Issues with python version

[Fplanas92]

In the instructions it is recommended Python version 3.7 or higher, but some of the dependencies are no longer supported for 3.7, such as numpy 1.22. The minimum is now Python 3.8.

With python 3.8 I get the error:

`
distributed.protocol.pickle - INFO - Failed to serialize {'trajectory': <PDBReader /data/users/fepd/trajectory-pymol.pdb with 101 frames of 4756 atoms>, 'config': {'run': True, 'method': 'jackknife', 'nsamplings': 10, 'dirnames': {'trj': 'trjfull', 'subtrj': 'resampling{nsampling}'}}}. Exception: cannot pickle '_io.BufferedReader' object
Traceback (most recent call last):
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/distributed/protocol/pickle.py", line 49, in dumps
result = pickle.dumps(x, **dump_kwargs)
TypeError: cannot pickle '_io.BufferedReader' object

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/data/users/fepd/miniconda3/envs/pyinknife-env/bin/pyinknife_run", line 33, in
sys.exit(load_entry_point('PyInKnife==2.0.0', 'console_scripts', 'pyinknife_run')())
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/PyInKnife-2.0.0-py3.8.egg/PyInKnife/pyinknife_run.py", line 202, in main
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/distributed/client.py", line 1576, in submit
futures = self._graph_to_futures(
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/distributed/client.py", line 2598, in _graph_to_futures
dsk = dsk.dask_distributed_pack(self, keyset, annotations)
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/dask/highlevelgraph.py", line 1076, in dask_distributed_pack
"state": layer.dask_distributed_pack(
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/dask/highlevelgraph.py", line 434, in dask_distributed_pack
dsk = toolz.valmap(dumps_task, dsk)
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/toolz/dicttoolz.py", line 83, in valmap
rv.update(zip(d.keys(), map(func, d.values())))
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/distributed/worker.py", line 4131, in dumps_task
d["kwargs"] = warn_dumps(task[3])
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/distributed/worker.py", line 4143, in warn_dumps
b = dumps(obj, protocol=4)
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/distributed/protocol/pickle.py", line 60, in dumps
result = cloudpickle.dumps(x, **dump_kwargs)
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/cloudpickle/cloudpickle_fast.py", line 73, in dumps
cp.dump(obj)
File "/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/cloudpickle/cloudpickle_fast.py", line 563, in dump
return Pickler.dump(self, obj)
TypeError: cannot pickle '_io.BufferedReader' object
distributed.nanny - INFO - Closing Nanny at 'tcp://127.0.0.1:42836'
/data/users/fepd/miniconda3/envs/pyinknife-env/lib/python3.8/site-packages/MDAnalysis/coordinates/chemfiles.py:59: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
MIN_CHEMFILES_VERSION = LooseVersion("0.9")
distributed.worker - INFO - Stopping worker at tcp://127.0.0.1:44685
distributed.scheduler - INFO - Remove worker <WorkerState 'tcp://127.0.0.1:44685', name: 0, status: closing, memory: 1, processing: 0>
distributed.core - INFO - Removing comms to tcp://127.0.0.1:44685
distributed.scheduler - INFO - Lost all workers
distributed.scheduler - INFO - Scheduler closing...
distributed.scheduler - INFO - Scheduler closing all comms
`

Could you have a look to see if it's something to be solved?

Thanks

[ValeSora]

Hi! Thank you for your report.

We just updated the codebase of PyInKnife2 to add some functionalities.

We tried the new code with Python 3.7 and 3.8 (using the latest numpy version for Python 3.8) and did not encounter the error you reported. Judging from the traceback, I think it may be related to your input trajectory causing some troubles to Dask, but it is worth checking whether it is related to the packages' versions.

Could I ask you to try the new code and report back to us if this error persists, providing the full command line you use to run PyInKnife2?

