ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2022-12-16T16:20:51+01:00https://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/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/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/222Format end of sequencing report change2022-12-16T16:21:27+01:00Jules SabbanFormat end of sequencing report changeWith the realese V2.03.2 annoncunced by Nanopore, the end of sequencing report will not be a PDF file, but an HTML file instead.
Make little modification in workflows/ont_qc/__init__.py#L65 script to keep it in files available on nG6.With the realese V2.03.2 annoncunced by Nanopore, the end of sequencing report will not be a PDF file, but an HTML file instead.
Make little modification in workflows/ont_qc/__init__.py#L65 script to keep it in files available on nG6.Jules SabbanJules Sabbanhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/221[IlluminaWF] Change algo use with BWA for ContaminationSearch analysis2022-12-16T16:21:28+01:00Jules Sabban[IlluminaWF] Change algo use with BWA for ContaminationSearch analysisCurrently, the **ContaminationSearch** analysis for illumina workflows is performed with `bwa aln`.
This algorithm is not optimal for the length of reads we currently have ; so we should use `bwa mem`.
Moreover, in the future pipeli...Currently, the **ContaminationSearch** analysis for illumina workflows is performed with `bwa aln`.
This algorithm is not optimal for the length of reads we currently have ; so we should use `bwa mem`.
Moreover, in the future pipeline under Nextflow we will use ***FastqScreen*** to make this analysis. This tool already use `bwa mem`.
So to have comparable results between the two pipelines, we must change `bwa aln` to `bwa mem`.Jules SabbanJules Sabbanhttps://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/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/186put the addrawfile component generic for any type of file to be saved2022-12-16T16:21:27+01:00Claire Kuchlyput the addrawfile component generic for any type of file to be savedNow the addrawfile component is only for fastq.gz files or with PacBio data we want to saves bam/xml and json files also.
So we want to add :
* [ ] management of any files to saved
* [ ] add calculation of the number of reads and base...Now the addrawfile component is only for fastq.gz files or with PacBio data we want to saves bam/xml and json files also.
So we want to add :
* [ ] management of any files to saved
* [ ] add calculation of the number of reads and bases for bam filesAudrey GibertAudrey Gibert2020-09-30https://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/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/173[Nanopore] Add graph for each sample on multiplex run2020-03-03T13:41:40+01:00Claire Kuchly[Nanopore] Add graph for each sample on multiplex runhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/167[Sequel2] make available BAM format from addrun2022-12-16T16:21:28+01:00Celine Vandecasteele[Sequel2] make available BAM format from addrunCurrently we can only make available fastq format when we add a run in NG6.
Data size on NG6 should be calculated from bam format.
#149Currently we can only make available fastq format when we add a run in NG6.
Data size on NG6 should be calculated from bam format.
#149Audrey GibertAudrey Giberthttps://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/165[Nanopore] Add "metadata_fast5.txt" in logs file on NG62020-02-06T14:12:27+01:00Roxane Boyer[Nanopore] Add "metadata_fast5.txt" in logs file on NG6See issue 45 from NGS_ONT project to find more.See issue 45 from NGS_ONT project to find more.https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/164[Hi-C] Hi-C pipeline developpement2022-12-16T16:21:28+01:00Claire Kuchly[Hi-C] Hi-C pipeline developpementImplementation of a new pipeline that takes Hi-C data :
* [ ] Implementation new CasavanG6workflow illumina_HiC_qc
* [ ] Implementation of juicer analyse - must make available the file merge_nodup.txt
* [ ] Implementation of juicer re...Implementation of a new pipeline that takes Hi-C data :
* [ ] Implementation new CasavanG6workflow illumina_HiC_qc
* [ ] Implementation of juicer analyse - must make available the file merge_nodup.txt
* [ ] Implementation of juicer result (file inter.txt) interface with smartyClaire KuchlyClaire Kuchly2020-04-30https://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/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/149[Sequel2] make new qc pipeline for Sequel2 data2022-12-16T16:21:28+01:00Claire Kuchly[Sequel2] make new qc pipeline for Sequel2 dataRaw data from Sequel2 instrument are different from the raw data of the RSII instrument.
We would create new pipeline :
This pipeline take CCS and CLR data.
This pipeline make available for :
* CCS data : subreads.ccs.bam file
* CL...Raw data from Sequel2 instrument are different from the raw data of the RSII instrument.
We would create new pipeline :
This pipeline take CCS and CLR data.
This pipeline make available for :
* CCS data : subreads.ccs.bam file
* CLR data : all files in output directory
Create of one analysis of run_stat.
? Make available fastq file.
?Claire KuchlyClaire Kuchly2020-01-31https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/148Add the duplicat rate without alignment in all illumina workflow2022-12-16T16:21:27+01:00Claire KuchlyAdd the duplicat rate without alignment in all illumina workflowAll the pipeline must have the duplication rate of all the samples : it must be a mandatory analysis.
Add to ng6workflow.pyAll the pipeline must have the duplication rate of all the samples : it must be a mandatory analysis.
Add to ng6workflow.pyClaire KuchlyClaire Kuchly2019-12-31https://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