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drugdata / D3R

Drug Design Data Resource is a suite of software to enable filtering, docking, and scoring of new sequences from wwpdb.
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Investigate why stage.3.blastnfilter failed on dataset.week.42 on version 1.6.0 #89

Closed coleslaw481 closed 7 years ago

coleslaw481 commented 8 years ago

blastnfilter failed with a non zero exit code. In blastnfilter.py.stderr file some exceptions were thrown. Below is edited output from blastnfilter.py.stderr file:

Running command: /usr/bin/blastnfilter.py --nonpolymertsv /data/celpp/2016/dataset.week.42/stage.2.dataimport/new_release_structure_nonpolymer.tsv --sequencetsv /data/celpp/2016/dataset.week.42/stage.2.dataimport/new_release_structure_sequence_canonical.tsv --pdbblastdb /data/celpp/2016/dataset.week.42/stage.1.makeblastdb --compinchi /data/celpp/2016/dataset.week.42/stage.2.dataimport/Components-inchi.ich --crystalpH /data/celpp/2016/dataset.week.42/stage.2.dataimport/new_release_crystallization_pH.tsv --pdbdb /data/pdb.extracted --log DEBUG --outdir /data/celpp/2016/dataset.week.42/stage.3.blastnfilter Although considered non fatal for processing of stage a non zero exit code: 2received. Standard out: The total number of structures is: 169 The total number of complexes is: 135 The total number of complexes with at least one dockable ligand is: 80 The total number of complexes with only one dockable ligand is: 56 The total number of monomers is: 132 The total number of monomers with one dockable ligand is: 42 The total number of multimers is: 37 The total number of multimers with one dockable ligand is: 14 Please set an rd mol object before calculating num of atoms Please set an rd mol object before calculating num of heavy atoms Please set an rd mol object before calculating num of atoms Please set an rd mol object before calculating num of heavy atoms Please set an rd mol object before calculating num of atoms Please set an rd mol object before calculating num of heavy atoms Please set an rd mol object before calculating num of atoms Please set an rd mol object before calculating num of heavy atoms Please set an rd mol object before calculating num of atoms Please set an rd mol object before calculating num of heavy atoms Please set an rd mol object before calculating num of atoms Please set an rd mol object before calculating num of heavy atoms Standard error : 2016-10-15 00:02:15,670 DEBUG d3r.blastnfilter Starting run 2016-10-15 00:02:15,670 DEBUG d3r.utilities.run Creating queries 2016-10-15 00:02:15,699 DEBUG d3r.utilities.in_put Found 169 queries from /data/celpp/2016/dataset.week.42/stage.2.dataimport/new_release_structure_sequence_canonical.tsv file 2016-10-15 00:02:15,703 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,756 DEBUG d3r.blast.query In set_ligand() . . . 2016-10-15 00:02:15,845 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,846 ERROR d3r.utilities.in_put Caught exception Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/d3r/utilities/in_put.py", line 95, in read_ligands inchi = words[2] IndexError: list index out of range 2016-10-15 00:02:15,847 ERROR d3r.utilities.in_put Caught exception Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/d3r/utilities/in_put.py", line 95, in read_ligands inchi = words[2] IndexError: list index out of range 2016-10-15 00:02:15,847 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,847 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,914 ERROR d3r.utilities.in_put Caught exception Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/d3r/utilities/in_put.py", line 95, in read_ligands inchi = words[2] IndexError: list index out of range 2016-10-15 00:02:15,915 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,915 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,921 ERROR d3r.utilities.in_put Caught exception Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/d3r/utilities/in_put.py", line 95, in read_ligands inchi = words[2] IndexError: list index out of range 2016-10-15 00:02:15,921 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,921 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,923 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,924 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,924 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,924 ERROR d3r.utilities.in_put Caught exception Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/d3r/utilities/in_put.py", line 95, in read_ligands inchi = words[2] IndexError: list index out of range 2016-10-15 00:02:15,924 DEBUG d3r.blast.query In set_ligand() . . 2016-10-15 00:02:15,941 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,941 DEBUG d3r.blast.query In set_ligand() 2016-10-15 00:02:15,942 DEBUG d3r.utilities.analysis Writing summary.txt file to /data/celpp/2016/dataset.week.42/stage.3.blastnfilter 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis INPUT SUMMARY 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis entries: 169 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis complexes: 135 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis dockable complexes: 56 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis monomers: 132 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis dockable monomers: 42 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis multimers: 37 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis dockable multimers: 14 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis FILTERING CRITERIA 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis No. of query sequences <= 1 2016-10-15 00:02:15,943 DEBUG d3r.utilities.analysis No. of dockable ligands = 1 2016-10-15 00:02:15,944 DEBUG d3r.utilities.analysis Percent identity >= 0.95 2016-10-15 00:02:15,944 DEBUG d3r.utilities.analysis Percent Coverage >= 0.9 2016-10-15 00:02:15,944 DEBUG d3r.utilities.analysis No. of hit sequences <= 2 2016-10-15 00:02:15,944 DEBUG d3r.utilities.analysis Structure determination method: x-ray diffraction 2016-10-15 00:02:15,944 DEBUG d3r.utilities.analysis 2016-10-15 00:02:15,944 DEBUG d3r.utilities.run # queries 169 2016-10-15 00:02:15,944 DEBUG d3r.utilities.run Blasting query: 1fcz 2016-10-15 00:02:15,944 DEBUG d3r.utilities.run Hit.set_pdb_dir 2016-10-15 00:02:15,944 DEBUG d3r.utilities.run Hit.set_pdb_dict 2016-10-15 00:02:15,944 DEBUG d3r.blast.hit Parsing /data/celpp/2016/dataset.week.42/stage.1.makeblastdb/pdb_seqres.txt 2016-10-15 00:02:51,848 DEBUG d3r.utilities.run Ligand.set_inchi_component 2016-10-15 00:02:51,863 ERROR d3r.blast.ligand Caught exception trying to read /data/celpp/2016/dataset.week.42/stage.2.dataimport/Components-inchi.ich file Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/d3r/blast/ligand.py", line 43, in set_inchi_component inchi = words[0] IndexError: list index out of range 2016-10-15 00:02:51,863 ERROR d3r.blast.ligand Caught exception trying to read /data/celpp/2016/dataset.week.42/stage.2.dataimport/Components-inchi.ich file Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/d3r/blast/ligand.py", line 44, in set_inchi_component resname = words[1] IndexError: list index out of range 2016-10-15 00:02:51,863 ERROR d3r.blast.ligand Caught exception trying to read /data/celpp/2016/dataset.week.42/stage.2.dataimport/Components-inchi.ich file Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/d3r/blast/ligand.py", line 43, in set_inchi_component inchi = words[0] IndexError: list index out of range 2016-10-15 00:02:51,908 DEBUG d3r.utilities.run query.run_blast 2016-10-15 00:02:51,908 DEBUG d3r.blast.query In run_blast() 2016-10-15 00:02:51,908 DEBUG d3r.blast.query Running blast_monomer

shuail commented 7 years ago

This bug is caused by the invalid operation to the top of the holo hit (try to extract the mcss info of the hit while the hit didn't have mcss info). Fix the bug by skipping the invalid holo hit and go to the next one in the holo list.