ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2018-06-19T15:08:13+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/2Purge : somme par projet incoherente2018-06-19T15:08:13+02:00Celine NoirotPurge : somme par projet incoherenteLa somme des données "purgeables" n'est pas coherente dans le table de puge.La somme des données "purgeables" n'est pas coherente dans le table de puge.V3.1 - PurgeClaire KuchlyClaire Kuchly2018-04-18https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/25after extending a part of project values in Data overview project are false2018-06-29T16:43:21+02:00Celine Noirotafter extending a part of project values in Data overview project are false![image](/uploads/cf5fda99787f29d34f38d5d4f20656a7/image.png)![image](/uploads/cf5fda99787f29d34f38d5d4f20656a7/image.png)V3.1 - PurgeCeline NoirotCeline Noirot2018-06-28https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/24deletion of demand purge don't work2018-06-29T15:54:26+02:00Celine Noirotdeletion of demand purge don't workReturn always error unable to delete.Return always error unable to delete.V3.1 - PurgeClaire KuchlyClaire Kuchly2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/16generate script to compute storage size for extention2019-07-23T14:15:59+02:00Celine Noirotgenerate script to compute storage size for extentionV3.1 - Purge2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/11Correct list of id analyse and run stored in db for a purge demand2018-08-02T14:55:49+02:00Celine NoirotCorrect list of id analyse and run stored in db for a purge demandWhen purge was created, a bug stored all values of a project
Correct the list of analyse id and run id before launching the purge
Think to also remove the purge id field to the analyses and the runsWhen purge was created, a bug stored all values of a project
Correct the list of analyse id and run id before launching the purge
Think to also remove the purge id field to the analyses and the runsV3.1 - PurgeCeline NoirotCeline Noirot2018-06-29https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/21Delete Analyse or run from project view or run view2018-08-14T14:13:03+02:00Celine NoirotDelete Analyse or run from project view or run viewIf the user enter an existing user on unix server, and this user do not have permission, the return is true/ok but the directory is not deleted
![image](/uploads/3b6913146624e853d83c524a728a59e4/image.png)If the user enter an existing user on unix server, and this user do not have permission, the return is true/ok but the directory is not deleted
![image](/uploads/3b6913146624e853d83c524a728a59e4/image.png)V3.2 - Slurm2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/19Bug project view nb run / analyse / size2018-06-20T16:49:27+02:00Celine NoirotBug project view nb run / analyse / size![ng6-project-bug](/uploads/a9a4a23eb23a55520cae49a853623d8e/ng6-project-bug.png)![ng6-project-bug](/uploads/a9a4a23eb23a55520cae49a853623d8e/ng6-project-bug.png)V3.1 - Purge2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/17Add project extention2018-07-18T15:48:10+02:00Celine NoirotAdd project extentionIf a project has a obsolete run (not all), all its run or analysis can be extentedIf a project has a obsolete run (not all), all its run or analysis can be extentedV3.1 - PurgeCeline NoirotCeline Noirot2018-06-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/38unable to delete runs or analyses from the ui2018-08-08T13:10:18+02:00Gerald Salingerald.salin@inra.frunable to delete runs or analyses from the uierror :
`08-08-18 08:07 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function ssh2_connect() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/nG6_ui_slurm/class.tx_nG6_eid.php in line 158. Request...error :
`08-08-18 08:07 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Call to undefined function ssh2_connect() | Error thrown in file /save/ng6-test/src/ng6-git-gsalin/nG6_ui_slurm/class.tx_nG6_eid.php in line 158. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?eID=tx_nG6&type=delete&del_level=analysis&data_folder=/work/ng6-test/jflow_mmanno/ng6&user_login=ng6-test&user_pwd=ng6L12*&user_id=4&ids=50717`V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.fr2018-08-28https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/97The makeflow command for md5sum is too long for the cluster2019-01-04T11:37:46+01:00Audrey GibertThe makeflow command for md5sum is too long for the clusterThe command for md5sum sent by Makeflow contains the paths of all samples. In 2 of our workflows, there are 672 samples, that is far too long to be accepted for the cluster.
>>>
2018/12/04 12:47:55.67 makeflow[46806] notice: job submis...The command for md5sum sent by Makeflow contains the paths of all samples. In 2 of our workflows, there are 672 samples, that is far too long to be accepted for the cluster.
>>>
2018/12/04 12:47:55.67 makeflow[46806] notice: job submission failed: no output from slurm
couldn't submit batch job, still trying...
>>>V3.2.1Audrey GibertAudrey Gibert2018-12-14https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/100Read and bases count are sometimes false2019-01-04T11:39:15+01:00Gerald Salingerald.salin@inra.frRead and bases count are sometimes falseSince the last ng6 update, the reads ans bases counts displayed for the runs are false.
