ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-12-16T16:21:28+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/164[Hi-C] Hi-C pipeline developpement2022-12-16T16:21:28+01:00Claire Kuchly[Hi-C] Hi-C pipeline developpementImplementation of a new pipeline that takes Hi-C data :
* [ ] Implementation new CasavanG6workflow illumina_HiC_qc
* [ ] Implementation of juicer analyse - must make available the file merge_nodup.txt
* [ ] Implementation of juicer re...Implementation of a new pipeline that takes Hi-C data :
* [ ] Implementation new CasavanG6workflow illumina_HiC_qc
* [ ] Implementation of juicer analyse - must make available the file merge_nodup.txt
* [ ] Implementation of juicer result (file inter.txt) interface with smartyClaire KuchlyClaire Kuchly2020-04-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/162Change the way the number of reads and the base pair for run information are ...2022-12-16T16:21:27+01:00Claire KuchlyChange the way the number of reads and the base pair for run information are calculated in the 10X analysisThe number of reads and base pair are calculed in all fileS ( R1, R2, I) or we want to have just the R1 and R2 informations.The number of reads and base pair are calculed in all fileS ( R1, R2, I) or we want to have just the R1 and R2 informations.Claire KuchlyClaire Kuchly2020-02-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/159On the "Download" page, selecting a whole project without expanding it bugs2022-12-16T16:21:27+01:00Romain ThervilleOn the "Download" page, selecting a whole project without expanding it bugsOn the download page:
https://ng6.toulouse.inra.fr/index.php?id=59
For the project "GutSpodo"
![Screen_Shot_2020-01-17_at_15.49.24](/uploads/3a8a01797b32ac31e6e9628e5a736202/Screen_Shot_2020-01-17_at_15.49.24.png)
"No run neither any a...On the download page:
https://ng6.toulouse.inra.fr/index.php?id=59
For the project "GutSpodo"
![Screen_Shot_2020-01-17_at_15.49.24](/uploads/3a8a01797b32ac31e6e9628e5a736202/Screen_Shot_2020-01-17_at_15.49.24.png)
"No run neither any analysis selected".
When expanding the project, there is no problem.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/152Tests a faire lors d'une mise en prod2020-07-09T14:07:54+02:00Celine NoirotTests a faire lors d'une mise en prodJ'aimerai que l'on liste l'ensemble des element a verifier lors d'une mise en prod pour eviter au mieux les bugs
tester :
* [ ] le download
* [ ] create symblink
* [ ] add project
* [ ] add run
* [ ] add analysis
* [ ] add raw files
* [...J'aimerai que l'on liste l'ensemble des element a verifier lors d'une mise en prod pour eviter au mieux les bugs
tester :
* [ ] le download
* [ ] create symblink
* [ ] add project
* [ ] add run
* [ ] add analysis
* [ ] add raw files
* [ ] vue projet
* [ ] vue run/downloads
* [ ] vue analyses/downloads
* [ ] verifier le application.properties est a jours en fonction des nouveaux dev
* [ ] verifier que le template dans typo3 est a jours en fonction des nouveaux devV4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/149[Sequel2] make new qc pipeline for Sequel2 data2022-12-16T16:21:28+01:00Claire Kuchly[Sequel2] make new qc pipeline for Sequel2 dataRaw data from Sequel2 instrument are different from the raw data of the RSII instrument.
We would create new pipeline :
This pipeline take CCS and CLR data.
This pipeline make available for :
* CCS data : subreads.ccs.bam file
* CL...Raw data from Sequel2 instrument are different from the raw data of the RSII instrument.
We would create new pipeline :
This pipeline take CCS and CLR data.
This pipeline make available for :
* CCS data : subreads.ccs.bam file
* CLR data : all files in output directory
Create of one analysis of run_stat.
? Make available fastq file.
?Claire KuchlyClaire Kuchly2020-01-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/148Add the duplicat rate without alignment in all illumina workflow2022-12-16T16:21:27+01:00Claire KuchlyAdd the duplicat rate without alignment in all illumina workflowAll the pipeline must have the duplication rate of all the samples : it must be a mandatory analysis.
Add to ng6workflow.pyAll the pipeline must have the duplication rate of all the samples : it must be a mandatory analysis.