Bests,
Valentina

[Fplanas92]

Hi,

I removed the package I installed just yesterday that came with numpy 1.22 and I reinstalled today with numpy 1.21.6. The installation worked only after removing pkg_resources==0.0.0.
Now when I run the code, it seems to work but it still returns some errors:

distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling2/cmpsn/null/6.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling2/cmpsn/null/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling2/hb/sc-sc/3.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling2/hb/sc-sc/3.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling2/sb/different_charge/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling2/sb/different_charge/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling2/cmpsn/rg/5.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling2/cmpsn/rg/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling2/cmpsn/rg/6.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling2/cmpsn/rg/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/cmpsn/null/6.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 6.0 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/cmpsn/null/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 4.5 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling2/cmpsn/rg/6.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling2/cmpsn/rg/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/hb/sc-sc/3.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --hb-co 3.5 --hydrogen-bonds --hb-class sc-sc --ff-masses charmm27 --verbose --hb-csv hb.csv --hb-graph hb-graph.dat
/data/users/fepd/miniconda3/envs/pyinteraph-env/lib/python3.7/site-packages/MDAnalysis/coordinates/base.py:892: UserWarning: Reader has no dt information, set to 1.0 ps
  warnings.warn("Reader has no dt information, set to 1.0 ps")
distributed.worker - INFO - Trajectory '/data/users/fepd/resampling4/resampling4.xtc' written. Frames: 50-100.
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/cmpsn/null/5.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.5 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/sb/different_charge/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 5.0 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/cmpsn/rg/6.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 6.0 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/cmpsn/null/6.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/cmpsn/null/6.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/hb/sc-sc/3.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/hb/sc-sc/3.5/hb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/cmpsn/null/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/cmpsn/null/4.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/sb/different_charge/4.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 4.0 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/sb/different_charge/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/sb/different_charge/5.0/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/cmpsn/null/5.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/cmpsn/null/5.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/cmpsn/rg/6.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/cmpsn/rg/6.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/hb/sc-sc/3.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/hb/sc-sc/3.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/null/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/null/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/null/6.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/null/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/cmpsn/rg/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 4.5 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/rg/6.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/rg/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/sb/different_charge/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/sb/different_charge/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/null/5.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/null/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/hb/sc-sc/3.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/hb/sc-sc/3.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/rg/6.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/rg/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/sb/different_charge/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/sb/different_charge/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/null/5.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/null/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/cmpsn/rg/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/cmpsn/rg/4.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/null/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/null/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/null/6.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/null/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/sb/different_charge/4.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/sb/different_charge/4.0/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/sb/different_charge/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 4.5 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/cmpsn/rg/5.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.5 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/rg/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/rg/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/cmpsn/null/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.0 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/cmpsn/null/6.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 6.0 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/sb/different_charge/4.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/sb/different_charge/4.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling3/cmpsn/rg/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling3/resampling3.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.0 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/sb/different_charge/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/sb/different_charge/4.5/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/cmpsn/null/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 4.5 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/sb/different_charge/4.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/sb/different_charge/4.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/cmpsn/rg/5.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/cmpsn/rg/5.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/rg/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/rg/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/cmpsn/null/6.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/cmpsn/null/6.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/cmpsn/null/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/cmpsn/null/5.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling3/cmpsn/rg/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling3/cmpsn/rg/5.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/sb/different_charge/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/sb/different_charge/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/cmpsn/null/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/cmpsn/null/4.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/cmpsn/null/5.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.5 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/rg/5.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/rg/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/sb/different_charge/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/sb/different_charge/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/null/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/null/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/rg/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/rg/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/null/6.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/null/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/null/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/null/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/cmpsn/rg/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.0 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/rg/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/rg/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/null/6.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/null/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/null/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/null/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/cmpsn/null/5.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/cmpsn/null/5.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling3/cmpsn/rg/5.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling3/cmpsn/rg/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/null/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/null/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/cmpsn/rg/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/cmpsn/rg/5.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/cmpsn/rg/5.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.5 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/null/5.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/null/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/cmpsn/null/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.0 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/sb/different_charge/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 4.5 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/sb/different_charge/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 5.0 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/null/5.