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Clustering error - Help, please

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Clustering error - Help, please

Hi, I'm trying to group structures into clusters, but I have an error and an empty log file. A few months ago (in February / March) I didn't have a problem with it, although I did it in the same way (I think so). I have no idea where this problem comes from.

Using the AbinitioRelax protocol, I obtained a silent file with 100,000 structures (centroid representations) for a certain amino acid sequence. Now I want to group the structures into clusters and sort by energy. I use the following commands:

. /home/bioinf/           (path to rosetta databases)

cluster @cluster_options > cluster.log

where the file cluster_options looks like:



    -silent ../silent_file.out


-radius 3

and here I only get the message  "Can't open @cluster_options" and an empty file cluster.log (this is probably not a problem with permissions to cluster_options file because everyone has full rights (-rwxrwxrwx)).

I also tried to write options with the command. I used the command:

cluster -in:file:silent ../silent_file.out -cluster:sort_groups_by_energy -cluster:radius 3 > cluster.log

and here I get:

option -i unrecognized - ignored

Usage: cluster <options> graphfile

    -C k - generate no more than k clusters (0)

       0 : no limit

    -c k - use clustering method k (0)

       0 : use modularity

       1 : use modularity quality

    -o <outfile> - output file (stdout)

    -v   - verbose mode

    -?   - print usage


Can you help me? Please. I have been tired of it for several weeks and I still can't see why I'm failing now, although a few months ago everything worked well. However, I don't know Rosetta very well, I just use what I learned in college and what I found on

I look forward to your reply.

Post Situation: 
Wed, 2020-06-17 11:19