Empty columns in results table after CCP4 installation

[otvrv]

Hey!

I am using AlphaPulldown's pipeline via python command line interface in a computer cluster and have successfully computed MSA and run the predictions. However, when i generate the results table, i see that columns Num_intf_residues and beyond are empty. I tried to find similar issues here on this case, but i don't truly know what could be happening since i followed the installation instructions described in the wiki section (pulling the image, creating sandbox, copying binaries to sandbox and building new image). CCP4 version is 9.0.003.

The script i submitted and logs:

#!/bin/bash
#SBATCH -J create_res_table
#SBATCH --time=40:00
#SBATCH --account=trim
#SBATCH -p sequana_gpu
#SBATCH -N 1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH -o logs/create_res_table_%j_out.txt
#SBATCH -e logs/create_res_table_%j_err.txt
#SBATCH --gpus=1


echo $SLURM_JOB_NODELIST
nodeset -e $SLURM_JOB_NODELIST
cd $SLURM_SUBMIT_DIR

singularity exec \
    --no-home \
    --bind $SCRATCH/testAPtrim/predictions-result:/mnt \
    $SCRATCH/containers/final_fold_analysis.sif \
    run_get_good_pae.sh \
    --output_dir=/mnt \
    --cutoff=10

Output:

core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: PyRosetta4.Release.python39.linux r377 2024.15+release.d972b59 d972b59c530a12affcbe0eb4a24eedc3ce7d5060 http://www.pyrosetta.org 2024-04-02T17:06:29
core.init: Rosetta extras: []
core.init: command: PyRosetta -ex1 -ex2aro -database /opt/conda/lib/python3.9/site-packages/pyrosetta/database
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=1538547376 seed_offset=0 real_seed=1538547376
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1538547376 RG_type=mt19937
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 985 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 1.00972 seconds.
core.import_pose.import_pose: File '/tmp/tmpwcke8i3h.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue VAL:CtermProteinFull 284
core.import_pose.import_pose: File '/tmp/tmp30n_2tvd.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue VAL:CtermProteinFull 284
core.import_pose.import_pose: File '/tmp/tmp_mabhfon.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue VAL:CtermProteinFull 284
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /opt/conda/lib/python3.9/site-packages/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/opt/conda/lib/python3.9/site-packages/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.956563 seconds to load from binary
core.import_pose.import_pose: File '/tmp/tmp3g6oclnc.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASP:CtermProteinFull 274
core.import_pose.import_pose: File '/tmp/tmpayhmwh0d.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASP:CtermProteinFull 274
core.import_pose.import_pose: File '/tmp/tmpadi8x33k.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASP:CtermProteinFull 274
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.import_pose.import_pose: File '/tmp/tmpxbssj4k6.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASP:CtermProteinFull 274
core.import_pose.import_pose: File '/tmp/tmp5rkj7o1c.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 305
core.import_pose.import_pose: File '/tmp/tmp5axeiy_z.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASP:CtermProteinFull 274
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.import_pose.import_pose: File '/tmp/tmpf8ak1cv3.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 305
core.import_pose.import_pose: File '/tmp/tmpy18oxgii.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 305
core.import_pose.import_pose: File '/tmp/tmpcvlpmbkv.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 305
