workflows issueshttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues2022-12-15T13:01:46+01:00https://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/102Add minimal sample2022-12-15T13:01:46+01:00Max RiedlAdd minimal sampleCreate a minimal sample containing config and gpf file.Create a minimal sample containing config and gpf file.Meesters, ChristianMax RiedlMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/119add snakemake-wrapper to mflow2022-12-15T13:32:22+01:00Meesters, Christianadd snakemake-wrapper to mflowneed to add snakemake-wrapper to easybuildneed to add snakemake-wrapper to easybuild0.5Meesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/47annotation file ammendmends2021-03-21T21:39:26+01:00Meesters, Christianannotation file ammendmends- mention that it performs structure based screening with VinaLC
- mention other features (e.g. modeller switches and how to obtain them)
- mention how to get a sample configuration
needs "constant" update- mention that it performs structure based screening with VinaLC
- mention other features (e.g. modeller switches and how to obtain them)
- mention how to get a sample configuration
needs "constant" updateversion 0.1Max RiedlMax Riedlhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/121ask Johannes about envmodules: in workflows2023-02-09T11:23:09+01:00Meesters, Christianask Johannes about envmodules: in workflowsA decision needs to be reached:
`
envmodules:
config["XXX"]
`
in workflows
or
`
envmodules:
'../file'
`
which would require a code change in snakemakeA decision needs to be reached:
`
envmodules:
config["XXX"]
`
in workflows
or
`
envmodules:
'../file'
`
which would require a code change in snakemakesnakemake-update / hpc-conformant workflowsMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/84avoid doubled write after splitting2022-01-04T17:50:08+01:00Meesters, Christianavoid doubled write after splittingVersion 0.4.7Max RiedlMax Riedlhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/18Check for Trinity_Home and other(?) variables2021-02-02T10:11:02+01:00Christian OttingCheck for Trinity_Home and other(?) variablessee titlesee titleChristian OttingChristian Ottinghttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/75cluster warns of not using "mem or mem-per-cpu" in job start also it is defin...2021-04-30T12:31:35+02:00Christian Ottingcluster warns of not using "mem or mem-per-cpu" in job start also it is defined in cluster config![image](/uploads/7c037ecbad591e2f67f69f0af13b49fd/image.png)![image](/uploads/7c037ecbad591e2f67f69f0af13b49fd/image.png)Meesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/55enable plotting of dags by mflow2021-02-11T09:28:12+01:00Meesters, Christianenable plotting of dags by mflowonly on login nodesonly on login nodesversion 0.3Meesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/114Error in workflow when ZINC15 natural-products is used2022-10-04T14:38:27+02:00Mona DawoodError in workflow when ZINC15 natural-products is usedDear Christian,
I used the workflow for Screening of natural-products from ZINC15 but I get an error.
here is the bath of my folder "/lustre/project/m2_jgu-smitt\Docking\Mona\DSC7
I used version 0\.4.16-foss-2021b-Python-3.9.6
**Here is...Dear Christian,
I used the workflow for Screening of natural-products from ZINC15 but I get an error.
here is the bath of my folder "/lustre/project/m2_jgu-smitt\Docking\Mona\DSC7
I used version 0\.4.16-foss-2021b-Python-3.9.6
**Here is the error**
Submitted job 45 with external jobid '11514822'.
[Tue Sep 20 21:58:26 2022]
Error in rule docking:
jobid: 45
output: /lustre/project/m2_jgu-smitt/Docking/Mona/DSC7/result/output/DSC3/subsets/DSC3.txt_ZINC_subsets_natural-products_0.txt.pdbqt.gz
shell:
(mkdir -p /lustre/project/m2_jgu-smitt/Docking/Mona/DSC7/result/output/DSC3/subsets
cd /lustre/project/m2_jgu-smitt/Docking/Mona/DSC7/result/output/DSC3/subsets
cp /lustre/project/m2_jgu-smitt/Docking/Mona/DSC7/result/receptor/DSC3.txt .
cp /lustre/project/m2_jgu-smitt/Docking/Mona/DSC7/result/grid/DSC3_grid.txt .
cp /lustre/project/m2_jgu-smitt/Docking/Mona/DSC7/result/library/ZINC_subsets_natural-products_0.txt .
space=$(grep 'spacing' /lustre/project/m2_jgu-smitt/Docking/Mona/DSC7/GRID/DSC3.gpf | cut -f2 -d' ')
srun vinalc --recList DSC3.txt --ligList ZINC_subsets_natural-products_0.txt --geoList DSC3_grid.txt --granularity $space
cd -)
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
cluster_jobid: 11514822
Error executing rule docking on cluster (jobid: 45, external: 11514822, jobscript: /lustre/miifs01/project/m2_jgu-smitt/Docking/Mona/DSC7/.snakemake/tmp.37jm2qq0/snakejob.docking.45.sh). For error details see the cluster log and the log files of the involved rule(s).
