ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2024-03-11T10:40:52+01:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/249remove archive option for download2024-03-11T10:40:52+01:00Gerald Salingerald.salin@inra.frremove archive option for downloaddue to url errors. Not so much used (~80 in 3 years, can be replaced by symbolic links or direct download from the downlaod areas of analysis)due to url errors. Not so much used (~80 in 3 years, can be replaced by symbolic links or direct download from the downlaod areas of analysis)V3.4.5Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/248allow to run jflow on genobioinfo2024-01-24T09:46:01+01:00Gerald Salingerald.salin@inra.frallow to run jflow on genobioinfogenologin is out, try to run jflow on genobioinfo :
- copy ng6-slurm:/usr/local/bioinfo/src/nG6 (ln de ng6-V3.4.4) from production to genobioinfo:/work/project/PlaGe/sbsuser/ng6-V3.4.4
- create /work/project/PlaGe/sbsuser/jflowSoftware ...genologin is out, try to run jflow on genobioinfo :
- copy ng6-slurm:/usr/local/bioinfo/src/nG6 (ln de ng6-V3.4.4) from production to genobioinfo:/work/project/PlaGe/sbsuser/ng6-V3.4.4
- create /work/project/PlaGe/sbsuser/jflowSoftware to store software needed by jflow and workflows
- compile/install last version of cctools (7.7). Install it in genobioinfo:/work/project/PlaGe/sbsuser/cctools (first compiled on esitoul-rocky-dev). The current version used on genologin fails on compiling on new infrastructure and compiled version copied on genobioinfo fails to run.
- create ng6 database on esitoul-rocky-dev from a backup (/save/ng6/backup_db)
- update /work/project/PlaGe/sbsuser/ng6-V3.4.4/application.properties for output folders (use /work/user/ng6/xxx)
run addrun workflow on test data failed with python3.6, at pickle.load stage....different tests showed the jflow code only works with python 3.4. Hard to find source code and compile it....I copied if from ng6-slurm scp /tools/python/3.4.3 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser and using it, the pipeline succeeded
`/work/project/PlaGe/sbsuser/Python-3.4.3/bin/python3.4 /work/project/PlaGe/sbsuser/ng6-V3.4.4/bin/ng6_cli.py addrun --project-name REPDEV --name GGTestPython3.4 --description makeflow7 --admin-login CTD --date 16/11/2023 --data-nature gDNA --sequencer aviti --species bos --type lane1 --sample type=se sample-id='V' read1='workflows/illumina_qc/data/casava_directory_test/Project_Demo_project/Sample_Demo/Demo_NoIndex_L001_R2_001.fastq.gz'`
To run illumina_qc workflow, we need specific version of some software and to update application.properties with new software location (but with same version) in /work/project/PlaGe/sbsuser/ng6-V3.4.4
Depending on software, a compilation was required or a simple copy worked :
```
1038 scp -r /usr/local/bioinfo/src/FastQC/FastQC_v0.11.2 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1040 scp -r /usr/local/bioinfo/src/fastq_illumina_filter/fastq_illumina_filter-0.1.tar.gz sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1045 scp -r /usr/local/bioinfo/src/FLASH/FLASH-1.2.6 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1047 scp -r /usr/local/bioinfo/src/FASTX-Toolkit/fastx_toolkit-0.0.14 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1049 scp -r /usr/local/bioinfo/src/STAR-2.7.10a_alpha_220314 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1050 scp -r /usr/local/bioinfo/src/STAR/STAR-2.7.10a_alpha_220314 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1059 scp -r /usr/local/bioinfo/src/STAR/STAR-2.7.10a_alpha_220314 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1060 scp -r /tools/java/jre1.8.0_45 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1062 scp -r /usr/local/bioinfo/src/TrimGalore/0.4.5.zip sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1063 scp -r /usr/local/bioinfo/src/Bismark/bismark_v0.19.0.tar.gz sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1064 scp -r /usr/local/bioinfo/src/bowtie/bowtie2-2.3.4.1-linux-x86_64.zip sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1069 scp -r /usr/local/bioinfo/src/cctools/cctools-6.0.14-x86_64-redhat7 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1079 scp -r /usr/local/bioinfo/src/picard-tools/picard-2.18.2 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
