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combogenomics / medusa

A draft genome scaffolder that uses multiple reference genomes in a graph-based approach.
http://combo.dbe.unifi.it/medusa/
GNU General Public License v3.0
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Medusa error #34

Closed kayobianco closed 2 years ago

kayobianco commented 2 years ago

hello everyone,

I installed medusa in an environment in conda, but I'm having difficulty using it. Can anyone help? best.

(medusa) kayobianco@ARQUEAS-XPS:~$ medusa -f /media/kayobianco/UBUNTU-HD/Illumina/Genomas/Neisseria_debora/N_meningitidis_CP021520 -i /media/kayobianco/UBUNTU-HD/Illumina/Genomas/Neisseria_debora/2779/unicycler_output/2779_assembly.fasta -o 2779_medusa_assembled -v INPUT FILE:/media/kayobianco/UBUNTU-HD/Illumina/Genomas/Neisseria_debora/2779/unicycler_output/2779_assembly.fasta

Running MUMmer.../home/kayobianco/miniconda3/envs/medusa/share/medusa-1.6-2/script//mummerRunner.sh: linha 11: nucmer: command not found /home/kayobianco/miniconda3/envs/medusa/share/medusa-1.6-2/script//mummerRunner.sh: linha 12: show-coords: command not found done.

Building the network...Traceback (most recent call last): File "/home/kayobianco/miniconda3/envs/medusa/share/medusa-1.6-2/script//netcon_mummer.py", line 6, in from cPickle import dump ModuleNotFoundError: No module named 'cPickle' Exception in thread "main" java.lang.RuntimeException: Error: Network construction failed. at Scaffolder.scaffolder(Unknown Source) at Scaffolder.runOnTerminal(Unknown Source) at Scaffolder.(Unknown Source) at Scaffolder.main(Unknown Source)

mgalardini commented 2 years ago

Hi, is mummer installed in the conda environment you are using? You can check by typing nucmer -h in your terminal. If you get an error then run this after activating the environment: conda install -c bioconda mummer4.