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/null/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/cmpsn/rg/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 4.5 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/rg/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/rg/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/cmpsn/rg/5.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/cmpsn/rg/5.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/cmpsn/rg/6.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 6.0 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/cmpsn/null/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/cmpsn/null/5.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/rg/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/rg/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/sb/different_charge/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/sb/different_charge/5.0/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/sb/different_charge/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/sb/different_charge/4.5/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/cmpsn/rg/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/cmpsn/rg/4.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/rg/5.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/rg/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/cmpsn/rg/6.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/cmpsn/rg/6.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/hb/sc-sc/3.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --hb-co 3.5 --hydrogen-bonds --hb-class sc-sc --ff-masses charmm27 --verbose --hb-csv hb.csv --hb-graph hb-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/null/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/null/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/rg/5.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/rg/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/sb/different_charge/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/sb/different_charge/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/null/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/null/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/sb/different_charge/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/sb/different_charge/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/rg/6.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/rg/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling4/sb/different_charge/4.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling4/resampling4.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 4.0 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/rg/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/rg/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/sb/different_charge/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/sb/different_charge/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/rg/6.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/rg/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/hb/sc-sc/3.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/hb/sc-sc/3.5/hb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
/data/users/fepd/miniconda3/envs/pyinteraph-env/lib/python3.7/site-packages/MDAnalysis/coordinates/base.py:892: UserWarning: Reader has no dt information, set to 1.0 ps
  warnings.warn("Reader has no dt information, set to 1.0 ps")
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/cmpsn/rg/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/cmpsn/rg/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/sb/different_charge/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/sb/different_charge/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling4/sb/different_charge/4.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling4/sb/different_charge/4.0/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/hb/sc-sc/3.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/hb/sc-sc/3.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - INFO - Trajectory '/data/users/fepd/resampling5/resampling5.xtc' written. Frames: 60-100.
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/hb/sc-sc/3.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/hb/sc-sc/3.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/sb/different_charge/4.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/sb/different_charge/4.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling4/sb/different_charge/4.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling4/sb/different_charge/4.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/cmpsn/null/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.0 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/cmpsn/null/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 4.5 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/sb/different_charge/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 5.0 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/cmpsn/rg/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.0 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/sb/different_charge/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 4.5 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/cmpsn/null/6.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 6.0 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/cmpsn/rg/5.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.5 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/cmpsn/null/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/cmpsn/null/5.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/cmpsn/null/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/cmpsn/null/4.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/sb/different_charge/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/sb/different_charge/5.0/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/cmpsn/rg/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 4.5 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/sb/different_charge/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/sb/different_charge/4.5/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/cmpsn/null/6.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/cmpsn/null/6.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/cmpsn/rg/5.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/cmpsn/rg/5.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/cmpsn/rg/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/cmpsn/rg/5.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/null/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/null/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/null/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/null/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/sb/different_charge/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/sb/different_charge/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/cmpsn/rg/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/cmpsn/rg/4.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/null/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/null/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/null/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/null/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/rg/5.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/rg/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/rg/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/rg/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/sb/different_charge/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/sb/different_charge/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/null/6.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/null/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/rg/5.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/rg/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/rg/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/rg/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/sb/different_charge/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/sb/different_charge/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/null/6.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/null/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/sb/different_charge/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/sb/different_charge/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/rg/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/rg/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/hb/sc-sc/3.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --hb-co 3.5 --hydrogen-bonds --hb-class sc-sc --ff-masses charmm27 --verbose --hb-csv hb.csv --hb-graph hb-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/rg/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/rg/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/cmpsn/null/5.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.5 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/cmpsn/rg/6.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 6.0 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/hb/sc-sc/3.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/hb/sc-sc/3.5/hb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
/data/users/fepd/miniconda3/envs/pyinteraph-env/lib/python3.7/site-packages/MDAnalysis/coordinates/base.py:892: UserWarning: Reader has no dt information, set to 1.0 ps
  warnings.warn("Reader has no dt information, set to 1.0 ps")
