ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2020-06-11T16:56:51+02:00https://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/138Display error in a project view : Table can not be sorted by date if the user...2020-04-03T15:58:05+02:00Audrey GibertDisplay error in a project view : Table can not be sorted by date if the user is not administratorMargot Zahm came to us because she can not sorter her project table by date :
![image](/uploads/80b4a32a42ffec62512a7fe598d11911/image.png)
![image](/uploads/f3bccdad743010390191f94004919555/image.png)
Order of dates is random
We could ...Margot Zahm came to us because she can not sorter her project table by date :
![image](/uploads/80b4a32a42ffec62512a7fe598d11911/image.png)
![image](/uploads/f3bccdad743010390191f94004919555/image.png)
Order of dates is random
We could not reproduce her bug because we were logged as CTD and it works perfectly for us...
One lead has been reported with the inspector column of web explorer :
what is sent in member view
![image](/uploads/2d8f69ffb2bbd8d28acc37314637bdeb/image.png)
what is sent in admin view
![image](/uploads/7114492349815c674d45ff5ba62c93f4/image.png)V4 - MaintenanceAudrey GibertAudrey Giberthttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/155Warning on hidden column while create a run, analyse or projet2020-01-10T10:24:43+01:00Celine NoirotWarning on hidden column while create a run, analyse or projet`
ng6-test@ng6-test: /work/ng6-test/jflow_rtherville $python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --admin-login cnoirot --run-id 15165 --data-file /work/ng6-test/jflow_rtherville/test.txt --analysis-name "A...`
ng6-test@ng6-test: /work/ng6-test/jflow_rtherville $python3.4 /save/ng6-test/src/ng6-git-rtherville/bin/ng6_cli.py addanalysis --admin-login cnoirot --run-id 15165 --data-file /work/ng6-test/jflow_rtherville/test.txt --analysis-name "Analyse de run" --analysis-description "68 + 20 Manech" --analysis-software "GATK..." --analysis-software-options "-" --analysis-software-version "GATK:3.7 - Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 - Bcftools:1.3.1"
parsing Makeflow...
checking Makeflow for consistency...
Makeflow has 1 rules.
starting workflow....
submitting job: /work/ng6-test/jflow_rtherville/work/addanalysis/wf000499/.working/153171b866/_Stash/0/0/0/w0000000 none /work/ng6-test/jflow_rtherville/work/addanalysis/wf000499/BasicAnalysis_default/analysis.cfg /work/ng6-test/jflow_rtherville/tmp/tmp22_7y9dk.dump
submitted job 16508
**/save/ng6-test/src/ng6-git-rtherville/src/weaver/../pymysql/cursors.py:146: Warning: Incorrect integer value: 'True' for column 'hidden' at row 1
result = self._query(query)
**
job 16508 completed
nothing left to do.
sending incremental file list
./
test.txt
sent 166 bytes received 34 bytes 400.00 bytes/sec
total size is 61 speedup is 0.30
###########
# Results #
###########
> V3.2.6Celine NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/153The DownloadSymlink workflow bugs when an analysis is an ONT Demultiplex2020-01-10T10:24:16+01:00Romain ThervilleThe DownloadSymlink workflow bugs when an analysis is an ONT Demultiplex**When does it happen?**
From the "download" page, when selecting an entire project that contains a demultiplex ONT analysis.
![2019-12-16_172314](/uploads/d98631c574a688f57a243b4984156f8d/2019-12-16_172314.png)
It's okay when the run ...**When does it happen?**
From the "download" page, when selecting an entire project that contains a demultiplex ONT analysis.
