ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2018-08-02T13:11:05+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/30RNAseq analysis2018-08-02T13:11:05+02:00Audrey GibertRNAseq analysisBug in the workflow illumina_rnaseq when the annotation file is added
RSeQC is involved, and the inner_distance.py even moreBug in the workflow illumina_rnaseq when the annotation file is added
RSeQC is involved, and the inner_distance.py even morehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/32add manual for purging data2018-08-02T14:57:31+02:00Gerald Salingerald.salin@inra.fradd manual for purging dataV4 - MaintenanceClaire KuchlyClaire Kuchlyhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/33correct source indent (tabs/white space) for all files2019-08-29T14:11:18+02:00Gerald Salingerald.salin@inra.frcorrect source indent (tabs/white space) for all filesV4 - MaintenanceRomain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/37Update documentation with rules and modules2018-09-07T12:03:51+02:00Celine NoirotUpdate documentation with rules and modulesBy upgrading jflow, new functionnalities have been added.
The documentation should also be upgrade.By upgrading jflow, new functionnalities have been added.
The documentation should also be upgrade.V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/46weaver : make patch for function.py2019-08-30T09:23:58+02:00Celine Noirotweaver : make patch for function.pyTODO
l214TODO
l214V4 - MaintenanceCeline NoirotCeline Noirothttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/52unable to use the modules functionality of jflow for insertsizes.py component2018-08-13T10:57:08+02:00Gerald Salingerald.salin@inra.frunable to use the modules functionality of jflow for insertsizes.py componentthe process of this module call a self.add_python_execution(inserts_metrics...)
the modules specified in application.properties for InsertSizes component is not managed in jflow as it is a PythonFunction
for the moment we have to put th...the process of this module call a self.add_python_execution(inserts_metrics...)
the modules specified in application.properties for InsertSizes component is not managed in jflow as it is a PythonFunction
for the moment we have to put this module load (module load system/R-3.4.3) in the bashrc fileV4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/55cutadapt output changed from 1.3 to 18 and 1.142018-08-13T19:10:53+02:00Gerald Salingerald.salin@inra.frcutadapt output changed from 1.3 to 18 and 1.14cutadpat component post-proccess failed :
the output no longer contains "Processed reads"
with cutadapt V1.3
`cutadapt version 1.3
Command line parameters: -b CTGTCTCTT -b ATACACATCT -b AGATCTAT -b AAGAGACAG --error-rate 0.1 --minimum-l...cutadpat component post-proccess failed :
the output no longer contains "Processed reads"
with cutadapt V1.3
`cutadapt version 1.3
Command line parameters: -b CTGTCTCTT -b ATACACATCT -b AGATCTAT -b AAGAGACAG --error-rate 0.1 --minimum-length 20 --times 4 --paired-output /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_cut.fastq --paired-output /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_cut.fastq -o /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R2_cut.fastq /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R2_tmp.fastq /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_tmp.fastq
Maximum error rate: 10.00%
No. of adapters: 4
Processed reads: 4344
Processed bases: 434400 bp (0.4 Mbp)
Trimmed reads: 2106 (48.5%)
Trimmed bases: 113988 bp (0.1 Mbp) (26.24% of total)
Too short reads: 377 (8.7% of processed reads)
Too long reads: 0 (0.0% of processed reads)
Total time: 0.28 s
Time per read: 0.064 ms
`
with cutadapt 18. and 1.14 :
`This is cutadapt 1.8.3 with Python 2.7.2
Command line parameters: -b CTGTCTCTT -b ATACACATCT -b AGATCTAT -b AAGAGACAG --error-rate 0.1 --minimum-length 20 --times 4 --paired-output /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_cut.fastq --paired-output /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_cut.fastq -o /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R2_cut.fastq /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R2_tmp.fastq /work/ng6-test/jflow_gsalin/work/illumina_matepair/wf000073/CutAdapt_default/B_CAGATC_L004_R1_tmp.fastq
Trimming 4 adapters with at most 10.0% errors in paired-end legacy mode ...
Finished in 0.18 s (41 us/read; 1.45 M reads/minute).