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.import_pose.import_pose: File '/tmp/tmp_couw3v5.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 301
core.import_pose.import_pose: File '/tmp/tmpnrs3hyc1.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 301
core.import_pose.import_pose: File '/tmp/tmpceezny1f.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 301
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.import_pose.import_pose: File '/tmp/tmpk4mkz16l.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASP:CtermProteinFull 274
core.import_pose.import_pose: File '/tmp/tmpm5_2ak2n.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue VAL:CtermProteinFull 284
core.import_pose.import_pose: File '/tmp/tmpy0ioainn.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASP:CtermProteinFull 274
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.import_pose.import_pose: File '/tmp/tmpj3x55_14.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 301
core.import_pose.import_pose: File '/tmp/tmp3h6al8ox.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 305
core.import_pose.import_pose: File '/tmp/tmpplpqc8bb.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 301
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.import_pose.import_pose: File '/tmp/tmprdibmej_.pdb' automatically determined to be of ty┌──────────────────────────────────────────────────────────────────────────────┐
│                                 PyRosetta-4                                  │
│              Created in JHU by Sergey Lyskov and PyRosetta Team              │
│              (C) Copyright Rosetta Commons Member Institutions               │
│                                                                              │
│ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │
│         See LICENSE.PyRosetta.md or email license@uw.edu for details         │
└──────────────────────────────────────────────────────────────────────────────┘
PyRosetta-4 2024 [Rosetta PyRosetta4.Release.python39.linux 2024.15+release.d972b59c530a12affcbe0eb4a24eedc3ce7d5060 2024-04-02T17:06:29] retrieved from: http://www.pyrosetta.org
Successfully parsed plddt values
Successfully parsed plddt values
Successfully parsed plddt values
Successfully parsed plddt values
Successfully parsed plddt values
Successfully parsed plddt values
Successfully parsed plddt values
Successfully parsed plddt values
Successfully parsed plddt values
Successfully parsed plddt values
pe PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue VAL:CtermProteinFull 284
core.import_pose.import_pose: File '/tmp/tmpfxsylfzz.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 301
core.import_pose.import_pose: File '/tmp/tmpemcd6v4h.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue VAL:CtermProteinFull 284
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.import_pose.import_pose: File '/tmp/tmpvfcp8npu.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASP:CtermProteinFull 274
core.import_pose.import_pose: File '/tmp/tmpvjp81h_g.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 301
core.import_pose.import_pose: File '/tmp/tmpyr_300zz.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ASP:CtermProteinFull 274
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
core.import_pose.import_pose: File '/tmp/tmp3pl5km2v.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue VAL:CtermProteinFull 284
core.import_pose.import_pose: File '/tmp/tmpx3p5z8oj.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue LEU:CtermProteinFull 305
core.import_pose.import_pose: File '/tmp/tmp7t7shs08.pdb' automatically determined to be of type PDB
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue VAL:CtermProteinFull 284
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015