![2019-12-16_172314](/uploads/d98631c574a688f57a243b4984156f8d/2019-12-16_172314.png)
It's okay when the run and analyzes are deployed and selected:
![2019-12-16_172422](/uploads/b95a120a14968d72406ad2d2d27e7f77/2019-12-16_172422.png)
**Why?**
In utils.py:
*12-16 13:19 Utils DEBUG get_directories_structure_and_content. src_directories = /save/ng6///data/run/fb3cdcb00, /save/ng6///data/analyze/e3df5acbb, /save/ng6///data/analyze/2753b0457, /save/ng6///data/run/b2e7de531, /save/ng6///data/analyze/ae6d2ec97, /save/ng6///data/analyze/cfec28f91
12-16 13:19 Utils DEBUG get_directories_structure_and_content. dest_directories = /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/RawData, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_RUNStats.64606, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_DemultiplexONT.64608, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/RawData, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_DemultiplexONT.64568, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_RUNStats.64567, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3-Climares-mtplx6-2-PAD92409.16250/Analyse_DemultiplexONT.64608, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT3-Climares-mtplx6-2-PAD92409.16250/Analyse_RUNStats.64606, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2-Climares-mtplx6-PAD92409.16245/Analyse_DemultiplexONT.64568, /work/lipm/gouzy/Project_CLIMARES.482/Run_ONT2-Climares-mtplx6-PAD92409.16245/Analyse_RUNStats.64567*
(The destination tab contains 2 versions of the same runs and analyzes, one with '-' separatores, one with '_'.)
This may be fixed with an update to the download page's javascript call:
http://ng6-test.toulouse.inra.fr:8080//run_workflow?username=ng6-test&password=aCYLKVdYzI8AaTcB%25C2%25A4%25C3%2596%25C3%25B3i%2540%25C3%2598%2515%25C3%25B6%2522&user_directory=/work/ng6-test/jflow_rtherville/&admin_login=CTD&data_id=15032&run_id=15032&analysis_id=57729::-::57730&workflow_class=DownloadSymlink&callback=jQuery111105034437105204775_1576513683378&_=1576513683383
(By removing the analyzes that have no directory.)
The workflow tries the following treatment:
ln -s /save/ng6/data/run/fb3cdcb00 /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/RawData
ln -s /save/ng6/data/analyze/e3df5acbb /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_RUNStats.64606
ln -s /save/ng6/data/analyze/2753b0457 /work/ng6/Project_CLIMARES.482/Run_ONT3_Climares_mtplx6_2_PAD92409.16250/Analyse_DemultiplexONT.64608
ln -s /save/ng6/data/run/b2e7de531 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/RawData
ln -s /save/ng6/data/analyze/ae6d2ec97 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_DemultiplexONT.64568
ln -s /save/ng6/data/analyze/cfec28f91 /work/ng6/Project_CLIMARES.482/Run_ONT2_Climares_mtplx6_PAD92409.16245/Analyse_RUNStats.64567
But fails, BECAUSE /save/ng6/data/analyze/2753b0457 AND /save/ng6/data/analyze/ae6d2ec97 DO NOT EXIST!V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/85Error addanalysis from graphic interface (firefox)2019-11-12T13:44:01+01:00Maxime MannoError addanalysis from graphic interface (firefox)I tried to launch a new analysis from the interface.
The window poped, but nothing append when I clicked on the "Run" button.
![image](/uploads/d4a6c90188f954c6d4f32c4c562b3a78/image.png)I tried to launch a new analysis from the interface.
The window poped, but nothing append when I clicked on the "Run" button.
![image](/uploads/d4a6c90188f954c6d4f32c4c562b3a78/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/132AligmentStats : Duplicate output is incorrect2019-10-28T10:44:11+01:00Audrey GibertAligmentStats : Duplicate output is incorrectIn Beestrong>NOVA12>AligmentStats, Duplicate table is almost correct!
[image](/uploads/f69faf5d6173d80430db07b47230557d/image.png)In Beestrong>NOVA12>AligmentStats, Duplicate table is almost correct!
[image](/uploads/f69faf5d6173d80430db07b47230557d/image.png)https://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/121purge email configuration2019-10-24T09:38:56+02:00Gerald Salingerald.salin@inra.frpurge email configurationcheck the recipient field, I think there were multiple copies of support.ng6 in the last purge session.check the recipient field, I think there were multiple copies of support.ng6 in the last purge session.V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/95Ajout d'analyse à un projet2019-10-21T11:52:25+02:00Philippe BardouAjout d'analyse à un projetImpossible d'ajouter une analyse à un projet via l'interface...
![Sélection_254](/uploads/c87f171a96f549d097dac188e11c7a20/Sélection_254.png)Impossible d'ajouter une analyse à un projet via l'interface...