1084 scp -r /tools/R/R-3.4.3 sbsuser@genobioinfo.toulouse.inrae.fr:/work/project/PlaGe/sbsuser/jflowSoftware/
```
I didn't managed to compile STAR, nor R-3.4.3
- stop here for STAR
- I used last version of R R-4.3.2 > compilation OK > test OK...but had to add 'Rpath = /work/project/PlaGe/sbsuser/jflowSoftware/R-4.3.2/bin/' and modify inserstssizes.py to modify PATH (Rscript is called by picard for CollectMetrics component to generate pdf file)V3.4.4Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/246allow to create symlinks on genobioinfo2023-11-14T05:38:23+01:00Gerald Salingerald.salin@inra.frallow to create symlinks on genobioinfoallow to choose the server where to create the cymbolic links (genologin pr genobioinfo)allow to choose the server where to create the cymbolic links (genologin pr genobioinfo)V3.4.3Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/245store ngl-bi analysis code in ng6 run2024-03-11T10:40:45+01:00Gerald Salingerald.salin@inra.frstore ngl-bi analysis code in ng6 runto allow the request for raw data path and update reasets path in NGL-Bi
in run table, add a new column ngl-bi-runcode-and-lane
check how to populate it from jflowto allow the request for raw data path and update reasets path in NGL-Bi
in run table, add a new column ngl-bi-runcode-and-lane
check how to populate it from jflowV3.4.5Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/244Purge management - In the "mail obsolete project" tab, the "nb run stored" an...2023-05-02T11:07:22+02:00Romain ThervillePurge management - In the "mail obsolete project" tab, the "nb run stored" and "project category" columns are wrongTo test, select the space "longterm_get".
- nb run stored = 1 instead of 2 for BETAGALL
- "project category" should be "finished" only when all data from the project has already been purgedTo test, select the space "longterm_get".
- nb run stored = 1 instead of 2 for BETAGALL
- "project category" should be "finished" only when all data from the project has already been purgedV3.4.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/242Infinite loading when deleting a run2022-12-16T16:20:51+01:00Romain ThervilleInfinite loading when deleting a runTests ongoing for the following:
Project SATI-1 (id 2017), Run SATI-1 (id 20284)
Project -> Select a run -> Delete -> ng6 credentialsTests ongoing for the following:
Project SATI-1 (id 2017), Run SATI-1 (id 20284)
Project -> Select a run -> Delete -> ng6 credentialsRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/241Jflow and SSL error2022-11-18T16:26:19+01:00Romain ThervilleJflow and SSL errorhttps://ng6.toulouse.inra.fr/jflow -> Code 500
```
Proxy Error
The proxy server could not handle the request GET /jflow.
Reason: Error during SSL Handshake with remote server
```https://ng6.toulouse.inra.fr/jflow -> Code 500
```
Proxy Error
The proxy server could not handle the request GET /jflow.
Reason: Error during SSL Handshake with remote server
```Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/240Purge process, some errors and suspected problems2023-10-04T11:13:50+02:00Romain ThervillePurge process, some errors and suspected problemsSure problem:
- Some projects with an active demand still appear in the "purgeable" list.
Maybe a problem:
- Make sure we don't check ".log.gz" files when looking for purgeable analyzes.
- Make sure the "purgeable" projects really do ha...Sure problem:
- Some projects with an active demand still appear in the "purgeable" list.
Maybe a problem:
- Make sure we don't check ".log.gz" files when looking for purgeable analyzes.