Add to ng6workflow.pyClaire KuchlyClaire Kuchly2019-12-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/147unable to authenticate with CTD account2020-06-11T17:05:23+02:00Gerald Salingerald.salin@inra.frunable to authenticate with CTD accountAlready happened last week....
this morning, Marine succeeded in login on ng6.
few minutes ago, impossible to login. Tested on my computer : same problem
>update the password (copy/paste from e-SIToul) solved the problem...
after succe...Already happened last week....
this morning, Marine succeeded in login on ng6.
few minutes ago, impossible to login. Tested on my computer : same problem
>update the password (copy/paste from e-SIToul) solved the problem...
after successful login, it seems the password is updated in the database :
$1$xxxxx instead of $2a$10$xxxxxyyyyRomain ThervilleRomain Therville2019-12-10https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/143illumina_10X debug due to test2022-12-16T16:21:27+01:00Audrey Gibertillumina_10X debug due to testDue to test before set up : bug in __init.py__ file of illumina_10X_qc workflowDue to test before set up : bug in __init.py__ file of illumina_10X_qc workflowAudrey GibertAudrey Giberthttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/142manage run 10X with samples with custom index that have to be processed like ...2022-12-16T16:21:27+01:00Claire Kuchlymanage run 10X with samples with custom index that have to be processed like 10X samplesLike SOCSMURIS projects : [mantis 4657](https://genomique.genotoul.fr/Mantis/view.php?id=4657), 10X samples and other samples in the same lane with longranger demultiplexing.
Rigth now, only sample with 10X indexes can be analyse with 1...Like SOCSMURIS projects : [mantis 4657](https://genomique.genotoul.fr/Mantis/view.php?id=4657), 10X samples and other samples in the same lane with longranger demultiplexing.
Rigth now, only sample with 10X indexes can be analyse with 10X illumina qc workflow.Claire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/136Fail to update a user's role on a project2020-06-11T17:08:53+02:00Romain ThervilleFail to update a user's role on a projectOn nG6 (prod), the user 513 was both member and admin on a project.
We should check if another user is concerned, and find why there were 2 rows in 'fe_rights' linking the user to the project.
Kanboard link : https://genomique.genotoul...On nG6 (prod), the user 513 was both member and admin on a project.
We should check if another user is concerned, and find why there were 2 rows in 'fe_rights' linking the user to the project.
Kanboard link : https://genomique.genotoul.fr/kanboard/?controller=TaskViewController&action=show&project_id=18&task_id=1132V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/125Differences between projet's hidden parameter and its run's hidden parameter2020-06-11T17:09:11+02:00Romain ThervilleDifferences between projet's hidden parameter and its run's hidden parameterSometimes (see exemple), hidden projects have visible analyses. Sometimes they do not.
http://ng6-test.toulouse.inra.fr
Project **FlaxCoreCol**
![2019-09-05_172449](/uploads/82d77c3e33ce35a60eb412286fa9d529/2019-09-05_172449.png)
Proj...Sometimes (see exemple), hidden projects have visible analyses. Sometimes they do not.
http://ng6-test.toulouse.inra.fr
Project **FlaxCoreCol**
![2019-09-05_172449](/uploads/82d77c3e33ce35a60eb412286fa9d529/2019-09-05_172449.png)
Project **FlaxCoreCol** Run **FlaxCoreCol-3** (recent)
![2019-09-05_172520](/uploads/bfbc0dea5ea36649347228321404ebd5/2019-09-05_172520.png)
Project **FlaxCoreCol** Run **FlaxCoreCol-4** (older)
![2019-09-05_172649](/uploads/05b5faaf00dc4f2f9d7ef39d0d8caca9/2019-09-05_172649.png)
(At least the icons are missing, but a check in the database is necessary.)V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/123Failed sub job is not catched by the main job2019-09-02T09:34:30+02:00Audrey GibertFailed sub job is not catched by the main jobMy illumina_qc workflow 2823 has a blue :nut_and_bolt: (écrou).
NG6 squeue says there is only the monitoring job alive. In the hidden directory `/work/ng6/jflow/work/illumina_qc/wf002823/.working/e125805cfa`, there is a slurm.status fil...My illumina_qc workflow 2823 has a blue :nut_and_bolt: (écrou).