AddRawFiles was modified to manage huge number of sample files (#97).
It seems the function counting the reads and bases is run too early.Since the last ng6 update, the reads ans bases counts displayed for the runs are false.
AddRawFiles was modified to manage huge number of sample files (#97).
It seems the function counting the reads and bases is run too early.V3.2.2Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.fr2019-01-10https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/114The analyse data do not end up in the right directory2019-08-06T15:25:20+02:00Romain ThervilleThe analyse data do not end up in the right directoryAfter an analyze run, some files are in the right directory, but most are not.
REPDEV project, Run ont_qc (30-07-19) :
http://ng6-test.toulouse.inra.fr/fileadmin/data_seqoccin/run/db3b81bfe/md5sum.txt
http://ng6-test.toulouse.inra.fr/f...After an analyze run, some files are in the right directory, but most are not.
REPDEV project, Run ont_qc (30-07-19) :
http://ng6-test.toulouse.inra.fr/fileadmin/data_seqoccin/run/db3b81bfe/md5sum.txt
http://ng6-test.toulouse.inra.fr/fileadmin/data_seqoccin/run/db3b81bfe/test.fastq.gz
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/RunStats_archive.tar.gz
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_cumulyield.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_channelbases.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_channelreads.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_distribquality.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_distriblength_bybases.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample.sequencing_summary.txt
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_seqrate.png
http://ng6-test.toulouse.inra.fr/fileadmin/data/analyze/9a1c63588/ONT_sample_distriblength.pngV3.2.4Romain ThervilleRomain Therville2019-08-30https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/134Debug about add index files in sample definition2019-10-28T10:29:19+01:00Claire KuchlyDebug about add index files in sample definitionwith the definition with index files for 10X analysis, error in illumina_qc launched.
in src/ng6/ng6workflow.py
```python
def __preprocess_samples__(self):
samples_ids = []
pidx = 1
nidx = 1
for index, ...with the definition with index files for 10X analysis, error in illumina_qc launched.
in src/ng6/ng6workflow.py
```python
def __preprocess_samples__(self):
samples_ids = []
pidx = 1
nidx = 1
for index, sample in enumerate(self.samples) :
if sample.name :
self.samples_names.append(sample.name)
else :
sample.name = 'SAMPLE_' + str(nidx)
nidx += 1
if sample.sample_id :
if sample.sample_id in samples_ids :
display_error_message( "Sample identifier %s must be uniq ( sample %s ).\n" % sample.sample_id, sample.name )
# add an automatic id for samples
else :
sample.sample_id = 'sample_' + str(pidx)
pidx += 1
samples_ids.append(sample.sample_id)
for rfile in sample.reads1 :
self.reads1_indexes.append(sample.sample_id)
self.reads1.append(rfile)
for rfile in sample.reads2 :
self.reads2_indexes.append(sample.sample_id)
self.reads2.append(rfile)
**for rfile in sample.index :
self.index.append(rfile)**
```Claire KuchlyClaire Kuchly2019-10-24https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/139Debug about add raw files due to 10X dev2020-06-15T10:26:45+02:00Claire KuchlyDebug about add raw files due to 10X devhttps://genomique.genotoul.fr/Mantis/view.php?id=4787 : add to raw files all reads and reads filtering.https://genomique.genotoul.fr/Mantis/view.php?id=4787 : add to raw files all reads and reads filtering.V3.2.8Claire KuchlyClaire Kuchly2019-11-07https://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/157Workflow addproject introuvable2020-06-11T17:12:34+02:00Romain ThervilleWorkflow addproject introuvableManque 1 import dans /workflows/addproject/__init__.py
Chargement infini en tentant addproject depuis l'interface web, et addproject est le seul workflow qui n'apparait pas dans get_available_workflows.
Plus d'infos dans le commit à sui...Manque 1 import dans /workflows/addproject/__init__.py
Chargement infini en tentant addproject depuis l'interface web, et addproject est le seul workflow qui n'apparait pas dans get_available_workflows.
Plus d'infos dans le commit à suivre.V3.2.6Romain ThervilleRomain Therville2020-01-16https://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/177No error message if login failed2020-06-11T16:56:51+02:00Celine NoirotNo error message if login failedSince last upgrade no error message :/Since last upgrade no error message :/V3.2.7Romain ThervilleRomain Therville2020-04-03https://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/192Project 'Mutua16s' always appears in the obsolete project list2021-03-25T14:29:06+01:00Romain ThervilleProject 'Mutua16s' always appears in the obsolete project listDuring the purge process, the alert mail for the Mutua16s project has been sent 19 times.
There should be only one mail per project.During the purge process, the alert mail for the Mutua16s project has been sent 19 times.
There should be only one mail per project.V3.2.7.5Romain ThervilleRomain Therville2021-02-08