Member Site › Forums › Rosetta 3 › Rosetta 3 – General › Clustering using an disrupted run silent file
- This topic has 9 replies, 4 voices, and was last updated 10 years ago by Anonymous.
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July 15, 2013 at 9:19 am #1657Anonymous
Hi all,
I was running rosetta but something happened and the job was stopped. I would like to use the already generated silent file to cluster but when I run the clustering algorithm I get a ‘could not make’ error which I suppose is due to the incomplete status. Had set to generate 10,000 but at the point of interruption there were 4767 structures. How do I edit the silent file for proper clustering of the 4767 decoys?
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July 15, 2013 at 11:22 am #9049Anonymous
Hi Paula,
Try after deleting the lines for the decoys for which the run was incomplete, if it actually appears in the silent file. If possible please provide the command you used and the error message you got. -
July 15, 2013 at 6:56 pm #9057Anonymous
The command line flag “-silent_read_through_errors” may also help to recover a corrupted silent file. (Just add it to any Rosetta run using the silent file as input.)
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July 17, 2013 at 9:57 am #9071Anonymous
Hi Paula,
Not sure whether this will work,but please run it after deleting ‘in:file:s’
flags:-database ../rosetta_database
-in:file:silent singh_silent.out
-in:file:fullatom
-cluster:radius -1
-cluster:sort_groups_by_energy
-out:file:silentRocco, could you please explain the difference between in:file:fullatom and in::file:fullatom ?
Thanks.
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September 24, 2014 at 1:09 pm #10315Anonymous
Hi,
I also try to work with the cluster tool in the same way like Paula. But the problem is, that Rosetta doesn`t find the structures and clusters. I have define the structures with the commando : -in:file:native .input/F_000*.pdb . What`s wrong?! -
July 17, 2013 at 8:31 am #9070Anonymous
Hi Moretti,
I added the flag ‘-silent_read_through_errors’ but I still get the same error.
ERROR: Could not make
ERROR:: Exit from: src/core/io/silent/SilentFileData.cc line: 287 -
July 17, 2013 at 8:34 am #9069Anonymous
Thanks for your reply.
Command: ../rosetta_source/bin/cluster.linuxgccrelease @flagsc > cluster.log
My flagsc:
-database ../rosetta_database
-in:file:silent singh_silent.out
-in::file:s
-in::file:fullatom
-cluster:radius -1
-cluster:sort_groups_by_energy
-out:file:silentERROR: Could not make
ERROR:: Exit from: src/core/io/silent/SilentFileData.cc line: 287I also looked at the silent file but I see that the last run had gone through my 71residues like in the 4766 run.
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July 17, 2013 at 6:09 pm #9076Anonymous
There’s none. The option parsing machinery should treat “::” and “:” identically. Which to use is a matter of preference. (The double colon matches the C++ namespace resolution of the options, but there was historically some issues (long since fixed) with Mac (?) computers where ‘:’ would work and ‘::’ wouldn’t.)
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July 17, 2013 at 6:13 pm #9077Anonymous
-out:file:silent takes a filename. The error you’re seeing is Rosetta complaining that it can’t create a file with the empty string as a name.
Use something like “-out:file:silent silentfile.out” instead. -
September 24, 2014 at 4:57 pm #10320Anonymous
What’s the full command you’re using, and what’s the error you’re getting? (Copy and paste tends to make debugging easier than paraphrasing.)
One possibility is that -in:file:native is expecting a single structure which is the native file to which RMS statistics are calculated – other than being used to calculate RMSD, the native file shouldn’t affect the clustering.
If you want to cluster PDBs, you need to use the “-s” option to specify them. So if you wanted to cluster the structure named like input/F_000*.pdb, then you’d use the option “-s input/F_000*.pdb” instead of Paula’s “-in:file:silent singh_silent.out” (which she used because she had a silent file instead of a PDB as input.)
Note that you need to give the names of the PDBs that you want to use – just a directory name won’t work. Also, remember it’s the shell that’s doing the wildcard (“*”) expansion, not Rosetta, so if you can’t do a “ls .input/F_000*.pdb” and get a list of filenames, then Rosetta won’t be able to find them.
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