ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2018-08-02T13:11:05+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/30RNAseq analysis2018-08-02T13:11:05+02:00Audrey GibertRNAseq analysisBug in the workflow illumina_rnaseq when the annotation file is added
RSeQC is involved, and the inner_distance.py even moreBug in the workflow illumina_rnaseq when the annotation file is added
RSeQC is involved, and the inner_distance.py even morehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/83copy to clipboard from download windows does not work2020-06-11T17:09:25+02:00Gerald Salingerald.salin@inra.frcopy to clipboard from download windows does not work![image](/uploads/6eaf4f5c375ebc0365c6f3bcb265ad13/image.png)
no errors, no action.
ZeroClipBoard.min.js was added from jflow project (not yet commited ni ng6), but clicking on the button doesn't copy the text to the clipboard.
maybe w...![image](/uploads/6eaf4f5c375ebc0365c6f3bcb265ad13/image.png)
no errors, no action.
ZeroClipBoard.min.js was added from jflow project (not yet commited ni ng6), but clicking on the button doesn't copy the text to the clipboard.
maybe we have to upgrade the ZeroClipBoard.min.js file (3 yers old)Romain ThervilleRomain Thervillehttps://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/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/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/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/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/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/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/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/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/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/166Infinite loop when trying to expand the 1QELD project in the download page2022-12-16T16:21:28+01:00Romain ThervilleInfinite loop when trying to expand the 1QELD project in the download pageWhen logged as CTD, on the download page, there is an infinite loop trying to call the AJAX "raw_data_description".
The project doesn't expand, the page is not stuck, but this results in a lot a pointless calls.
Screenshot below:
![scr...When logged as CTD, on the download page, there is an infinite loop trying to call the AJAX "raw_data_description".
The project doesn't expand, the page is not stuck, but this results in a lot a pointless calls.
Screenshot below:
![screenshot_bug_nG6_1QELD](/uploads/8c59366a852bc9f4616a3a18720fe205/screenshot_bug_nG6_1QELD.png)Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/175In the web interface, the addAnalysis "Run" button doesn't do anything2020-06-11T16:51:47+02:00Romain ThervilleIn the web interface, the addAnalysis "Run" button doesn't do anythingThis happens on nG6 and nG6-test.
Nothing in the the browser's "network" and "console" debug tabs.This happens on nG6 and nG6-test.
Nothing in the the browser's "network" and "console" debug tabs.V3.2.7Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/180Analysis sort by data in project view2020-05-05T14:40:13+02:00Celine NoirotAnalysis sort by data in project viewUnable to sort project analysis by date
![image](/uploads/f37bbc5558f1d7655864dd3a3ef086cb/image.png)Unable to sort project analysis by date
![image](/uploads/f37bbc5558f1d7655864dd3a3ef086cb/image.png)V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/184Database inconstistency in nG62022-12-16T16:21:27+01:00Romain ThervilleDatabase inconstistency in nG6**Problem:**
673 links project/run while the run doesn't exist anymore.
The most recent run in this series was made Monday 3 April 2017 22:00:00.
(This error impacts at least the migration process.)
SELECT * FROM `tx_nG6_project_run` WH...**Problem:**
673 links project/run while the run doesn't exist anymore.
The most recent run in this series was made Monday 3 April 2017 22:00:00.
(This error impacts at least the migration process.)
SELECT * FROM `tx_nG6_project_run` WHERE run_id NOT IN (SELECT uid FROM tx_nG6_run)
**Tests:**
Deleting the run via the web interface also deletes the link. So the inconstistency doesn't come from here.
**To do:**
* [ ] Remove the obsolete links
* [ ] Test if the purge process is responsible. (It shouldn't delete the run nor the link.)
* [ ] Update the database structure to add an integrity constaint.