![Sélection_254](/uploads/c87f171a96f549d097dac188e11c7a20/Sélection_254.png)V3.2.5.2Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/124Analysis added to a run have no space_id2019-09-27T14:50:59+02:00Romain ThervilleAnalysis added to a run have no space_idError:
python3.4 /usr/local/bioinfo/src/nG6/bin/ng6_cli.py addanalysis
data-file 15/ng6.jobs --analysis-name "Variant calling 88"
analysis-description "68 + 20 Manech" --analysis-software "GATK..."
analysis-software-options "-" --ana...Error:
python3.4 /usr/local/bioinfo/src/nG6/bin/ng6_cli.py addanalysis
data-file 15/ng6.jobs --analysis-name "Variant calling 88"
analysis-description "68 + 20 Manech" --analysis-software "GATK..."
analysis-software-options "-" --analysis-software-version "GATK:3.7
Picard:2.1.1 - Bwa:0.7.15 - Samtools:1.3.1 - FastQC:v0.11.2 -
Bcftools:1.3.1" --admin-login sigenae --project-id 1144
**Error: 'NoneType' object has no attribute 'space_id'**
Origin:
Issue#114
src/ng6/ng6workflow.py
```
if addto == "project": cmpt_object.project = self.project
elif addto == "run": cmpt_object.run = self.runobj
#We replace the default space_id
if cmpt_object.space_id == "default" and cmpt_object.space_id != cmpt_object.run.space_id:
cmpt_object.space_id = cmpt_object.run.space_id
```
We should set the space_id according to the project containing the run, not the run itself.V3.2.5.2Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/27Project view : hidden run and analyses are counted2019-09-18T17:27:36+02:00Celine NoirotProject view : hidden run and analyses are countedIn data overview hidden project are counted
![image](/uploads/14b9494bc2aedd913f56bf7bf8c0c025/image.png)In data overview hidden project are counted
![image](/uploads/14b9494bc2aedd913f56bf7bf8c0c025/image.png)V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/8Metacharacter "&" in password creates a bug2019-09-12T09:27:13+02:00Audrey GibertMetacharacter "&" in password creates a bugWhen "&" is in the password, the registered password stops just before the "&" :
Example:
if "hgff&ld" is written,
the registered password in the database is "hgff"When "&" is in the password, the registered password stops just before the "&" :
Example:
if "hgff&ld" is written,
the registered password in the database is "hgff"V3.2.6Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/104loadin icon go on display while an error is raised2019-08-30T13:22:58+02:00Roxane Boyerloadin icon go on display while an error is raisedwhile downloading data with 'symlink', even if an error is raised the message is not displayed and the user has to wait :
![image](/uploads/fb5a7e6c8e7dac37eaac89bd231ce4da/image.png)while downloading data with 'symlink', even if an error is raised the message is not displayed and the user has to wait :
![image](/uploads/fb5a7e6c8e7dac37eaac89bd231ce4da/image.png)V3.2.5Romain ThervilleRomain Thervillehttps://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/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/103ONT - Bug with gzipped input fastq file2019-06-11T15:13:44+02:00Maxime MannoONT - Bug with gzipped input fastq fileThe new automatised pipeline launch the ont_qc with a gzipped input fastq file, and the analysis failedThe new automatised pipeline launch the ont_qc with a gzipped input fastq file, and the analysis failedV3.2.4Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/89run date in tx_ng6_run is wrong2019-02-11T18:36:40+01:00Gerald Salingerald.salin@inra.frrun date in tx_ng6_run is wrongrunning a workflow with a run date D will be displayed D-1dayrunning a workflow with a run date D will be displayed D-1dayV3.2.3https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/90Lost of Porechop version2019-02-11T17:24:49+01:00Maxime MannoLost of Porechop version![2018-11-05_100514](/uploads/c5a7c2dc48cd73b91c20252710124b20/2018-11-05_100514.png)![2018-11-05_100514](/uploads/c5a7c2dc48cd73b91c20252710124b20/2018-11-05_100514.png)V3.2.3Maxime MannoMaxime Mannohttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/74ONT-QC bug with l502019-01-04T17:45:19+01:00Maxime MannoONT-QC bug with l50we removed the L50 from the R script, and the workflow need this informationwe removed the L50 from the R script, and the workflow need this informationV3.2.2Maxime MannoMaxime Mannohttps://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.fr2019-01-10