snakemake_rapidrun_obitools issueshttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues2022-11-25T13:14:56Zhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/13Enhancements2022-11-25T13:14:56ZvmarquesEnhancements- Clean the test configs
- write simple command to relaunch at the ecotag step & other steps in case of crash- Clean the test configs
- write simple command to relaunch at the ecotag step & other steps in case of crashhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/16Warning: the following output files of rule demulti__obisplit were not presen...2022-09-01T08:26:14ZmbrunoWarning: the following output files of rule demulti__obisplit were not present when the DAG was createdProblem with wildcard "sample"Problem with wildcard "sample"mbrunombrunohttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/8donnees test run ffausse2021-06-21T13:49:09Zpeguerinpierre-edouard.guerin@cefe.cnrs.frdonnees test run ffausseil faut mettre à jour les données test car les runs sont toujours faussesil faut mettre à jour les données test car les runs sont toujours fausseshttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/1Error step 2 - merge reads2021-06-21T13:48:27ZvmarquesError step 2 - merge readsIl y a une erreur au tout début de la pipeline.
Au moment de merger les reads en utilisant la commande illuminapaired, les fichiers se créent bien mais l'opération s'arrête puis efface les fichiers car ils seraient 'corrupted'.
Donc l...Il y a une erreur au tout début de la pipeline.
Au moment de merger les reads en utilisant la commande illuminapaired, les fichiers se créent bien mais l'opération s'arrête puis efface les fichiers car ils seraient 'corrupted'.
Donc la pipeline s'arrête.
J'ai essayé en lançant la pipeline globale, puis uniquement l'étape 02_ pour un résultat semblable.
```
Error in rule illuminapairedend:
[Tue Jun 2 12:54:49 2020]
Error in rule illuminapairedend:
[Tue Jun 2 12:54:49 2020]
[Tue Jun 2 12:54:49 2020]
Removing output files of failed job illuminapairedend since they might be corrupted:
01_illuminapairedend/191017_SN234_A_L001_AIMI-148.fastq
```peguerinpierre-edouard.guerin@cefe.cnrs.frpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/6soigner presentation et doc2021-06-21T13:35:08Zpeguerinpierre-edouard.guerin@cefe.cnrs.frsoigner presentation et docS'inspirer de cette présentation
https://github.com/ifremer-bioinformatics/samba
Le wiki est à refaire/mettre à jour entierementS'inspirer de cette présentation
https://github.com/ifremer-bioinformatics/samba
Le wiki est à refaire/mettre à jour entierementhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/11Error running the pipeline2021-03-26T09:47:36ZvmarquesError running the pipelineI have an error while running the pipeline, at the step 15_
Here is the output from the nohup:
```
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
Activating c...I have an error while running the pipeline, at the step 15_
Here is the output from the nohup:
```
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
[Thu Mar 25 05:37:34 2021]
Finished job 6215.
6205 of 6251 steps (99%) done
Select jobs to execute...
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
[Thu Mar 25 05:37:34 2021]
rule taxonomic_assignment:
input: results/14_dereplicate_runs/LaPerouse/teleo/200206_SN6662_A_L001_AIMI-188.uniq.fasta
output: results/15_taxonomic_assignment/LaPerouse/teleo/200206_SN6662_A_L001_AIMI-188.tag.u.fasta
log: logs/15_taxonomic_assignment/LaPerouse/teleo/200206_SN6662_A_L001_AIMI-188.log
jobid: 6214
wildcards: projmarkrun=LaPerouse/teleo/200206_SN6662_A_L001_AIMI-188
threads: 8
[Thu Mar 25 05:37:34 2021]
Finished job 6245.
6206 of 6251 steps (99%) done
[Thu Mar 25 05:37:34 2021]
Finished job 6230.
6207 of 6251 steps (99%) done
Select jobs to execute...
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver.Run Snakemake with --verbose to see the full solver output for debugging the problem.
Select jobs to execute...
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver.Run Snakemake with --verbose to see the full solver output for debugging the problem.
Activating conda environment: /media/vmarques/DATA/working/laperouse/snakemake_rapidrun_obitools/.snakemake/conda/17f3e483
[Thu Mar 25 05:37:35 2021]
Finished job 6235.
6208 of 6251 steps (99%) done
Select jobs to execute...
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver.Run Snakemake with --verbose to see the full solver output for debugging the problem.
[Thu Mar 25 05:37:35 2021]
Finished job 6225.
6209 of 6251 steps (99%) done
Select jobs to execute...
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver.Run Snakemake with --verbose to see the full solver output for debugging the problem.
[Thu Mar 25 05:37:36 2021]
Finished job 6220.
6210 of 6251 steps (99%) done
Select jobs to execute...
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver.Run Snakemake with --verbose to see the full solver output for debugging the problem.
[Thu Mar 25 05:37:36 2021]
Finished job 6240.
6211 of 6251 steps (99%) done
Select jobs to execute...
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver.Run Snakemake with --verbose to see the full solver output for debugging the problem.
[Thu Mar 25 05:37:38 2021]
Finished job 6.
6212 of 6251 steps (99%) done
Select jobs to execute...
Failed to solve scheduling problem with ILP solver. Falling back to greedy solver.Run Snakemake with --verbose to see the full solver output for debugging the problem.
```
I am on a new server at marbechttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/2Error illuminapairedend2021-01-19T11:11:58ZvmarquesError illuminapairedendJ'ai une erreur avec cette pipeline quand je lance l'étape 02_ assembly.
Voici l'erreur:
```
KeyError in line 61 of /media/superdisk/edna/working/laperouse/snakemake_rapidrun_obitools/02_assembly/Snakefile:
'nb_chunk'
File "/media/s...J'ai une erreur avec cette pipeline quand je lance l'étape 02_ assembly.
Voici l'erreur:
```
KeyError in line 61 of /media/superdisk/edna/working/laperouse/snakemake_rapidrun_obitools/02_assembly/Snakefile:
'nb_chunk'
File "/media/superdisk/edna/working/laperouse/snakemake_rapidrun_obitools/02_assembly/Snakefile", line 61, in <module>
```
Ca a l'air d'être lié à ta modification pour couper le fichier et accélérer la performance de cette première étape sous obitools.
Je te met le chemin du dossier où j'ai testé ça:
```
/media/superdisk/edna/working/laperouse/snakemake_rapidrun_obitools
```peguerinpierre-edouard.guerin@cefe.cnrs.frpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/3my first issue2021-01-19T11:11:35ZPichotmy first issuepeguerinpierre-edouard.guerin@cefe.cnrs.frpeguerinpierre-edouard.guerin@cefe.cnrs.frhttps://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/issues/4pas compris2020-10-28T15:40:43Zpeguerinpierre-edouard.guerin@cefe.cnrs.frpas comprisprobprob