“OSError: [Errno 2]” in “clustering.py”

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    • October 11, 2014 at 9:30 pm #2028
      Anonymous

        Dear friends,
        I am trying to use “clustering.py” but I was told “OSError: [Errno 2] No such file or directory”. Can I ask how to solve this?

        I am sorry but it seems I have been asking technical questions all the time. Please tell me if there is something I can read to prepare my knowledge to debug. For example, how can I actually debug this python problem based on the error message?

        Thank you very much.

        Yours sincerely
        Cheng

        The following is the command line and prompt.

        /mnt/hgfs/Cheng/Rosetta$ python ~/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools/scripts/clustering.py –pdb_list=/mnt/hgfs/Cheng/Rosetta/list_of_pdbs.txt –rosetta=~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/cluster.linuxgccrelease –database=~/Cheng/rosetta_2014.30.57114_bundle/main/database –options=/mnt/hgfs/Cheng/Rosetta/cluster.options cluster_summary.txt cluster_histogram.txt
        Parsing pdb file scores
        Running cluster
        Traceback (most recent call last):
        File “/home/dancebean/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools/scripts/clustering.py”, line 59, in
        cluster_output = subprocess.Popen(command,stdout=subprocess.PIPE).communicate()[0]
        File “/usr/lib/python2.7/subprocess.py”, line 710, in __init__
        errread, errwrite)
        File “/usr/lib/python2.7/subprocess.py”, line 1327, in _execute_child
        raise child_exception
        OSError: [Errno 2] No such file or directory

      • October 14, 2014 at 5:29 pm #10432
        Anonymous

          It looks like it’s having problems finding the clustering executable. Try changing what you pass to the –rosetta option to be an absolute path without a tilde (~) – there might be an issue regarding the home directory expansion. (Alternatively, using a space instead of an equals sign would likely fix the issue, as that gives the shell an opportunity to do the tilde substitution.)

        • October 15, 2014 at 10:39 am #10438
          Anonymous

            Hi R Moretti,
            Thank you. I will use absolute path as a thumb of rule to debug.

            After running

            python /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools/scripts/clustering.py –pdb_list /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/list_of_pdbs.txt –rosetta /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/cluster.linuxgccrelease –database /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database –options /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.3_clustering/cluster.options cluster_summary.txt cluster_histogram.txt

            for a list of 100 PDBs, I was told ERROR:

            Parsing pdb file scores
            Running cluster
            ERROR: Could not make
            ERROR:: Exit from: src/core/io/silent/SilentFileData.cc line: 386
            Parsing cluster output
            Clusters: 1
            Structures: 100

            But I can still get cluster_summary.txt and cluster_histogram.txt (attached).

            Is this due to too few PDBs for clustering? As I check on

            https://www.rosettacommons.org/docs/latest/cluster.html

            It seems that I need at least 400 structures:

            “Starting with a subset of structures (the first 400 structures)”

            Is there a minimum range of PDBs required for cluster?

            Thank you very much.

            Yours sincerely
            Cheng

          • October 17, 2014 at 12:10 pm #10455
            Anonymous

              Hi R Moretti,
              Yes, you are right. After changing “-out:file:silent” into “-out:file:silent /path/to/cluster.out”, I can run the “clustering.py” successfully. :)

              I was assuming the output would be with a default name if I did not specify its name.

              Thank you.

              Yours sincerely
              Cheng

            • October 16, 2014 at 4:21 pm #10449
              Anonymous

                That error you’re getting is because Rosetta can’t open up a file for output … which isn’t surprising, as it looks like it’s trying to open up a file with an empty filename. (The filename should be printed after the “make”.)

                Why it’s trying to open up a silent file with an empty name, I’m not sure. What’s the content of your cluster.options file?

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