=== Summary ===
Total read pairs processed: 4,344
Read 1 with adapter: 3,610 (83.1%)
Read 2 with adapter: 0 (0.0%)
Pairs that were too short: 377 (8.7%)
Pairs written (passing filters): 3,967 (91.3%)
Total basepairs processed: 814,063 bp
Read 1: 434,400 bp
Read 2: 379,663 bp
Total written (filtered): 686,031 bp (84.3%)
Read 1: 342,864 bp
Read 2: 343,167 bp
`V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/63overriding batch_option values possible?2018-08-14T15:44:30+02:00Gerald Salingerald.salin@inra.froverriding batch_option values possible?to configure time according to the sequencer (or the number of reads?)to configure time according to the sequencer (or the number of reads?)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/71clean pipeline outputs if succeeded2018-09-06T15:09:01+02:00Gerald Salingerald.salin@inra.frclean pipeline outputs if succeededallow the deletion of files in the worflow output dir to save dik spaceallow the deletion of files in the worflow output dir to save dik spaceV4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/83copy to clipboard from download windows does not work2020-06-11T17:09:25+02:00Gerald Salingerald.salin@inra.frcopy to clipboard from download windows does not work![image](/uploads/6eaf4f5c375ebc0365c6f3bcb265ad13/image.png)
no errors, no action.
ZeroClipBoard.min.js was added from jflow project (not yet commited ni ng6), but clicking on the button doesn't copy the text to the clipboard.
maybe w...![image](/uploads/6eaf4f5c375ebc0365c6f3bcb265ad13/image.png)
no errors, no action.
ZeroClipBoard.min.js was added from jflow project (not yet commited ni ng6), but clicking on the button doesn't copy the text to the clipboard.
maybe we have to upgrade the ZeroClipBoard.min.js file (3 yers old)Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/87Enhancing the display of a project search result2019-08-29T14:24:03+02:00Audrey GibertEnhancing the display of a project search resultI was looking for project Epi on the ng6 project page.
It appears on the 2nd page of search result because according to ng6, space character comes after letters.I was looking for project Epi on the ng6 project page.
It appears on the 2nd page of search result because according to ng6, space character comes after letters.Romain ThervilleRomain Thervillehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/91[methylseq] do not store files for analyses Alignment and Metylation extractor2018-11-06T17:50:17+01:00Gerald Salingerald.salin@inra.fr[methylseq] do not store files for analyses Alignment and Metylation extractorthese data are too huge and for no use after the quality pipeline is overthese data are too huge and for no use after the quality pipeline is overV4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/92AddRawFilesComponent is not displayed on ng6 interface2018-11-08T17:18:58+01:00Audrey GibertAddRawFilesComponent is not displayed on ng6 interface![image](/uploads/ddcac4b0e5f54501039d0cd6b28e5daf/image.png)![image](/uploads/ddcac4b0e5f54501039d0cd6b28e5daf/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/93rsync error in addrawfiles is not reported by the workflow2018-11-13T14:33:47+01:00Audrey Gibertrsync error in addrawfiles is not reported by the workflowexample for workflow 467
logs in 181108_A00318_0024_BHCFFJDSXX_1541824203/JflowOutputs
```
rsync: writefd_unbuffered failed to write 80 bytes to socket [generator]: Broken pipe (32)
rsync error: error in rsync protocol data stream (code...example for workflow 467
logs in 181108_A00318_0024_BHCFFJDSXX_1541824203/JflowOutputs
```
rsync: writefd_unbuffered failed to write 80 bytes to socket [generator]: Broken pipe (32)
rsync error: error in rsync protocol data stream (code 12) at io.c(1532) [generator=3.0.9]
slurmstepd: error: Detected 1 oom-kill event(s) in step 1733125.batch cgroup.
