample=Crichardtii Traceback: File "/home/amesclir/local/bin/odp/scripts/odp", line 1828, in

conchoecia commented 1 year ago

Looks like you're trying to run the script in the install directory. Can you try again by running the program in a different directory? Can you also please post your config file?

amesclir commented 1 year ago

I have try to run it in a another folder, and I had the same error. This is the config file

this file is called config.yaml

ignore_autobreaks: True # Skip steps to find breaks in synteny blocks diamond_or_blastp: "diamond" # "diamond" or "blastp" 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: Arabidopsisthaliana: proteins: /home/amesclir/local/bin/odp_run/genomes/Arabidopsisthaliana.fna chrom: /home/amesclir/local/bin/odp_run/genomes/Arabidopsisthaliana.chrom genome: /home/amesclir/local/bin/odp_run/genomes/Arabidopsisthaliana.faa Ceratopterisrichardtii: proteins: /home/amesclir/local/bin/odp_run/genomes/Ceratopterisrichardtii.fna chrom: /home/amesclir/local/bin/odp_run/genomes/Ceratopterisrichardtii.chrom genome: /home/amesclir/local/bin/odp_run/genomes/Ceratopterisrichardtii.faa

changsarahl commented 1 year ago

Hi, was this issue resolved? I have a similar issue with list index out or range

InputFunctionException in rule hmm_against_prots in file /home/krablab/odp/scripts/odp, line 1935: Error: IndexError: list index out of range Wildcards: coloredby=BCnS_LGs sample=Asap Traceback: File "/home/krablab/odp/scripts/odp", line 1939, in

conchoecia commented 9 months ago

Should be fixed with recent commits, including https://github.com/conchoecia/odp/commit/ba6c45375c2bf5e75a9ff0779e5d75b5509209db

Please run git pull to update the software directory, then try again. Closing for now.