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/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/188[IlluminaWF]Hiding some analyses per defaut2020-07-15T10:02:05+02:00Audrey Gibert[IlluminaWF]Hiding some analyses per defautBy default, there is only the "log files" analysis that is hidden :
![image](/uploads/6603fbe0bddccccce2c13a16675d8079/image.png)
We should also hide
* Subset read files
* alignment
* alignmentStats
* InsertSizes
*...By default, there is only the "log files" analysis that is hidden :
![image](/uploads/6603fbe0bddccccce2c13a16675d8079/image.png)
We should also hide
* Subset read files
* alignment
* alignmentStats
* InsertSizes
* DemultiplexStatsV4 - MaintenanceAudrey GibertAudrey Gibert2021-07-01https://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/183WF AddAnalysis : rsync errors in error output2020-10-02T19:33:12+02:00Audrey GibertWF AddAnalysis : rsync errors in error outputWhen there is a lot of files to be sent to NG6 with the Addanalysis workflow, the rsync command seems to have some trouble.
I had 6 file groups to send, only 1/6 worked without error message.
The error message looks like this :
```bash...When there is a lot of files to be sent to NG6 with the Addanalysis workflow, the rsync command seems to have some trouble.
I had 6 file groups to send, only 1/6 worked without error message.
The error message looks like this :
```bash
rsync: sender failed to remove PL1_Pool2_11_BD20_2017.2.fq.gz: No such file or directory (2)
rsync: sender failed to remove PL1_Pool2_11_BD20_2017.rem.1.fq.gz: No such file or directory (2)
rsync: sender failed to remove PL1_Pool2_11_BD20_2017.rem.2.fq.gz: No such file or directory (2)
rsync: sender failed to remove PL1_Pool2_12_BK28_2018.1.fq.gz: No such file or directory (2)
rsync: sender failed to remove PL1_Pool2_12_BK28_2018.2.fq.gz: No such file or directory (2)
rsync: sender failed to remove PL1_Pool2_12_BK28_2018.rem.1.fq.gz: No such file or directory (2)
rsync: sender failed to remove PL1_Pool2_12_BK28_2018.rem.2.fq.gz: No such file or directory (2)
rsync: sender failed to remove PL1_Pool2_14_A69_2013.1.fq.gz: No such file or directory (2)
rsync: sender failed to remove PL1_Pool2_14_A69_2013.2.fq.gz: No such file or directory (2)
rsync: sender failed to remove PL1_Pool2_14_A69_2013.rem.1.fq.gz: No such file or directory (2)
...
rsync: send_files failed to open "/work/ng6/jflow/work/data/analyze/efa9850d7/PL1_Pool2_9_BE53_2017.1.fq.gz": Not a directory (20)
rsync: sender failed to remove PL1_Pool2_6_BD73_2017.rem.2.fq.gz: Not a directory (20)
rsync: send_files failed to open "/work/ng6/jflow/work/data/analyze/efa9850d7/PL1_Pool2_9_BE53_2017.2.fq.gz": Not a directory (20)
rsync: sender failed to remove PL1_Pool2_7_BK70_2_2018.1.fq.gz: Not a directory (20)
rsync: send_files failed to open "/work/ng6/jflow/work/data/analyze/efa9850d7/PL1_Pool2_9_BE53_2017.rem.1.fq.gz": Not a directory (20)
rsync: sender failed to remove PL1_Pool2_7_BK70_2_2018.2.fq.gz: Not a directory (20)
rsync: send_files failed to open "/work/ng6/jflow/work/data/analyze/efa9850d7/PL1_Pool2_9_BE53_2017.rem.2.fq.gz": Not a directory (20)
rsync: sender failed to remove PL1_Pool2_7_BK70_2_2018.rem.1.fq.gz: Not a directory (20)
rsync: sender failed to remove PL1_Pool2_7_BK70_2_2018.rem.2.fq.gz: Not a directory (20)
rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1052) [sender=3.0.9]
```
Md5sum is the same between the files to send, and the files in NG6, so no rush in here. But maybe this feature can be improved..V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/181make filenames in NG6 uniq2020-05-15T07:36:11+02:00Gerald Salingerald.salin@inra.frmake filenames in NG6 uniqin NG6 FAQ, for downloading :
On a Windows workstation (Command lines), copy/paste this list in a file "listOfFiles" (B**e aware that if the same filename is found in different url, the local file will be overriden**). Then you can down...in NG6 FAQ, for downloading :
On a Windows workstation (Command lines), copy/paste this list in a file "listOfFiles" (B**e aware that if the same filename is found in different url, the local file will be overriden**). Then you can download curl for Windows (https://curl.haxx.se/download.html), extract the archive, and run this following command in a windows prompt
should not happen.
prefix the filename so that it is uniq (add the name of the parent folder which is uniq? the run Id + analysis Id?)V4 - Maintenancehttps://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/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/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.