- Make sure the "purgeable" projects really do have expired files in their runs/analyzes.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/239error displaying workflow status if too much runs present2022-11-07T16:33:55+01:00Gerald Salingerald.salin@inra.frerror displaying workflow status if too much runs presenterror in web developper interface of the browser : Request-URI Too Long The requested URL's length exceeds the capacity limit for this server.error in web developper interface of the browser : Request-URI Too Long The requested URL's length exceeds the capacity limit for this server.V3.4.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/238add user not working2022-10-14T15:36:00+02:00Gerald Salingerald.salin@inra.fradd user not workingthe user receives an email telling him he can access a project, but it is not right.
the record is not stored in database.
due to the ng6 extension install in typo3 which asks for a primary key > uid was selected, but it is not auto in...the user receives an email telling him he can access a project, but it is not right.
the record is not stored in database.
due to the ng6 extension install in typo3 which asks for a primary key > uid was selected, but it is not auto incremented
Apply solved the problem : ALTER TABLE `fe_rights`MODIFY `uid` int(11) NOT NULL AUTO_INCREMENT;V3.4.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/237readstat image visualization not displayed when samples are compared2022-10-11T13:27:10+02:00Gerald Salingerald.salin@inra.frreadstat image visualization not displayed when samples are comparedV3.4.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/236structure of ng6 extension tables changes at each new deployment2022-10-10T11:15:44+02:00Gerald Salingerald.salin@inra.frstructure of ng6 extension tables changes at each new deploymentdescription field of tx_ng6_run chnages from text to VARCHAR(255) as well as primary(uid) of table fe_rights.
it seems ext_tables.php fil is executed when deplying a new version. This file was never updatedescription field of tx_ng6_run chnages from text to VARCHAR(255) as well as primary(uid) of table fe_rights.
it seems ext_tables.php fil is executed when deplying a new version. This file was never updateV3.4.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/235Hide and unhide a run2022-10-07T17:07:32+02:00Jules SabbanHide and unhide a runWhen I hide a run : every analysis bellow are hidden too
When I unhide a run : every analysis bellow are unhidden too
The behavouir we want when I unhide a run : nothing at analysis level OR unhide every analysis except 'Log files' ...When I hide a run : every analysis bellow are hidden too
When I unhide a run : every analysis bellow are unhidden too
The behavouir we want when I unhide a run : nothing at analysis level OR unhide every analysis except 'Log files' analysis.
The behavouir we want when I hide a run : nothing at analysis level OR same as now (to be discuss).
---
At analysis level, everything works well.
When I hide an analysis : the run above is no hidden : OK !
When I unhide an analysis : the run above is not unhidden : OK !V3.4Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/234add logging through typo3 in ng6 extension2022-09-27T18:26:23+02:00Gerald Salingerald.salin@inra.fradd logging through typo3 in ng6 extensiondo not use error_log anymore
look at ng6.php code to implement loggingdo not use error_log anymore
look at ng6.php code to implement loggingV3.4https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/233add support to typo3 v112022-10-07T17:07:41+02:00Gerald Salingerald.salin@inra.fradd support to typo3 v11typo3 v10 is maintained until beginning of 2023.
typo3 V11 is maintained until october 2024.
https://typo3.org/cms/roadmap/maintenance-releases
update nG6 extension source code to be compatible with typo3 V11typo3 v10 is maintained until beginning of 2023.
typo3 V11 is maintained until october 2024.
