Dear all,
Recently I’ve been using VFVS for rigid docking, and I obtained 50,000 ligands through this step. Now, I have wrote a script file to generate a Tranches file called AA from the above 50,000 ligands as the input ligands-library for my next flexible docking. But some errors occurred when operating the flexible docking, job submitted but immediately failed. I think this problem is from the input ligands-library, and I can sure that entered input receptor files are correct. I browsed all the discussion on VFVS community, but still didn’t solve my problem. This step has been block me for a long time, I hope to get your help. Could you help me?
Attached are some input files, the AAAAAA.tar, AAAAAD.tar and AAAAAT.tar are some samples from the AA folds. Hopping to help you understand my problem. Thank you!
all.ctrl:
steps_per_job=1
cpus_per_step=36
queues_per_step=36
cpus_per_queue=36
central_todo_list_splitting_size=10000
ligands_todo_per_queue=500
ligands_per_refilling_step=100
verbosity_logfiles=debug
store_queue_log_files=all_uncompressed
ligand_check_interval=100
other are default
collections:
AAAAAA_00000 499
AAAAAA_00001 500
AAAAAA_00002 500
AAAAAA_00003 500
AAAAAA_00004 500
AAAAAB_00000 500
AAAAAB_00001 500
AAAAAB_00002 500
AAAAAB_00003 500
AAAAAB_00004 500
AAAAAC_00000 500
AAAAAC_00001 500
AAAAAC_00002 500
AAAAAC_00003 500
AAAAAC_00004 500
AAAAAD_00000 500
AAAAAD_00001 500
AAAAAD_00002 500
AAAAAD_00003 500
AAAAAD_00004 500
AAAAAE_00000 500
AAAAAE_00001 500
AAAAAE_00002 500
AAAAAE_00003 500
AAAAAE_00004 500
…
.out file:
++ grep -m 1 ‘^error_response=’ …/workflow/control/all.ctrl
++ tr -d ‘[[:space:]]’
++ awk -F ‘[=#]’ ‘{print $2}’
- VF_ERROR_RESPONSE=fail
- export VF_ERROR_RESPONSE
++ grep -m 1 ‘^tempdir_default=’ …/workflow/control/all.ctrl
++ tr -d ‘[[:space:]]’
++ awk -F ‘[=#]’ ‘{print $2}’ - export VF_TMPDIR=/tmp
- VF_TMPDIR=/tmp
- ‘[’ ‘!’ -d /tmp/lichunqiong ‘]’
++ grep -m 1 ‘^tempdir_fast=’ …/workflow/control/all.ctrl
++ tr -d ‘[[:space:]]’
++ awk -F ‘[=#]’ ‘{print $2}’ - export VF_TMPDIR_FAST=/dev/shm
- VF_TMPDIR_FAST=/dev/shm
- ‘[’ ‘!’ -d /tmp/lichunqiong ‘]’
++ cat …/workflow/control/all.ctrl
++ grep -m 1 ‘^job_letter=’ - line=job_letter=t
- export VF_JOBLETTER=t
- VF_JOBLETTER=t
++ grep -m 1 ‘^error_sensitivity=’ …/workflow/control/all.ctrl
++ tr -d ‘[[:space:]]’
++ awk -F ‘[=#]’ ‘{print $2}’ - VF_ERROR_SENSITIVITY=normal
- [[ normal == \h\i\g\h ]]
- check_queue_end1
- VF_CONTROLFILE=
++ ls ‘…/workflow/control/-’
++ true - ‘[’ -z ‘’ ‘]’
- export VF_CONTROLFILE=…/workflow/control/all.ctrl
- VF_CONTROLFILE=…/workflow/control/all.ctrl
++ cat …/workflow/control/all.ctrl
++ grep stop_after_next_check_interval= - line=stop_after_next_check_interval=false
- stop_after_next_check_interval=false
- ‘[’ false = true ‘]’
- no_collections_incomplete=0
- i=0
- ‘[’ 0 == 0 ‘]’
++ grep -c ‘[^[:blank:]]’
++ cat …/workflow/ligand-collections/todo/todo.all …/workflow/ligand-collections/todo/todo.all.0000 ‘…/workflow/ligand-collections/todo/1//’ ‘…/workflow/ligand-collections/current/1//’ - no_collections_incomplete=200
- i=1
- ‘[’ 1 == 5 ‘]’
- sleep 1
- ‘[’ 200 == 0 ‘]’
- [[ 200 = \0 ]]
++ grep -m 1 time= …/workflow/job-files/main/1.job - job_line=’#SBATCH --time=7-00:00:00’
- timelimit=7-00:00:00
- timelimit=7:00:00:00
++ awk -F : ‘{print $4 + $3 * 60 + $2 * 3600 + $1 * 3600 * 24}’
++ echo -n 7:00:00:00 - export VF_TIMELIMIT_SECONDS=604800
- VF_TIMELIMIT_SECONDS=604800
++ cat …/workflow/control/all.ctrl
++ grep queues_per_step= - line=queues_per_step=36
- export VF_QUEUES_PER_STEP=36
- VF_QUEUES_PER_STEP=36
++ tr -d ‘[[:space:]]’
++ grep -m 1 ‘^prepare_queue_todolists=’ …/workflow/control/all.ctrl
++ awk -F ‘[=#]’ ‘{print $2}’ - prepare_queue_todolists=true
- ‘[’ TRUE == TRUE ‘]’
- cd helpers
- bash prepare-todolists.sh 1 1 36
