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keiserlab / e3fp

3D molecular fingerprints
GNU Lesser General Public License v3.0
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E3FP fingerprint generate.py fails when it encounters a fingerprint that already exists #19

Closed 8li closed 7 years ago

8li commented 7 years ago

Fingerprint generation (using generate.py in serial mode) fails when it encounters a fingerprint that already exists:

Generating Fingerprints of conformers in /netapp/home/ali/projects/e3fp/confgen/hashed/e2 using /netapp/home/ali/projects/e3fp/e3fpgen/generate.py
2017-05-16 15:13:11,139|WARNING|Only 1 processes available. 'mpi' mode not available.
2017-05-16 15:13:11,139|INFO|Parallelizer initialized with mode 'serial' and 1 processors.
2017-05-16 15:13:11,139|INFO|Initializing E3FP generation.
2017-05-16 15:13:11,140|INFO|Getting SDF files
2017-05-16 15:13:11,238|INFO|SDF File Number: 3192
2017-05-16 15:13:11,239|INFO|Out Directory Basename: /netapp/home/ali/projects/e3fp/e3fpgen/e3fpgen_nompi/e2
2017-05-16 15:13:11,239|INFO|Out Extension: .fp.bz2
2017-05-16 15:13:11,239|INFO|Database File: fingerprints.fps.bz2
2017-05-16 15:13:11,239|INFO|Max First Conformers: -1
2017-05-16 15:13:11,239|INFO|Bits: 4096
2017-05-16 15:13:11,239|INFO|Level/Max Iterations: 5
2017-05-16 15:13:11,239|INFO|Shell Radius Multiplier: 1.718
2017-05-16 15:13:11,239|INFO|Stereo Mode: True
2017-05-16 15:13:11,239|INFO|Connected-only mode: on
2017-05-16 15:13:11,239|INFO|Parallel Mode: serial
2017-05-16 15:13:11,240|INFO|Starting
2017-05-16 15:13:11,620|WARNING|All fingerprint files for CHEMBL309766 already exist. Skipping.
2017-05-16 15:13:11,638|ERROR|Error running: ('/netapp/home/ali/projects/e3fp/confgen/hashed/e2/CHEMBL309766.sdf.bz2',)
Traceback (most recent call last):
  File "build/bdist.macosx-10.7-x86_64/egg/python_utilities/parallel.py", line 328, in serial_run
    yield (result, data)
GeneratorExit
8li commented 7 years ago

Fingerprint generation (using generate.py in mpi mode on a cluster) hangs when it encounters fingerprints that already exist:

Generating Fingerprints of conformers in /netapp/home/ali/projects/e3fp/confgen/hashed/27 using /netapp/home/ali/pr
ojects/e3fp/e3fpgen/generate.py
2017-05-16 22:06:50,964|INFO|Parallelizer initialized with mode 'mpi' and 10 processors.
2017-05-16 22:06:50,964|INFO|Initializing E3FP generation.
2017-05-16 22:06:50,964|INFO|Getting SDF files
2017-05-16 22:06:51,112|INFO|SDF File Number: 3181
2017-05-16 22:06:51,113|INFO|Out Directory Basename: /netapp/home/ali/projects/e3fp/e3fpgen/e3fpgen_mpi/27
2017-05-16 22:06:51,113|INFO|Out Extension: .fp.bz2
2017-05-16 22:06:51,113|INFO|Database File: fingerprints.fps.bz2
2017-05-16 22:06:51,113|INFO|Max First Conformers: -1
2017-05-16 22:06:51,113|INFO|Bits: 4096
2017-05-16 22:06:51,113|INFO|Level/Max Iterations: 5
2017-05-16 22:06:51,113|INFO|Shell Radius Multiplier: 1.718
2017-05-16 22:06:51,113|INFO|Stereo Mode: True
2017-05-16 22:06:51,113|INFO|Connected-only mode: on
2017-05-16 22:06:51,113|INFO|Parallel Mode: mpi
2017-05-16 22:06:51,113|INFO|Starting
2017-05-16 22:06:51,166|WARNING|All fingerprint files for CHEMBL379501 already exist. Skipping.
2017-05-16 22:06:51,167|INFO|Generated fingerprints for CHEMBL379501
2017-05-16 22:06:51,175|WARNING|All fingerprint files for CHEMBL1302425 already exist. Skipping.
2017-05-16 22:06:51,182|WARNING|All fingerprint files for CHEMBL401071 already exist. Skipping.
2017-05-16 22:06:51,209|WARNING|All fingerprint files for CHEMBL2064514 already exist. Skipping.
2017-05-16 22:06:51,302|WARNING|All fingerprint files for CHEMBL122199 already exist. Skipping.
2017-05-16 22:06:51,337|WARNING|All fingerprint files for CHEMBL572000 already exist. Skipping.
2017-05-16 22:06:51,777|WARNING|All fingerprint files for CHEMBL373498 already exist. Skipping.
2017-05-16 22:06:51,925|WARNING|All fingerprint files for CHEMBL2204472 already exist. Skipping.
2017-05-16 22:06:52,211|WARNING|All fingerprint files for CHEMBL219947 already exist. Skipping.

This run was executed to resume a previous run, so the output directory already contained hundreds of previously generated fingerprints. As of 22:58, this file has not been updated, and no additional fingerprints were generated.