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keiserlab / e3fp

3D molecular fingerprints
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Fix clobbering in output log files #17

Open 8li opened 7 years ago

8li commented 7 years ago

The $LOGFILE produced by this call:

python e3fp/e3fp/fingerprint/generate.py $SDFDIR -o $OUTDIR -l $LOGFILE -b 4096 -p $NSLOTS --parallel_mode mpi

contains clobbered lines like this:

2017-05-09 10:15:37,194|INFO|Generating fingerprints for CHEMBL1001642017-05-09 10:15:37,277|INFO|Generating fingerprints for CHEMBL100109.
8li commented 7 years ago

I am also noticing strange output which may or may not be related to the same issue:

Expt run on iq35
Anaconda env used: e3fp_git
Activating environment e3fp_git
Generating Fingerprints of conformers in /netapp/home/ali/projects/e3fp/confgen/hashed/22 using /netapp/home/ali/projects/e3fp/e
3fpgen/generate.py
2017-05-17 15:00:52,270|WARNING|All fingerprint files for CHEMBL381755 already exist. Skipping.
017-05-17 15:00:52,224|WARNING|All fingerprint files for CHEMBL104857 already exist. Skipping.
les
2017-05-17 15:00:51,883|INFO|SDF File Number: 3140
2017-05-17 15:00:51,883|INFO|Out Directory Basename: /netapp/home/ali/projects/e3fp/e3fpgen/e3fpgen_mpi/22
2017-05-17 15:00:51,883|INFO|Out Extension: .fp.bz2
2017-05-17 15:00:51,883|INFO|Database File: /netapp/home/ali/projects/e3fp/e3fpgen/e3fpgen_mpi/22.fps.bz2
2017-05-17 15:00:51,883|INFO|Max First Conformers: -1
2017-05-17 15:00:51,883|INFO|Bits: 4096
2017-05-17 15:00:51,883|INFO|Level/Max Iterations: 5
2017-05-17 15:00:51,884|INFO|Shell Radius Multiplier: 1.718
2017-05-17 15:00:51,884|INFO|Stereo Mode: True
2017-05-17 15:00:51,884|INFO|Connected-only mode: on
2017-05-17 15:00:51,884|INFO|Parallel Mode: mpi
2017-05-17 15:00:51,884|INFO|Starting
2017-05-17 15:00:51,958|INFO|Generated fingerprints for CHEMBL2172080

Notice, that the logging lines seem to be writing in a strange order--the warnings about existing molecules are first, and the mode information usually comes before the SDF file information.

EDIT 1: Also, "Generated fingerprints for CHEMBL2172080" is weird, because (1) there is no corresponding "Generating line" and (2) upon checking, the fingerprints are already present in the output folder.

EDIT 2: This error came from using an older version of generate.py, but using the latest repo of E3FP