- echo -e ‘\n * Preparing the to-do lists for jobline 1\n’
- Preparing the to-do lists for jobline 1
-
trap time_near_limit 10
-
trap termination_signal 1 2 3 9 15
-
trap clean_up EXIT
-
mkdir -p /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/
-
vf_controlfile_temp=/dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/controlfile
-
cp …/…/workflow/control/all.ctrl /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/controlfile
++ grep -m 1 ‘^collection_folder=’ /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/controlfile
++ tr -d ‘[[:space:]]’
++ awk -F ‘[=#]’ ‘{print $2}’ -
collection_folder=…/input-files/ligand-library
-
collection_folder=…/input-files/ligand-library
++ grep -m 1 ‘^ligands_todo_per_queue=’ /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/controlfile
++ tr -d ‘[[:space:]]’
++ awk -F ‘[=#]’ ‘{print $2}’ -
ligands_todo_per_queue=500
++ awk -F ‘[=#]’ ‘{print $2}’
++ tr -d ‘[[:space:]]’
++ grep -m 1 ‘^ligands_per_refilling_step=’ /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/controlfile -
ligands_per_refilling_step=100
-
initial_todolist=true
-
[[ ! 1 1 36 = \q\u\i\e\t ]]
-
echo
-
ligands_todo=
-
queue_collection_numbers=
-
todofile_queue_old_temp=/dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.queue.old
++ seq 1 1 -
for queue_no_2 in ‘$(seq 1 ${steps_per_job})’
++ seq 1 36 -
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-1
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=0
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=0
-
todofile_queue_new_temp[${queue_no_2}0000${queue_no_3}]=/dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.queue.new.1-1-1
-
‘[’ -s …/…/workflow/ligand-collections/todo/1/1/1-1-1 ‘]’
-
‘[’ -s …/…/workflow/ligand-collections/current/1/1/1-1-1 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-2
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=0
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=0
-
todofile_queue_new_temp[${queue_no_2}0000${queue_no_3}]=/dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.queue.new.1-1-2
-
‘[’ -s …/…/workflow/ligand-collections/todo/1/1/1-1-2 ‘]’
-
‘[’ -s …/…/workflow/ligand-collections/current/1/1/1-1-2 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-3
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=0
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=0
…
todofile_queue_new_temp[${queue_no_2}0000${queue_no_3}]=/dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.queue.new.1-1-35
- ‘[’ -s …/…/workflow/ligand-collections/todo/1/1/1-1-35 ‘]’
- ‘[’ -s …/…/workflow/ligand-collections/current/1/1/1-1-35 ‘]’
- for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
- queue_no=1-1-36
- ligands_todo[${queue_no_2}0000${queue_no_3}]=0
- queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=0
- todofile_queue_new_temp[${queue_no_2}0000${queue_no_3}]=/dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.queue.new.1-1-36
- ‘[’ -s …/…/workflow/ligand-collections/todo/1/1/1-1-36 ‘]’
- ‘[’ -s …/…/workflow/ligand-collections/current/1/1/1-1-36 ‘]’
- [[ ! 1 1 36 = \q\u\i\e\t ]]
- echo ‘Starting the (re)filling of the todolists of the queues.’
Starting the (re)filling of the todolists of the queues. - echo
++ seq 1 1
-
for queue_no_2 in ‘$(seq 1 ${steps_per_job})’
++ seq 1 36 -
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-1
-
echo ‘Before (re)filling the todolists the queue 1-1-1 had 0 ligands todo distributed in 0 collections.’
Before (re)filling the todolists the queue 1-1-1 had 0 ligands todo distributed in 0 collections. -
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-2
-
echo ‘Before (re)filling the todolists the queue 1-1-2 had 0 ligands todo distributed in 0 collections.’
Before (re)filling the todolists the queue 1-1-2 had 0 ligands todo distributed in 0 collections.
