After successfully completing VFVS_GK tutorial1, tried to do the tutorial 2 with the suggested settings:-
$ cat all.ctrl | grep -v "#" | sed '/^$/d'
*************************************************************** Job Resource Configuration
job_letter=t
batchsystem=SLURM
partition=shared
timelimit=3-00:00:00
steps_per_job=1
cpus_per_step=8
queues_per_step=8
cpus_per_queue=1
********************************************************************* Workflow Options
central_todo_list_splitting_size=1000
ligands_todo_per_queue=1000
ligands_per_refilling_step=1000
collection_folder=…/input-files/ligand-library
ligand_library_format=pdbqt
minimum_time_remaining=10
dispersion_time_min=3
dispersion_time_max=10
verbosity_commands=standard
verbosity_logfiles=standard
store_queue_log_files=all_compressed_error_uncompressed
keep_ligand_summary_logs=true
error_sensitivity=normal
error_response=fail
tempdir_default=/tmp
tempdir_fast=/dev/shm
outputfiles_level=collection
prepare_queue_todolists=true
***************************************************************** Virtual Screenign Options
docking_scenario_names=qvina02_rigid_receptor1:smina_rigid_receptor1
docking_scenario_programs=docking_scenario_programs=qvina02:smina_rigid
docking_scenario_replicas=1:1
docking_scenario_inputfolders=…/input-files/qvina02_rigid_receptor1:…/input-files/smina_rigid_receptor1
******************************************************************* Terminating Variables
stop_after_next_check_interval=false
ligand_check_interval=10
stop_after_collection=false
stop_after_job=false
I downloaded a subset of REAL Lib following tutorial2 as follows:-
This is the contents of my input-files/ligand-library/CF/ dir
ls -lah input-files/ligand-library/CF/ | cut -d" " -f3-4 --complement
total 40M
drwxr-xr-x 2 4.0K Oct 13 14:41 .
drwxr-xr-x 3 4.0K Oct 13 11:10 …
-rw-r–r-- 1 20K Jan 5 2019 CFCDAD.tar
-rw-r–r-- 1 20K Jan 5 2019 CFCDAE.tar
-rw-r–r-- 1 4.4M Jan 5 2019 CFCDBD.tar
-rw-r–r-- 1 7.2M Jan 5 2019 CFCDBE.tar
-rw-r–r-- 1 8.9M Jan 5 2019 CFCDCD.tar
-rw-r–r-- 1 7.8M Jan 5 2019 CFCDCE.tar
-rw-r–r-- 1 5.4M Jan 5 2019 CFCDDD.tar
-rw-r–r-- 1 2.0M Oct 13 14:41 CFCDDE.tar
-rw-r–r-- 1 1.4M Jan 5 2019 CFCDED.tar
-rw-r–r-- 1 460K Jan 5 2019 CFCDEE.tar
-rw-r–r-- 1 100K Jan 5 2019 CFCDFD.tar
-rw-r–r-- 1 60K Jan 5 2019 CFCDFE.tar
-rw-r–r-- 1 10K Jan 5 2019 CFCEAE.tar
-rw-r–r-- 1 50K Jan 5 2019 CFCEBD.tar
-rw-r–r-- 1 320K Jan 5 2019 CFCEBE.tar
-rw-r–r-- 1 30K Jan 5 2019 CFCECD.tar
-rw-r–r-- 1 130K Jan 5 2019 CFCECE.tar
-rw-r–r-- 1 30K Jan 5 2019 CFCEDD.tar
-rw-r–r-- 1 20K Jan 5 2019 CFCEDE.tar
-rw-r–r-- 1 10K Jan 5 2019 CFCEED.tar
-rw-r–r-- 1 10K Jan 5 2019 CFCEFD.tar
-rw-r–r-- 1 40K Jan 5 2019 CFDDBD.tar
-rw-r–r-- 1 350K Jan 5 2019 CFDDBE.tar
-rw-r–r-- 1 50K Jan 5 2019 CFDDCD.tar
-rw-r–r-- 1 250K Jan 5 2019 CFDDCE.tar
-rw-r–r-- 1 80K Jan 5 2019 CFDDDD.tar
-rw-r–r-- 1 140K Jan 5 2019 CFDDDE.tar
-rw-r–r-- 1 20K Jan 5 2019 CFDDED.tar
-rw-r–r-- 1 70K Jan 5 2019 CFDDEE.tar
-rw-r–r-- 1 10K Jan 5 2019 CFDDFD.tar
-rw-r–r-- 1 10K Jan 5 2019 CFDDFE.tar
-rw-r–r-- 1 20K Jan 5 2019 CFDEBE.tar
-rw-r–r-- 1 20K Jan 5 2019 CFDECE.tar
-rw-r–r-- 1 10K Jan 5 2019 CFDEDE.tar
-rw-r–r-- 1 10K Jan 5 2019 CFDEFE.tar
This is the content of my tools/templates/todo.all
$ cat tools/templates/todo.all
CFDEBE_00000 48
CFDEFE_00000 1
CFDECE_00000 22
CFDEDE_00000 2
CFDDEE_00000 183
CFDDED_00000 22
CFDDFE_00000 18
CFDDFD_00000 9
CFDDCE_00000 649
CFDDCD_00000 107
CFDDDE_00000 366
CFDDDD_00000 186
CFDDBE_00000 990
CFDDBD_00000 91
CFCEAE_00000 18
CFCEDE_00000 35
CFCEDD_00000 48
CFCEED_00000 5
CFCEBE_00000 827
CFCEBD_00000 102
CFCECD_00000 52
CFCECE_00000 289
CFCEFD_00000 12
CFCDBD_00001 1935
CFCDBD_00002 1752
CFCDBD_00003 1500
CFCDBD_00004 1415