NG6 squeue says there is only the monitoring job alive. In the hidden directory `/work/ng6/jflow/work/illumina_qc/wf002823/.working/e125805cfa`, there is a slurm.status file:
```bash
/work/ng6/jflow/work/illumina_qc/wf002823/.working/e125805cfa $ ll
total 770K
-rw-r--r-- 1 ng6 NG6 191K Aug 29 22:30 Makeflow
-rw-r--r-- 1 ng6 NG6 366K Aug 29 23:48 Makeflow.makeflowlog
-rw-r--r-- 1 ng6 NG6 17 Aug 29 22:30 slurm.status.7509032
-rwxr-xr-x 1 ng6 NG6 299 Aug 29 22:30 slurm.wrapper
drwxr-xr-x 3 ng6 NG6 4.0K Aug 29 22:30 _Stash
```
but the associated job is cancelled for out of memory
```bash
seff 7509032
Job ID: 7509032
Cluster: genobull
User/Group: ng6/NG6
State: CANCELLED (exit code 0)
Cores: 1
CPU Utilized: 04:26:42
CPU Efficiency: 90.79% of 04:53:46 core-walltime
Job Wall-clock time: 04:53:46
Memory Utilized: 2.93 GB
Memory Efficiency: 100.00% of 2.93 GB
```
-> Erros was not catched, this is a problem!https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/115Login fail if acount has no usergroup2020-01-30T14:21:19+01:00Maxime MannoLogin fail if acount has no usergroup> De : ng6-support-request@groupes.renater.fr <ng6-support-request@groupes.renater.fr> De la part de Maria Bernard
> Envoyé : lundi 12 août 2019 08:37
> À : ng6-support@groupes.renater.fr; William Orlando Burgos Paz <wburgos@agrosavi...> De : ng6-support-request@groupes.renater.fr <ng6-support-request@groupes.renater.fr> De la part de Maria Bernard
> Envoyé : lundi 12 août 2019 08:37
> À : ng6-support@groupes.renater.fr; William Orlando Burgos Paz <wburgos@agrosavia.co>
> Objet : RE: [ng6-support] [HiSeq] IMAGE project - WP 4 Cattle sequence Calidad muestras : datas available
>
> Hello everyone,
>
> I added wburgos user to the IMAGE project, but its login password failed. Could you help him to solve the problem ?
>
> One thing more, the “contact us” link do not point anymore to the ng6 support email address.
>
> Have a good day
**Account NG6** : wburgos
No usergroup (Is NULL in the database)
**Issue** :
If trying to connect with this account, we observe a login failure and it became impossible to login with this account or an other even with the good password.
If we change the usergroup and refresh the nG6 page after the first login failure, everthing goes ok. In fact it seem's that we were login with wburgos but we were blocked by the lack of usegroup.https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/109ftp server architecture2019-08-30T09:27:13+02:00Celine Noirotftp server architectureKeep/generate run/analysis architecture for a project when ftp server will be available.Keep/generate run/analysis architecture for a project when ftp server will be available.V4 - MaintenanceGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/108export metadata2019-08-30T09:27:13+02:00Celine Noirotexport metadataadd a functionality to export all metadata of project, run, analysis.add a functionality to export all metadata of project, run, analysis.V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/105sort order not numeric in contaminationsearch table2019-10-28T15:44:50+01:00Gerald Salingerald.salin@inra.frsort order not numeric in contaminationsearch table![image](/uploads/c5da447e601b3750890b5432d22e18a3/image.png)![image](/uploads/c5da447e601b3750890b5432d22e18a3/image.png)V4 - MaintenanceAudrey GibertAudrey Giberthttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/94[ont_qc] ne pas mettre en dur la compression2019-02-11T17:17:45+01:00Gerald Salingerald.salin@inra.fr[ont_qc] ne pas mettre en dur la compressionself.compression = "gz" dans la fonction process de __init__ du pipelineself.compression = "gz" dans la fonction process de __init__ du pipelinehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/93rsync error in addrawfiles is not reported by the workflow2018-11-13T14:33:47+01:00Audrey Gibertrsync error in addrawfiles is not reported by the workflowexample for workflow 467
logs in 181108_A00318_0024_BHCFFJDSXX_1541824203/JflowOutputs
```
rsync: writefd_unbuffered failed to write 80 bytes to socket [generator]: Broken pipe (32)
rsync error: error in rsync protocol data stream (code...example for workflow 467
logs in 181108_A00318_0024_BHCFFJDSXX_1541824203/JflowOutputs
```
rsync: writefd_unbuffered failed to write 80 bytes to socket [generator]: Broken pipe (32)
rsync error: error in rsync protocol data stream (code 12) at io.c(1532) [generator=3.0.9]
slurmstepd: error: Detected 1 oom-kill event(s) in step 1733125.batch cgroup.
```https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/92AddRawFilesComponent is not displayed on ng6 interface2018-11-08T17:18:58+01:00Audrey GibertAddRawFilesComponent is not displayed on ng6 interface![image](/uploads/ddcac4b0e5f54501039d0cd6b28e5daf/image.png)![image](/uploads/ddcac4b0e5f54501039d0cd6b28e5daf/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/91[methylseq] do not store files for analyses Alignment and Metylation extractor2018-11-06T17:50:17+01:00Gerald Salingerald.salin@inra.fr[methylseq] do not store files for analyses Alignment and Metylation extractorthese data are too huge and for no use after the quality pipeline is overthese data are too huge and for no use after the quality pipeline is overV4 - Maintenance