… -
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-35
-
echo ‘Before (re)filling the todolists the queue 1-1-35 had 0 ligands todo distributed in 0 collections.’
Before (re)filling the todolists the queue 1-1-35 had 0 ligands todo distributed in 0 collections. -
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-36
-
echo ‘Before (re)filling the todolists the queue 1-1-36 had 0 ligands todo distributed in 0 collections.’
Before (re)filling the todolists the queue 1-1-36 had 0 ligands todo distributed in 0 collections. -
echo
-
status=false
-
k=1
-
max_iter=1000
-
modification_time_difference=0
++ date +%s -
start_time_waiting=1597634634
++ grep -m 1 ‘^dispersion_time_min=’ /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/controlfile
++ tr -d ‘[[:space:]]’
++ awk -F ‘[=#]’ ‘{print $2}’ -
dispersion_time_min=3
++ tr -d ‘[[:space:]]’
++ grep -m 1 ‘^dispersion_time_max=’ /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/controlfile
++ awk -F ‘[=#]’ ‘{print $2}’ -
dispersion_time_max=10
++ shuf -i 3-10 -n1 -
modification_time_treshhold=10
-
modification_time_treshhold_lockedfile=300
-
[[ false = \f\a\l\s\e ]]
++ stat -c %Z …/…/workflow/ligand-collections/todo/todo.all -
modification_time=1597634580
-
‘[’ 1597634580 -eq 1597634580 ‘]’
++ date +%s -
modification_time_difference=54
-
‘[’ 54 -ge 10 ‘]’
-
mv …/…/workflow/ligand-collections/todo/todo.all …/…/workflow/ligand-collections/todo/todo.all.locked
-
cp …/…/workflow/ligand-collections/todo/todo.all.locked /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
++ realpath …/…/workflow/ligand-collections/todo/todo.all.locked
++ xargs basename
++ xargs basename
++ awk -F . ‘{print $3}’ -
current_todo_list_index=0000
-
‘[’ 0000 -eq 0000 ‘]’
-
cp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all …/…/workflow/ligand-collections/var/todo.all.0000.bak.1
-
status=true
-
trap ‘error_response_std $LINENO’ ERR
-
touch_locked_pid=’#!’
-
[[ true = \f\a\l\s\e ]]
-
watch -m -n 1 touch …/…/workflow/ligand-collections/var/todo.all.locked
++ date +%s -
end_time_waiting=1597634634
++ cat /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
++ grep -c ‘[^[:blank:]]’ -
no_collections_incomplete=100
-
[[ 100 = \0 ]]
-
grep ‘[^[:blank:]]’
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_of_refilling_steps=5
++ grep -cv ‘^\s*$’ /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
no_collections_remaining=100
-
no_collections_assigned=0
-
no_collections_beginning=100
++ date +%s -
start_time_seconds=1597634634
++ seq 1 5 -
for refill_step in ‘$(seq 1 ${no_of_refilling_steps})’
-
step_limit=100
++ seq 1 1 -
for queue_no_2 in ‘$(seq 1 ${steps_per_job})’
++ seq 1 36 -
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-1
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 100 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAA_00000 499’
-
next_ligand_collection=AAAAAA_00000
-
‘[’ AAAAAA_00000 = Binary ‘]’
-
echo ‘AAAAAA_00000 499’
-
no_to_add=499
-
‘[’ 499 -eq 499 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=499
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=99
-
no_collections_assigned=1
-
‘[’ 499 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-2
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 99 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAA_00001 500’
-
next_ligand_collection=AAAAAA_00001
-
‘[’ AAAAAA_00001 = Binary ‘]’
-
echo ‘AAAAAA_00001 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=98
-
no_collections_assigned=2
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-3
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 98 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAA_00002 500’
-
next_ligand_collection=AAAAAA_00002
-
‘[’ AAAAAA_00002 = Binary ‘]’
-
echo ‘AAAAAA_00002 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=97
-
no_collections_assigned=3
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-4
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 97 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAA_00003 500’
-
next_ligand_collection=AAAAAA_00003
-
‘[’ AAAAAA_00003 = Binary ‘]’
-
echo ‘AAAAAA_00003 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=96
-
no_collections_assigned=4
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-5
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 96 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAA_00004 500’
-
next_ligand_collection=AAAAAA_00004
-
‘[’ AAAAAA_00004 = Binary ‘]’
-
echo ‘AAAAAA_00004 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=95
-
no_collections_assigned=5
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-6
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 95 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAB_00000 500’
-
next_ligand_collection=AAAAAB_00000
-
‘[’ AAAAAB_00000 = Binary ‘]’
-
echo ‘AAAAAB_00000 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=94
-
no_collections_assigned=6
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-7