Error:

I1205 17:01:17.823477 22362358437056 get_good_inter_pae.py:120] now processing TRIM4_homo_2er
W1205 17:01:18.466206 22362358437056 pdb_analyser.py:197] Skipping interface due to unexpected format: None
I1205 17:01:24.372085 22362358437056 get_good_inter_pae.py:168] done for TRIM4_homo_2er 1 out of 12 finished.
I1205 17:01:24.372440 22362358437056 get_good_inter_pae.py:120] now processing TRIM5_homo_2er
W1205 17:01:24.984574 22362358437056 pdb_analyser.py:197] Skipping interface due to unexpected format: None
I1205 17:01:25.906690 22362358437056 get_good_inter_pae.py:168] done for TRIM5_homo_2er 2 out of 12 finished.
I1205 17:01:25.907000 22362358437056 get_good_inter_pae.py:120] now processing TRIM2_and_TRIM5
W1205 17:01:26.624629 22362358437056 pdb_analyser.py:197] Skipping interface due to unexpected format: None
I1205 17:01:27.568456 22362358437056 get_good_inter_pae.py:168] done for TRIM2_and_TRIM5 3 out of 12 finished.
I1205 17:01:27.568645 22362358437056 get_good_inter_pae.py:120] now processing TRIM2_homo_2er
W1205 17:01:28.012139 22362358437056 pdb_analyser.py:197] Skipping interface due to unexpected format: None
I1205 17:01:29.282416 22362358437056 get_good_inter_pae.py:168] done for TRIM2_homo_2er 4 out of 12 finished.
I1205 17:01:29.282649 22362358437056 get_good_inter_pae.py:120] now processing TRIM3_homo_2er
W1205 17:01:29.792085 22362358437056 pdb_analyser.py:197] Skipping interface due to unexpected format: None
I1205 17:01:30.774157 22362358437056 get_good_inter_pae.py:168] done for TRIM3_homo_2er 5 out of 12 finished.
I1205 17:01:30.774350 22362358437056 get_good_inter_pae.py:120] now processing TRIM4_and_TRIM5
W1205 17:01:31.390140 22362358437056 pdb_analyser.py:197] Skipping interface due to unexpected format: None
I1205 17:01:32.324669 22362358437056 get_good_inter_pae.py:168] done for TRIM4_and_TRIM5 6 out of 12 finished.
I1205 17:01:32.324857 22362358437056 get_good_inter_pae.py:120] now processing predictions_with_good_interpae.csv
W1205 17:01:32.325329 22362358437056 get_good_inter_pae.py:164] predictions_with_good_interpae.csv does not have ranking_debug.json. Skipped.
I1205 17:01:32.325397 22362358437056 get_good_inter_pae.py:168] done for predictions_with_good_interpae.csv 7 out of 12 finished.
I1205 17:01:32.325439 22362358437056 get_good_inter_pae.py:120] now processing pi_score_outputs
W1205 17:01:32.325700 22362358437056 get_good_inter_pae.py:164] pi_score_outputs does not have ranking_debug.json. Skipped.
I1205 17:01:32.325747 22362358437056 get_good_inter_pae.py:168] done for pi_score_outputs 8 out of 12 finished.
I1205 17:01:32.325785 22362358437056 get_good_inter_pae.py:120] now processing TRIM2_and_TRIM3
W1205 17:01:32.791718 22362358437056 pdb_analyser.py:197] Skipping interface due to unexpected format: None
I1205 17:01:33.790646 22362358437056 get_good_inter_pae.py:168] done for TRIM2_and_TRIM3 9 out of 12 finished.
I1205 17:01:33.790920 22362358437056 get_good_inter_pae.py:120] now processing TRIM3_and_TRIM4
W1205 17:01:34.458729 22362358437056 pdb_analyser.py:197] Skipping interface due to unexpected format: None
I1205 17:01:35.442256 22362358437056 get_good_inter_pae.py:168] done for TRIM3_and_TRIM4 10 out of 12 finished.
I1205 17:01:35.442455 22362358437056 get_good_inter_pae.py:120] now processing TRIM3_and_TRIM5
W1205 17:01:35.913053 22362358437056 pdb_analyser.py:197] Skipping interface due to unexpected format: None
I1205 17:01:36.854231 22362358437056 get_good_inter_pae.py:168] done for TRIM3_and_TRIM5 11 out of 12 finished.
I1205 17:01:36.854418 22362358437056 get_good_inter_pae.py:120] now processing TRIM2_and_TRIM4
W1205 17:01:37.521888 22362358437056 pdb_analyser.py:197] Skipping interface due to unexpected format: None
I1205 17:01:38.514947 22362358437056 get_good_inter_pae.py:168] done for TRIM2_and_TRIM4 12 out of 12 finished.

I would appreciate any help/tips. Also, thank you for all the effort spent in developing and maintaining this amazing project.

Best regards,
Otavio.

[DimaMolod]

Hi Otavio!
Sorry, installing CCP4 directly into the sandbox turned out to be unstable, with multiple reports of missing values in the outputs from our users. Most likely this is caused by incompatibilities between newer CCP4 releases and the Docker analysis pipeline.

Because of this, we have reintroduced a standalone analysis pipeline here:
https://github.com/KosinskiLab/AlphaJudge

For interactive inspection and visualization of the results (aka old jupyter-notebook), you can also use APLit:
https://github.com/KosinskiLab/aplit

Feel free to try both, and any feedback is very welcome!
Best wishes,
Dima