* [x] Check if the analyzes have the same problem (project/analyze, run/analyze, analyze/result).Romain ThervilleRomain Therville2020-06-12https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/187An update to analysis.py has introduced a bug and stopped to workflows in pro...2022-12-16T16:21:27+01:00Romain ThervilleAn update to analysis.py has introduced a bug and stopped to workflows in progressThe commit eb9dd0cb292d57be2c1ec9f74e9e54d94d4e2bed (issue #129) has introduced the following error:
Traceback (most recent call last):
File "/work/ng6/jflow/work/illumina_diversity_qc/wf006442/.working/7d7ab284d7/_Stash/0/0/0/w000069...The commit eb9dd0cb292d57be2c1ec9f74e9e54d94d4e2bed (issue #129) has introduced the following error:
Traceback (most recent call last):
File "/work/ng6/jflow/work/illumina_diversity_qc/wf006442/.working/7d7ab284d7/_Stash/0/0/0/w0000699", line 92, in <module>
outputs = add_analysis(*new_args)
File "/work/ng6/jflow/work/illumina_diversity_qc/wf006442/.working/7d7ab284d7/_Stash/0/0/0/w0000699", line 73, in add_analysis
analysis.post_process()
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.2/src/weaver/../../workflows/components/fastqc.py", line 124, in post_process
job 32605 completed
/work/ng6/jflow/work/illumina_diversity_qc/wf006442/.working/7d7ab284d7/_Stash/0/0/0/w0000742 none /work/ng6/jflow/work/illumina_diversity_qc/wf006442/Flash_default/analysis.cfg /work/ng6/jflow/tmp/tmp29fg5x0m.dump /work/ng6/jflow/work/illumina_diversity_qc/wf006442/FastqIlluminaFilter_default/analysis.cfg failed with exit code 1
sample + ".per_tile_quality.png"), "ptqpng")
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.2/src/weaver/../ng6/analysis.py", line 625, in _save_file
return self.get_web_filepath(file_name, 'fileadmin')
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.2/src/weaver/../ng6/analysis.py", line 774, in get_web_filepath
return base_filepath + os.path.join(self.get_directory(), file_name)
File "/tools/python/3.4.3/lib/python3.4/posixpath.py", line 82, in join
path += b
TypeError: unsupported operand type(s) for +=: 'NoneType' and 'str'
For the time being, I've rolled back to a previous version.
Problem : To test the build, I've used a simple addanalysis. It wasn't enough.
The tests in issue #152 should cover more user cases, they are currently to weak.
A big shell script to test everything at once would be great.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/194The Downloadsymlink workflow stays stuck when ng6 ssh user has a rsa passphrase2021-05-04T11:49:20+02:00Romain ThervilleThe Downloadsymlink workflow stays stuck when ng6 ssh user has a rsa passphrase**Symptoms:**
- Creating symbolic links through the web interface results in an infinite loading.
- The associated workflow doesn't end.
- The workflow debug returns the following :
Traceback (most recent call last):
File "/work/ng6/j...**Symptoms:**
- Creating symbolic links through the web interface results in an infinite loading.
- The associated workflow doesn't end.
- The workflow debug returns the following :
Traceback (most recent call last):
File "/work/ng6/jflow/work/downloadsymlink/wf008708/.working/f85edccc0a/_Stash/0/0/0/w0000000", line 86, in <module>
outputs = create_symbolik_link(*new_args)
File "/work/ng6/jflow/work/downloadsymlink/wf008708/.working/f85edccc0a/_Stash/0/0/0/w0000000", line 79, in create_symbolik_link
s.cmd('bash %s'%user_script)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.4/src/weaver/../ng6/utils.py", line 568, in cmd
return self.ssh_results(pid, f)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.4/src/weaver/../ng6/utils.py", line 561, in ssh_results
got = self._read(f)
File "/usr/local/bioinfo/src/ng6_sources/ng6-V3.2.7.4/src/weaver/../ng6/utils.py", line 538, in _read
x = os.read(f, 1024)
**Cause of the problem:**
When lauching an SSH connection with the ng6 user (Python : s = SSH(username, password, server_params[0]) ), a passphrase defined in /home/ng6/.ssh/id_rsa is asked.V4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/215SQL error in ./nG6/src/pymysql/cursors.py2022-12-16T16:21:27+01:00Jules SabbanSQL error in ./nG6/src/pymysql/cursors.pyNew error encountered during illumina_qc :
```
/usr/local/bioinfo/src/nG6/src/pymysql/cursors.py:146: Warning: Data truncated for column 'description' at row 1
result = self._query(query)
```
Maybe related to last plugin nG6 / typo3 ...New error encountered during illumina_qc :
```
/usr/local/bioinfo/src/nG6/src/pymysql/cursors.py:146: Warning: Data truncated for column 'description' at row 1
result = self._query(query)
```
Maybe related to last plugin nG6 / typo3 updates ?Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://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 Kuchly