```https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/94[ont_qc] ne pas mettre en dur la compression2019-02-11T17:17:45+01:00Gerald Salingerald.salin@inra.fr[ont_qc] ne pas mettre en dur la compressionself.compression = "gz" dans la fonction process de __init__ du pipelineself.compression = "gz" dans la fonction process de __init__ du pipelinehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/105sort order not numeric in contaminationsearch table2019-10-28T15:44:50+01:00Gerald Salingerald.salin@inra.frsort order not numeric in contaminationsearch table![image](/uploads/c5da447e601b3750890b5432d22e18a3/image.png)![image](/uploads/c5da447e601b3750890b5432d22e18a3/image.png)V4 - MaintenanceAudrey GibertAudrey Giberthttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/108export metadata2019-08-30T09:27:13+02:00Celine Noirotexport metadataadd a functionality to export all metadata of project, run, analysis.add a functionality to export all metadata of project, run, analysis.V4 - Maintenancehttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/109ftp server architecture2019-08-30T09:27:13+02:00Celine Noirotftp server architectureKeep/generate run/analysis architecture for a project when ftp server will be available.Keep/generate run/analysis architecture for a project when ftp server will be available.V4 - MaintenanceGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/115Login fail if acount has no usergroup2020-01-30T14:21:19+01:00Maxime MannoLogin fail if acount has no usergroup> De : ng6-support-request@groupes.renater.fr <ng6-support-request@groupes.renater.fr> De la part de Maria Bernard
> Envoyé : lundi 12 août 2019 08:37
> À : ng6-support@groupes.renater.fr; William Orlando Burgos Paz <wburgos@agrosavi...> De : ng6-support-request@groupes.renater.fr <ng6-support-request@groupes.renater.fr> De la part de Maria Bernard
> Envoyé : lundi 12 août 2019 08:37
> À : ng6-support@groupes.renater.fr; William Orlando Burgos Paz <wburgos@agrosavia.co>
> Objet : RE: [ng6-support] [HiSeq] IMAGE project - WP 4 Cattle sequence Calidad muestras : datas available
>
> Hello everyone,
>
> I added wburgos user to the IMAGE project, but its login password failed. Could you help him to solve the problem ?
>
> One thing more, the “contact us” link do not point anymore to the ng6 support email address.
>
> Have a good day
**Account NG6** : wburgos
No usergroup (Is NULL in the database)
**Issue** :
If trying to connect with this account, we observe a login failure and it became impossible to login with this account or an other even with the good password.
If we change the usergroup and refresh the nG6 page after the first login failure, everthing goes ok. In fact it seem's that we were login with wburgos but we were blocked by the lack of usegroup.https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/123Failed sub job is not catched by the main job2019-09-02T09:34:30+02:00Audrey GibertFailed sub job is not catched by the main jobMy illumina_qc workflow 2823 has a blue :nut_and_bolt: (écrou).
NG6 squeue says there is only the monitoring job alive. In the hidden directory `/work/ng6/jflow/work/illumina_qc/wf002823/.working/e125805cfa`, there is a slurm.status fil...My illumina_qc workflow 2823 has a blue :nut_and_bolt: (écrou).
NG6 squeue says there is only the monitoring job alive. In the hidden directory `/work/ng6/jflow/work/illumina_qc/wf002823/.working/e125805cfa`, there is a slurm.status file:
```bash
/work/ng6/jflow/work/illumina_qc/wf002823/.working/e125805cfa $ ll
total 770K
-rw-r--r-- 1 ng6 NG6 191K Aug 29 22:30 Makeflow
-rw-r--r-- 1 ng6 NG6 366K Aug 29 23:48 Makeflow.makeflowlog
-rw-r--r-- 1 ng6 NG6 17 Aug 29 22:30 slurm.status.7509032
-rwxr-xr-x 1 ng6 NG6 299 Aug 29 22:30 slurm.wrapper
drwxr-xr-x 3 ng6 NG6 4.0K Aug 29 22:30 _Stash
```
but the associated job is cancelled for out of memory
```bash
seff 7509032
Job ID: 7509032
Cluster: genobull
User/Group: ng6/NG6
State: CANCELLED (exit code 0)
Cores: 1
CPU Utilized: 04:26:42
CPU Efficiency: 90.79% of 04:53:46 core-walltime
Job Wall-clock time: 04:53:46
Memory Utilized: 2.93 GB
Memory Efficiency: 100.00% of 2.93 GB
```
-> Erros was not catched, this is a problem!