no apparent download of the receptor file
Dear Christian,
Welcome back from your holiday. I hope you spent a nice time. I tried to write on the https://gitlab.rlp.net/hpc-jgu-lifescience but somehow it says (the message was recognized as spasm and discarded), and I couldnot post the error there.
As I said in the last issue I keep getting an error and I even tried today after your message. I got the same error, I used version 0.4.16-foss-2021b-Python-3.9.6 and also 0.4.17-foss-2021b-Python-3.9.6, with both I got the same error. somehow the software could not make the pdbqt of the protein I think, because if I tried to run a trail with one of my old proteins it works. also, I tried different proteins from PDB but it is the same error always.
here is the recent bath that I used "/lustre/project/m2_jgu-smitt/Docking/Mona/trail4" and I used version 0.4.17.
here is the error once again
Error in rule prepareReceptor:
jobid: 15
output: /lustre/scratch/m2_jgu-smitt/PDB/receptor/3JXF.pdb
Traceback (most recent call last):
File "/cluster/easybuild/broadwell/software/snakemake/6.10.0-foss-2021b/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 593, in _callback
raise ex
File "/cluster/easybuild/broadwell/software/Python/3.9.6-GCCcore-11.2.0/lib/python3.9/concurrent/futures/thread.py", line 52, in run
result = self.fn(*self.args, **self.kwargs)
File "/cluster/easybuild/broadwell/software/snakemake/6.10.0-foss-2021b/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 579, in cached_or_run
run_func(*args)
File "/cluster/easybuild/broadwell/software/snakemake/6.10.0-foss-2021b/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 2461, in run_wrapper
raise ex
File "/cluster/easybuild/broadwell/software/snakemake/6.10.0-foss-2021b/lib/python3.9/site-packages/snakemake/executors/__init__.py", line 2418, in run_wrapper
run(
File "/cluster/easybuild/broadwell/software/mflow/0.4.17-foss-2021b-Python-3.9.6/workflows/life-science/StructureBasedScreening/workflows/preparation.smk", line 155, in __rule_prepareReceptor
File "/cluster/easybuild/broadwell/software/snakemake/6.10.0-foss-2021b/lib/python3.9/site-packages/snakemake/script.py", line 1371, in script
executor.evaluate()
File "/cluster/easybuild/broadwell/software/snakemake/6.10.0-foss-2021b/lib/python3.9/site-packages/snakemake/script.py", line 381, in evaluate
self.execute_script(fd.name, edit=edit)
File "/cluster/easybuild/broadwell/software/snakemake/6.10.0-foss-2021b/lib/python3.9/site-packages/snakemake/script.py", line 582, in execute_script
self._execute_cmd(
File "/cluster/easybuild/broadwell/software/snakemake/6.10.0-foss-2021b/lib/python3.9/site-packages/snakemake/script.py", line 414, in _execute_cmd
return shell(
File "/cluster/easybuild/broadwell/software/snakemake/6.10.0-foss-2021b/lib/python3.9/site-packages/snakemake/shell.py", line 266, in __new__
raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'module purge && module load bio/Biopython/1.75-foss-2019b-Python-3.7.4; set -euo pipefail; /cluster/easybuild/broadwell/software/Python/3.9.6-GCCcore-11.2.0/bin/python3.9 /lustre/miifs01/project/m2_jgu-smitt/Docking/Mona/trail4/.snakemake/scripts/tmp5vls93te.prepareReceptor.py' returned non-zero exit status 127.
It would really be great if you have a look at it. Thank you so much in advance
cordial regards
Mona