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/cmpsn/null/5.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/cmpsn/null/5.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/cmpsn/rg/6.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/cmpsn/rg/6.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling5/sb/different_charge/4.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling5/resampling5.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 4.0 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/null/5.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/null/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - INFO - Trajectory '/data/users/fepd/resampling6/resampling6.xtc' written. Frames: 70-100.
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/rg/6.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/rg/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling5/sb/different_charge/4.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling5/sb/different_charge/4.0/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/null/5.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/null/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/hb/sc-sc/3.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/hb/sc-sc/3.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/cmpsn/rg/6.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/cmpsn/rg/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/hb/sc-sc/3.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/hb/sc-sc/3.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/sb/different_charge/4.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/sb/different_charge/4.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/cmpsn/null/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 4.5 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/cmpsn/rg/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.0 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/hb/sc-sc/3.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --hb-co 3.5 --hydrogen-bonds --hb-class sc-sc --ff-masses charmm27 --verbose --hb-csv hb.csv --hb-graph hb-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling5/sb/different_charge/4.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling5/sb/different_charge/4.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/cmpsn/rg/6.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 6.0 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/sb/different_charge/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 5.0 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/cmpsn/rg/5.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.5 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/cmpsn/null/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.0 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/cmpsn/rg/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/cmpsn/rg/5.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/cmpsn/null/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/cmpsn/null/4.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/hb/sc-sc/3.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/hb/sc-sc/3.5/hb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/cmpsn/rg/6.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/cmpsn/rg/6.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/sb/different_charge/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/sb/different_charge/5.0/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/cmpsn/rg/5.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/cmpsn/rg/5.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/cmpsn/rg/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 4.5 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/rg/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/rg/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/null/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/null/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/hb/sc-sc/3.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/hb/sc-sc/3.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/cmpsn/null/5.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/cmpsn/null/5.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/rg/6.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/rg/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/null/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/null/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/rg/5.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/rg/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/cmpsn/rg/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/cmpsn/rg/4.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/rg/6.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/rg/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/rg/5.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/rg/5.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/sb/different_charge/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/sb/different_charge/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/null/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/null/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/rg/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/rg/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/hb/sc-sc/3.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/hb/sc-sc/3.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/sb/different_charge/5.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/sb/different_charge/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/rg/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/rg/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/cmpsn/null/6.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 6.0 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/rg/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/rg/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/sb/different_charge/4.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 4.0 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/sb/different_charge/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --sb-co 4.5 --salt-bridges --sb-mode different_charge --ff-masses charmm27 --verbose --sb-csv sb.csv --sb-graph sb-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/null/5.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/null/5.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/cmpsn/null/6.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/cmpsn/null/6.0/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/sb/different_charge/4.0/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/sb/different_charge/4.0/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/sb/different_charge/4.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/sb/different_charge/4.5/sb-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
/data/users/fepd/miniconda3/envs/pyinteraph-env/lib/python3.7/site-packages/MDAnalysis/coordinates/base.py:892: UserWarning: Reader has no dt information, set to 1.0 ps
  warnings.warn("Reader has no dt information, set to 1.0 ps")
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/sb/different_charge/4.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/sb/different_charge/4.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/sb/different_charge/4.5/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/sb/different_charge/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - INFO - Trajectory '/data/users/fepd/resampling7/resampling7.xtc' written. Frames: 80-100.
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling6/cmpsn/null/5.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling6/resampling6.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.5 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/sb/different_charge/4.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/sb/different_charge/4.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/sb/different_charge/4.5/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/sb/different_charge/4.5/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/null/6.0/20.0/hubs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/null/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --hubs --hubs-cutoff 3 --hubs-pdb hubs.pdb
distributed.worker - ERROR - filter_graph run in /data/users/fepd/resampling6/cmpsn/null/5.5/20.0 exited with code 1. Command line: filter_graph --input-dat /data/users/fepd/resampling6/cmpsn/null/5.5/cmpsn-graph_all.dat --filter-threshold 20.0 --output-dat filtered_graph.dat
distributed.worker - ERROR - graph_analysis run in /data/users/fepd/resampling6/cmpsn/null/6.0/20.0/ccs exited with code 1. Command line: graph_analysis --adj-matrix /data/users/fepd/resampling6/cmpsn/null/6.0/20.0/filtered_graph.dat --reference /data/users/fepd/reference.pdb --components --components-pdb cc.pdb
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling7/cmpsn/rg/4.5 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling7/resampling7.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 4.5 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling7/cmpsn/rg/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling7/resampling7.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.0 --cmpsn --cmpsn-correction rg --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat
distributed.worker - ERROR - pyinteraph run in /data/users/fepd/resampling7/cmpsn/null/5.0 exited with code 1. Command line: pyinteraph --trj /data/users/fepd/resampling7/resampling7.xtc --top /data/users/fepd/reference.pdb --ref /data/users/fepd/reference.pdb --cmpsn-co 5.0 --cmpsn --cmpsn-correction null --ff-masses charmm27 --verbose --cmpsn-residues ALA,ARG,ASN,ASP,CYS,GLN,GLU,HIS,ILE,LEU,LYS,MET,PHE,PRO,SER, THR,TRP,TYR,VAL --cmpsn-csv cmpsn.csv --cmpsn-graph cmpsn-graph.dat