CFCDBD_00005 1451
CFCDBD_00006 1792
CFCDBD_00000 2147
CFCDBE_00007 1773
CFCDBE_00008 2620
CFCDBE_00009 374
CFCDBE_00004 1659
CFCDBE_00005 2118
CFCDBE_00006 2149
CFCDBE_00001 1957
CFCDBE_00000 2141
CFCDBE_00002 1713
CFCDBE_00003 2197
CFCDCE_00000 1780
CFCDCE_00001 1828
CFCDCE_00002 1924
CFCDCE_00003 1765
CFCDCE_00004 1748
CFCDCE_00005 1267
CFCDCE_00006 2040
CFCDCE_00007 1523
CFCDCE_00008 1593
CFCDCE_00009 2016
CFCDCE_00010 2335
CFCDCE_00011 347
CFCDCD_00000 1393
CFCDCD_00001 1301
CFCDCD_00002 1384
CFCDCD_00011 1291
CFCDCD_00013 1328
CFCDCD_00012 1288
CFCDCD_00014 1436
CFCDCD_00015 1608
CFCDCD_00016 471
CFCDCD_00003 1510
CFCDCD_00004 1311
CFCDCD_00005 1474
CFCDCD_00006 1658
CFCDCD_00007 1383
CFCDCD_00008 1315
CFCDCD_00009 1467
CFCDCD_00010 1539
CFCDAE_00000 27
CFCDAD_00000 31
CFCDFD_00000 229
CFCDFE_00000 116
CFCDDD_00003 1277
CFCDDD_00004 1215
CFCDDD_00005 1109
CFCDDD_00006 1146
CFCDDD_00007 1455
CFCDDD_00008 1184
CFCDDD_00009 1194
CFCDDD_00010 1322
CFCDDD_00011 44
CFCDDD_00000 1310
CFCDDD_00001 1263
CFCDDD_00002 1268
CFCDDE_00000 1550
CFCDDE_00001 1253
CFCDDE_00002 1618
CFCDDE_00003 470
CFCDEE_00000 1105
CFCDED_00000 1256
CFCDED_00001 1149
CFCDED_00002 1035
This Job output section of the workflow/output-files/jobs/job-1.1_52434964.out
*** Job Output ***
===========================================================
* Preparing the to-do lists for jobline 1
Starting the (re)filling of the todolists of the queues.
Before (re)filling the todolists the queue 1-1-1 had 0 ligands todo distributed in 0 collections.
Before (re)filling the todolists the queue 1-1-2 had 0 ligands todo distributed in 0 collections.
Before (re)filling the todolists the queue 1-1-3 had 0 ligands todo distributed in 0 collections.
Before (re)filling the todolists the queue 1-1-4 had 0 ligands todo distributed in 0 collections.
Before (re)filling the todolists the queue 1-1-5 had 0 ligands todo distributed in 0 collections.
Before (re)filling the todolists the queue 1-1-6 had 0 ligands todo distributed in 0 collections.
Before (re)filling the todolists the queue 1-1-7 had 0 ligands todo distributed in 0 collections.
Before (re)filling the todolists the queue 1-1-8 had 0 ligands todo distributed in 0 collections.
After (re)filling the todolists the queue 1-1-1 has 1061 ligands todo distributed in 10 collections.
After (re)filling the todolists the queue 1-1-2 has 1542 ligands todo distributed in 3 collections.
After (re)filling the todolists the queue 1-1-3 has 1024 ligands todo distributed in 6 collections.
After (re)filling the todolists the queue 1-1-4 has 2390 ligands todo distributed in 5 collections.
After (re)filling the todolists the queue 1-1-5 has 1752 ligands todo distributed in 1 collections.
After (re)filling the todolists the queue 1-1-6 has 1500 ligands todo distributed in 1 collections.
After (re)filling the todolists the queue 1-1-7 has 1415 ligands todo distributed in 1 collections.
After (re)filling the todolists the queue 1-1-8 has 1451 ligands todo distributed in 1 collections.
The todo lists for the queues were (re)filled in 0 second(s) (waiting time not included).
The waiting time was 0 second(s).
Starting job step 1 on host compute0013.
Job step 1 is starting queue 1-1-1 on host compute0013.
Job step 1 is starting queue 1-1-2 on host compute0013.
Job step 1 is starting queue 1-1-3 on host compute0013.
Job step 1 is starting queue 1-1-4 on host compute0013.
Job step 1 is starting queue 1-1-5 on host compute0013.
Job step 1 is starting queue 1-1-6 on host compute0013.
Job step 1 is starting queue 1-1-7 on host compute0013.
Job step 1 is starting queue 1-1-8 on host compute0013.
Error was trapped
Error in bash script one-step.sh
Error on line 187
Any help will be appreciated.