https://typo3.org/cms/roadmap/maintenance-releases
update nG6 extension source code to be compatible with typo3 V11V3.4Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/232download symlink finished without error, but no data is available2022-10-06T21:29:54+02:00Gerald Salingerald.salin@inra.frdownload symlink finished without error, but no data is availablein case the analyze name contains some special characters, the output folder and/or the symbolic links can't be created :
mkdir -p -m 755 /outputFolder/Analyse_Demultiplexed_subreads_**(**bam**)**.XXX ;
ln -s /inputFolder/file.xml /outp...in case the analyze name contains some special characters, the output folder and/or the symbolic links can't be created :
mkdir -p -m 755 /outputFolder/Analyse_Demultiplexed_subreads_**(**bam**)**.XXX ;
ln -s /inputFolder/file.xml /outputFolder/file.xml;
avoid these characters in the names of run/analysis/projects or replace them when creating the symlinksV3.4https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/231The "addfiles" workflow changes the rights to the target directory to root:root2022-09-27T14:58:40+02:00Romain ThervilleThe "addfiles" workflow changes the rights to the target directory to root:rootThis happened on august 26th, 2022 (09:18 am)
**Target directory :** /data_seqoccin/analyze/99200b167
```
ng6@genologin1 /save/ng6/data_seqoccin/analyze $ stat 99200b167
File: ‘99200b167’
Size: 4096 Blocks: 1 IO ...This happened on august 26th, 2022 (09:18 am)
**Target directory :** /data_seqoccin/analyze/99200b167
```
ng6@genologin1 /save/ng6/data_seqoccin/analyze $ stat 99200b167
File: ‘99200b167’
Size: 4096 Blocks: 1 IO Block: 262144 directory
Device: 3ah/58d Inode: 297274441 Links: 2
Access: (0751/drwxr-x--x) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2022-08-29 00:31:23.219591326 +0200
Modify: 2022-08-26 09:18:24.227200000 +0200
Change: 2022-08-26 09:18:52.285248179 +0200
Birth: -
```
**Logs :** /work/ng6/jflow/ng6.log
```
08-26 09:18 Analysis.sync DEBUG Synchronizing analysis id=80043 from /work/ng6/jflow/work/data_seqoccin/analyze/99200b167 to /save/ng6//data_seqoccin/analyze/99200b167
08-26 09:18 Analysis.sync DEBUG rsync -avh --remove-sent-files /work/ng6/jflow/work/data_seqoccin/analyze/99200b167/ /save/ng6//data_seqoccin/analyze/99200b167
08-26 09:18 Analysis.sync DEBUG Synchronization done for analysis id=80043(retcode=0)
```
**Workflow :** /work/ng6/jflow/work/addfiles/wf005296
**Tests :**
I tried launching addfiles from the ng6 website, the jflow directory AND the file transfered where both "root:root". It seems the workflow is launched by the user root from the web interface...V3.3Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/230[contaminationSearch] Bwa mem configuration causes some misunderstandings in ...2022-12-16T16:21:27+01:00Claire Kuchly[contaminationSearch] Bwa mem configuration causes some misunderstandings in the calculation of the contamination and explodes the CPU quotat of ng6After several month of bwa meme use for calculation of contamination rate, it appears several problems :
- the calcul of contamination rate is not adapted for what we want to see.
- after a run of NovaSeq we see an large increase of ng...After several month of bwa meme use for calculation of contamination rate, it appears several problems :
- the calcul of contamination rate is not adapted for what we want to see.
- after a run of NovaSeq we see an large increase of ng6 cPU quota due to the parameters used for launched bwa mem analyzis.Claire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/229The project name 'xxx' does not exists ->Erreur de handshake SSL lors de la c...2022-10-06T18:55:47+02:00Romain ThervilleThe project name 'xxx' does not exists ->Erreur de handshake SSL lors de la connexion à la BDDPlus d'informations dans le mantis:
https://genomique.genotoul.fr/Mantis/view.php?id=5221#c18361Plus d'informations dans le mantis:
https://genomique.genotoul.fr/Mantis/view.php?id=5221#c18361V3.4https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/228Using addanalysis on a run unhides it.2022-06-16T16:54:26+02:00Romain ThervilleUsing addanalysis on a run unhides it.(This explains a lot. How can a run be visible if no one uses "unhide" in the ng6 http logs?)
This can definitely be tested easily, but I'll ask Jules if I need an exemple.(This explains a lot. How can a run be visible if no one uses "unhide" in the ng6 http logs?)
This can definitely be tested easily, but I'll ask Jules if I need an exemple.V3.3Romain ThervilleRomain Therville