ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-12-16T16:21:27+01:00https://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/185Adding a warning to prevent users from lauching 20+ direct url downloads at t...2022-12-16T16:21:28+01:00Romain ThervilleAdding a warning to prevent users from lauching 20+ direct url downloads at the same timeThis morning, the nG6 virtual server had a 40+ load average.
The cause seems to be a big number of direct downloads (urldownload method) from a single user.
We should add a warning like:
"If you need to recover a large number of files, ...This morning, the nG6 virtual server had a 40+ load average.
The cause seems to be a big number of direct downloads (urldownload method) from a single user.
We should add a warning like:
"If you need to recover a large number of files, please copy the links and only launch 2 to 3 downloads at the same time (Either with the wget command, or with your web browser). Thank you."Romain ThervilleRomain Thervillehttps://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/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/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/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/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/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/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 Therville2019-12-10