I am not sure if this is just a communication issue between the workers, or if it relates to an error to pyinknife.

Best,
Ferran

[ManuPer3z]

Hi @Fplanas92

The error you're encountering is related to the serialization of objects. Specifically, Python is having trouble pickling (serializing) the _io.BufferedReader object. Serialization is the process of converting an object's state to a byte stream, and this is commonly done using Python's pickle module.

When dealing with distributed computing (which seems to be the case given the presence of distributed in your stack trace), data has to be sent between different processes or even different machines. To do that, data is serialized on one end and deserialized on the other.

There are a few general strategies you might consider:

Avoid Serializing Unsupported Objects: Some objects just aren't meant to be serialized. If possible, see if there's a way to avoid sending the problematic object (in this case, the _io.BufferedReader object) between processes.

Convert to a Serializable Format: Sometimes you can convert an object into another format that's easier to serialize. For example, if you have a file reader object, you might read the data into a string or bytes object and send that instead.

Custom Serialization: For objects that can't be easily serialized using Python's built-in tools, you can sometimes implement custom serialization and deserialization functions.

Let's relate these general strategies to your specific error:

The error arises when trying to serialize an object that contains a PDBReader with a trajectory from a .pdb file. The PDBReader appears to have an open file handle (_io.BufferedReader) associated with it, which cannot be serialized.
Here are steps you can take to potentially resolve the issue:

Ensure Everything is Updated: Before making any code changes, ensure that all libraries and packages are updated. Sometimes these kinds of issues are recognized and fixed in newer versions of the libraries.

Preprocess the Data: Instead of serializing the PDBReader object directly, you might read the necessary data from the .pdb file into memory first (as arrays, lists, etc.), and then serialize and send that processed data. This way, you avoid trying to serialize the open file handle.

Custom Serialization: If the PDBReader object must be sent as-is, you could potentially implement custom serialization methods for it. However, this can be complex and might not be the best route unless truly necessary.

Check Library Support & Documentation: Given that this is a specific issue related to the PyInKnife library and MDAnalysis, it's possible that there are known workarounds or solutions in the community or documentation. It's worth checking if this is a recognized issue, and if there are recommended solutions.

Best Regards,