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 94 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAB_00001 500’
-
next_ligand_collection=AAAAAB_00001
-
‘[’ AAAAAB_00001 = Binary ‘]’
-
echo ‘AAAAAB_00001 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=93
-
no_collections_assigned=7
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-8
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 93 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAB_00002 500’
-
next_ligand_collection=AAAAAB_00002
-
‘[’ AAAAAB_00002 = Binary ‘]’
-
echo ‘AAAAAB_00002 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=92
-
no_collections_assigned=8
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-9
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 92 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAB_00003 500’
-
next_ligand_collection=AAAAAB_00003
-
‘[’ AAAAAB_00003 = Binary ‘]’
-
echo ‘AAAAAB_00003 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=91
-
no_collections_assigned=9
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-10
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 91 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAB_00004 500’
-
next_ligand_collection=AAAAAB_00004
-
‘[’ AAAAAB_00004 = Binary ‘]’
-
echo ‘AAAAAB_00004 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=90
-
no_collections_assigned=10
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-11
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 90 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAC_00000 500’
-
next_ligand_collection=AAAAAC_00000
-
‘[’ AAAAAC_00000 = Binary ‘]’
-
echo ‘AAAAAC_00000 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=89
-
no_collections_assigned=11
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-12
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 89 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAC_00001 500’
-
next_ligand_collection=AAAAAC_00001
-
‘[’ AAAAAC_00001 = Binary ‘]’
-
echo ‘AAAAAC_00001 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=88
-
no_collections_assigned=12
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-13
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 88 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAC_00002 500’
-
next_ligand_collection=AAAAAC_00002
-
‘[’ AAAAAC_00002 = Binary ‘]’
-
echo ‘AAAAAC_00002 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=87
-
no_collections_assigned=13
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-14
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 87 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAC_00003 500’
-
next_ligand_collection=AAAAAC_00003
-
‘[’ AAAAAC_00003 = Binary ‘]’
-
echo ‘AAAAAC_00003 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=86
-
no_collections_assigned=14
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-15
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 86 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length=‘AAAAAC_00004 500’
-
next_ligand_collection=AAAAAC_00004
-
‘[’ AAAAAC_00004 = Binary ‘]’
-
echo ‘AAAAAC_00004 500’
-
no_to_add=500
-
‘[’ 500 -eq 500 ‘]’
-
ligands_todo[${queue_no_2}0000${queue_no_3}]=500
-
queue_collection_numbers[${queue_no_2}0000${queue_no_3}]=1
-
tail -n +2 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
mv /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all.tmp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all
-
no_collections_remaining=85
-
no_collections_assigned=15
-
‘[’ 500 -lt 100 ‘]’
-
for queue_no_3 in ‘$(seq 1 ${queues_per_step})’
-
queue_no=1-1-16
-
‘[’ 0 -lt 100 ‘]’
-
‘[’ 85 -eq 0 ‘]’
++ head -n 1 /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all -
next_ligand_collection_and_length='AAAAAD_00000 500 ’
-
next_ligand_collection=AAAAAD_00000
-
‘[’ AAAAAD_00000 = Binary ‘]’
-
echo 'AAAAAD_00000 500 ’
-
no_to_add=
-
‘[’ ‘’ -eq ‘’ ‘]’
prepare-todolists.sh: line 481: [: : integer expression expected -
echo ’ * Warning: Could not get the length of collection AAAAAD_00000. Found value is: . Exiting.’
- Warning: Could not get the length of collection AAAAAD_00000. Found value is: . Exiting.
- exit 1
- clean_up
- cp /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/todo.all …/…/workflow/ligand-collections/todo/todo.all.locked
- mv …/…/workflow/ligand-collections/todo/todo.all.locked …/…/workflow/ligand-collections/todo/todo.all
- rm -r /dev/shm/lichunqiong/VFVS/t/1/prepare-todolists/
- kill ‘#!’
- true
++ error_response_std 287
++ echo ‘Error was trapped’
Error was trapped
++ echo ‘Error in bash script /var/spool/slurmd/job18163064/slurm_script’
Error in bash script /var/spool/slurmd/job18163064/slurm_script
++ echo ‘Error on line 287’
Error on line 287
++ echo ’ *** Final Job Information *** ’
*** Final Job Information ***
++ echo ======================================================================
++ echo
++ echo ‘Starting time:’ Mon Aug 17 11:23:53 CST 2020
Starting time: Mon Aug 17 11:23:53 CST 2020
+++ date
++ echo 'Ending time: ’ Mon Aug 17 11:23:54 CST 2020
Ending time: Mon Aug 17 11:23:54 CST 2020
++ echo
++ exit 1