Thank you so much in advance
cordial regards
Monahttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/97files in sandbox need cleanup2022-01-06T16:02:22+01:00Meesters, Christianfiles in sandbox need cleanupsee titlesee titleMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/67Handle Logs ins snakemake for portability of statistical analysis2021-04-30T09:33:54+02:00Christian OttingHandle Logs ins snakemake for portability of statistical analysisChristian OttingChristian Ottinghttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/122how to mix conda and envmodules?2023-02-09T11:23:27+01:00Meesters, Christianhow to mix conda and envmodules?question to Johannes?question to Johannes?snakemake-update / hpc-conformant workflowsMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/123localrules: arbitrarily in every workflow?2023-02-09T11:25:09+01:00Meesters, Christianlocalrules: arbitrarily in every workflow?May all plotting rules and similar declared "local"? It is not necessary to submit a job per plot, or?May all plotting rules and similar declared "local"? It is not necessary to submit a job per plot, or?snakemake-update / hpc-conformant workflowsMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/65Merging a cluster-config should overwrite existing rules2022-01-04T22:09:35+01:00Christian OttingMerging a cluster-config should overwrite existing rulesIt is no use for me if I can't use my cluster-config, also maybe do not merge with --clusterconfig and only do so with the --merge-clusterconfig command.It is no use for me if I can't use my cluster-config, also maybe do not merge with --clusterconfig and only do so with the --merge-clusterconfig command.Meesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/120mflow exec to snakemake >=7.19.12023-02-09T11:21:23+01:00Meesters, Christianmflow exec to snakemake >=7.19.1Currently mflow executes snakemake with a json profile and the plugin in mind - now snakemake needs native support of mflow, including all new flags.Currently mflow executes snakemake with a json profile and the plugin in mind - now snakemake needs native support of mflow, including all new flags.snakemake-update / hpc-conformant workflowsMeesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/95New error in workflow version 0.4.72022-02-09T07:52:05+01:00Mona DawoodNew error in workflow version 0.4.7Hello, I used the new version of the workflow and I got the folloing error:
Error in rule docking:
jobid: 110
output: /lustre/project/m2_jgu-smitt/Docking/Mona/m23/result/output/1ITQ/FG/1ITQ.txt_ZINC_FG_FGABRN_0.txt.pdbqt.gz
...Hello, I used the new version of the workflow and I got the folloing error:
Error in rule docking:
jobid: 110
output: /lustre/project/m2_jgu-smitt/Docking/Mona/m23/result/output/1ITQ/FG/1ITQ.txt_ZINC_FG_FGABRN_0.txt.pdbqt.gz
shell:
(
mkdir -p /lustre/project/m2_jgu-smitt/Docking/Mona/m23/result/output/1ITQ/FG
cd /lustre/project/m2_jgu-smitt/Docking/Mona/m23/result/output/1ITQ/FG
cp /lustre/project/m2_jgu-smitt/Docking/Mona/m23/result/receptor/1ITQ.txt .
cp /lustre/project/m2_jgu-smitt/Docking/Mona/m23/result/grid/1ITQ_grid.txt .
cp /lustre/project/m2_jgu-smitt/Docking/Mona/m23/result/library/ZINC_FG_FGABRN_0.txt .
space=$(grep 'spacing' /lustre/project/m2_jgu-smitt/Docking/Mona/m23/GRID/1ITQ.gpf | cut -f2 -d' ')
mpirun vinalc --recList 1ITQ.txt --ligList ZINC_FG_FGABRN_0.txt --geoList 1ITQ_grid.txt --granularity $space
cd -
)
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
cluster_jobid: 10212912
Error executing rule docking on cluster (jobid: 110, external: 10212912, jobscript: /lustre/miifs01/project/m2_jgu-smitt/Docking/Mona/m23/.snakemake/tmp.naye6nqc/snakejob.docking.110.sh). For error details see the cluster log and the log files of the involved rule(s).
Thank you so muchhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/52ProtTrans: pub-ready plots2021-02-11T09:21:51+01:00Meesters, ChristianProtTrans: pub-ready plotsNot an issue, rather quickly forgotten meta-info:
convert Michal's R-script according to https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html
> In the R script, an S4 object named snakemake analogous to the Python case abov...Not an issue, rather quickly forgotten meta-info:
convert Michal's R-script according to https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html
> In the R script, an S4 object named snakemake analogous to the Python case above is available and allows access to input and output files and other parameters. Here the syntax follows that of S4 classes with attributes that are R lists, e.g. we can access the first input file with snakemake@input[[1]] (note that the first file does not have index 0 here, because R starts counting from 1). Named input and output files can be accessed in the same way, by just providing the name instead of an index, e.g. snakemake@input[["myfile"]].version 0.2Christian OttingChristian Ottinghttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/19provide log directory via tag2021-02-25T09:51:06+01:00Christian Ottingprovide log directory via tag-l --log /path/for/logs-l --log /path/for/logsversion 0.3Meesters, ChristianMeesters, Christianhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/73Remove LOG workaround when #67 is fixed - CANT PUBLISH BEFORE2021-04-30T09:34:50+02:00Christian OttingRemove LOG workaround when #67 is fixed - CANT PUBLISH BEFOREWhile #67 is not fixed logs will be gathered manually for report.smk such that it works on MOGONWhile #67 is not fixed logs will be gathered manually for report.smk such that it works on MOGONhttps://gitlab.rlp.net/hpc-jgu-lifescience/workflows/-/issues/118retrieve configs from worklfow folder2022-12-15T13:23:00+01:00Meesters, Christianretrieve configs from worklfow folderget the _whole_ config from a workflow folder instead of the per-workflow yaml file, onlyget the _whole_ config from a workflow folder instead of the per-workflow yaml file, only0.5Meesters, ChristianMeesters, Christian