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

[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

[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.)

[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

[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

[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?

[Author]

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