* Extracting JH/JHEADB.tar to /dev/shm/cgorgulla/

Bugs
#1

Stopped a run and tried to analyze the data.
Installed VFTools and added them to path.
Used:
vfvs_pp_ranking_all.sh …/…/output-files/complete/ 2 meta_collection

I got some ranked results. But it seemed wrong. Then I removed the incomplete results and came no ranked results.

The terminal output is attached as rank.log

It looks like the script is trying to tar in your temporary folder and fails.

  • Extracting JH/JHEAAE.tar to /dev/shm/cgorgulla/…

Is this some bug that needs to be fixed or I need to change some parameter?

#2

Dear Evangelos,

welcome to the forum.

Did you run the tutorial, or your own virtual screening?

Why did the result seemed wrong?

If you stopped the a run, then it is normal that intermediate results of ligand collections which are not yet completed are stored in the “incomplete” folder. If you remove that folder, and if not collections have yet been fully completed, naturally nothing is left, and thus it is expected that in this you do not see any results.

Best,
Christoph

#3

Hi Christoph,
I run the tutorial2 preparation from Scratch.
But I selected a large tranche with millions of compounds that took quite sometime.
So I stopped the run.
Then I tried
vfvs_pp_ranking_all.sh …/…/output-files/complete/ 2 meta_collection

should I redirect the tar to some of my folders somehow?

Recently I finished with a smaller tranche that should have completed without stopping and I will test it. But does it mean that I cannot stop and analyze a run!?!

#4

ok I repeated [ep202@login05 pp]$ vfvs_pp_ranking_all.sh …/output-files/complete/ 2 meta_collection

with a complete run and I still get error messages. I also do not understand why the tar files should be extracted in /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926042166145
and not extracted in my folders. Is there some bug or the way I installed VFTools?

Here is the complete terminal output:

[ep202@login05 ranking]$
[ep202@login05 ranking]$ vfvs_pp_ranking_all.sh …/…/output-files/complete/ 2 meta_collection

  • Starting to prepare the firstposes of docking-scenario qvina02_rigid_receptor1
    [1]+ Running vfvs_pp_ranking_single.sh $input_folder/$folder ${library_format} &
  • Starting to prepare the firstposes of docking-scenario smina_rigid_receptor1
         Creating a single file with all first poses

         Creating a single file with all first poses

  • Extracting JH/JHEAAE.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926042166145

  • Adding file …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEAAE.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEAAE.tar/*: Not a directory

  • Extracting JH/JHEAAE.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926078808240

  • Adding file …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEAAE.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEAAE.tar/*: Not a directory

  • Extracting JH/JHEAAF.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926042166145

  • Adding file …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEAAF.tar/* to firstposes.all

  • Extracting JH/JHEAAF.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926078808240

  • Adding file …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEAAF.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEAAF.tar/*: Not a directory

  • Extracting JH/JHEADB.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926042166145

  • Adding file …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEADB.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEAAF.tar/*: Not a directory

  • Extracting JH/JHEADB.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926078808240
    gzip: …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEADB.tar/*: Not a directory

  • Adding file …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEADB.tar/* to firstposes.all

  • Extracting JH/JHEBBD.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926042166145

  • Adding file …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEBBD.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEADB.tar/*: Not a directory

  • Extracting JH/JHEBBD.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926078808240
    gzip: …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEBBD.tar/*: Not a directory

  • Adding file …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEBBD.tar/* to firstposes.all

  • Extracting JH/JHEBBG.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926042166145

  • Adding file …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEBBG.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEBBG.tar/*: Not a directory

  • Extracting JH/JHEBCC.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926042166145

  • Adding file …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEBCC.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEBBD.tar/*: Not a directory

  • Extracting JH/JHEBBG.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926078808240

  • Adding file …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEBBG.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEBCC.tar/*: Not a directory

  • Extracting JH/JHEBCF.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926042166145

  • Adding file …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEBCF.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEBBG.tar/: Not a directory
    gzip: …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEBCF.tar/    : Not a directory

  • Extracting JH/JHEBCG.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926042166145

  • Extracting JH/JHEBCC.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926078808240

  • Adding file …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEBCC.tar/* to firstposes.all

  • Adding file …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEBCG.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//qvina02_rigid_receptor1/summaries/JH/JHEBCG.tar/: Not a directory
    gzip: …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEBCC.tar/    : Not a directory

  • Cleaning the temporary files *

  • Extracting JH/JHEBCF.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926078808240

  • All first poses have been united in the file firstposes.all

  • Adding file …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEBCF.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEBCF.tar/*: Not a directory

  • Extracting JH/JHEBCG.tar to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1615400926078808240

  • Adding file …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEBCG.tar/* to firstposes.all
    gzip: …/…/…/output-files/complete//smina_rigid_receptor1/summaries/JH/JHEBCG.tar/*: Not a directory

  • Cleaning the temporary files *

  • All first poses have been united in the file firstposes.all

         Creating a single file with all first poses

ls: cannot access …/…/…/output-files/incomplete//qvina02_rigid_receptor1/summaries: No such file or directory

  • Cleaning the temporary files *

  • All first poses have been united in the file firstposes.all.incomplete

         Creating a single file with all first poses

ls: cannot access …/…/…/output-files/incomplete//smina_rigid_receptor1/summaries: No such file or directory

  • Cleaning the temporary files *

  • All first poses have been united in the file firstposes.all.incomplete
    cat: firstposes.all.incomplete: No such file or directory
    Error was trapped which is a nonstandard error.
    Error in bash script vfvs_pp_ranking_single.sh
    Error on line 54

cat: firstposes.all.incomplete: No such file or directory
Error was trapped which is a nonstandard error.
Error in bash script vfvs_pp_ranking_single.sh
Error on line 54

  • The first-poses of all docking runs have been prepared

[ep202@login05 ranking]$

#5

Hi,
I get the same issue, something like this:

  • Extracting IA/IACBBE to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1626192226344828915

tar: …/…/…/output-files/complete//vina_files/summaries/IA/IACBBE: Cannot read: Is a directory

tar: At beginning of tape, quitting now

tar: Error is not recoverable: exiting now

ls: cannot access ‘/dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1626192226344828915/IACBBE’: No such file or directory

rm: cannot remove ‘/dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1626192226344828915/IACBBE/’: No such file or directory

  • Extracting IA/IACBCE to /dev/shm/cgorgulla/vfvs_pp_firstposes_all_unite_1626192226344828915

Were you able to figure it out?

Janujan

#6

Hi Janujan,
I believe submitting by sbatch

sbatch -p short -o rank_report.txt -e rank_errorreport.txt -c 4 -t 12:00:00 vfvs_pp_ranking_all.sh …/…/output-files/complete/ 1 meta_tranche

it has worked although I am not sure how/why