ng6 issueshttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues2019-07-23T09:22:06+02:00https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/111[ont-qc] Adding logs to ont-qc analysis2019-07-23T09:22:06+02:00Maxime Manno[ont-qc] Adding logs to ont-qc analysis#### It should have log files from :
* [x] the Merkaat pipeline log
* [x] final status run summary log#### It should have log files from :
* [x] the Merkaat pipeline log
* [x] final status run summary logV3.2.4Maxime MannoMaxime Manno2019-07-31https://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/101adapt visualisation of ONT versions (gridion and promethion)2019-01-15T14:01:26+01:00Maxime Mannoadapt visualisation of ONT versions (gridion and promethion)The scripts parse-version for ONT gridion and promethion have been modified. We need to update and adapt the visualisationThe scripts parse-version for ONT gridion and promethion have been modified. We need to update and adapt the visualisationV3.2.3Maxime 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.fr2019-01-10https://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/64Test pipelines with slurm with real data2018-12-20T18:27:43+01:00Maxime MannoTest pipelines with slurm with real data* [x] illumina_qc
* [x] illumina_rnaseq (without annotation which is buggy)
* [x] illumina_diversity_qc
* [ ] gene_diversity
* [ ] illumina_matepair
* [x] ont_qc
* [ ] radseq
* [x] download_url
* [x] download_symlink
* [x] down...* [x] illumina_qc
* [x] illumina_rnaseq (without annotation which is buggy)
* [x] illumina_diversity_qc
* [ ] gene_diversity
* [ ] illumina_matepair
* [x] ont_qc
* [ ] radseq
* [x] download_url
* [x] download_symlink
* [x] download_archiveV3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/57[illumina_diversity_qc] no blastn on genologin2018-12-20T18:26:55+01:00Gerald Salingerald.salin@inra.fr[illumina_diversity_qc] no blastn on genologinwith module load bioinfo/blast-2.2.26
we can only access blastall blastclust blastpgpwith module load bioinfo/blast-2.2.26
we can only access blastall blastclust blastpgphttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/98update user not working2018-12-20T18:24:47+01:00Gerald Salingerald.salin@inra.frupdate user not working![image](/uploads/dcc565f70a9e98cc10254b37cca1ac02/image.png)
![image](/uploads/1c0595fae6c3f7a384db569c20874537/image.png)![image](/uploads/dcc565f70a9e98cc10254b37cca1ac02/image.png)
![image](/uploads/1c0595fae6c3f7a384db569c20874537/image.png)V3.2.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/88sending email from update user window does not work2018-12-20T18:05:34+01:00Gerald Salingerald.salin@inra.frsending email from update user window does not workno email is sent, no error ion the javascript console....no email is sent, no error ion the javascript console....V3.2.1https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/99delete data for a purge demand sometimes does not work2018-12-20T18:03:53+01:00Gerald Salingerald.salin@inra.frdelete data for a purge demand sometimes does not work![image](/uploads/b473a3c59c2274e805d8cf0d8c714dfb/image.png)
the interface is freezed and nothing happens
in case the folder contains a lot of files![image](/uploads/b473a3c59c2274e805d8cf0d8c714dfb/image.png)
the interface is freezed and nothing happens
in case the folder contains a lot of filesV3.2.1Gerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.frhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/96Extra space between md5 and file name in md5sum.txt2018-12-14T18:44:42+01:00Roxane BoyerExtra space between md5 and file name in md5sum.txtThere are 3 spaces instead of 2 in the md5sum file :
```
3efa244db27854b63b740a31e16e85e6 ESE00019_AAGTCCAA-TACTCATA-AH2MC2BBXY_L002_R1.fastq.gz
ff0510e4615e75a5b5cccac402262e88 ESE00107_GTTCCAAT-GCAGAATT-AH2MC2BBXY_L002_R2.fastq.gz...There are 3 spaces instead of 2 in the md5sum file :
```
3efa244db27854b63b740a31e16e85e6 ESE00019_AAGTCCAA-TACTCATA-AH2MC2BBXY_L002_R1.fastq.gz
ff0510e4615e75a5b5cccac402262e88 ESE00107_GTTCCAAT-GCAGAATT-AH2MC2BBXY_L002_R2.fastq.gz
```
md5sum -c md5sum.txt
md5sum: PLF7_GCCGCG-C28GH_L001_R1.fastq.gz: Aucun fichier ou dossier de ce type
PLF7_GCCGCG-C28GH_L001_R1.fastq.gz : Échec d'ouverture ou de lecture.Roxane BoyerRoxane Boyerhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/65workflows monitoring not working on ng62018-10-22T13:10:03+02:00Gerald Salingerald.salin@inra.frworkflows monitoring not working on ng6connecte as admin on ng6
go to ADMINISTRATIOn > workflows monitoring
after few seconds, seems jflow server is not reachable....whereas the workflow status on the runs is working well....
![image](/uploads/67802eca658b20942873a2fbda5562d1...connecte as admin on ng6
go to ADMINISTRATIOn > workflows monitoring
after few seconds, seems jflow server is not reachable....whereas the workflow status on the runs is working well....
![image](/uploads/67802eca658b20942873a2fbda5562d1/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/82Error downloading data with symlink and url2018-10-22T12:59:40+02:00Gerald Salingerald.salin@inra.frError downloading data with symlink and urlcan select data to download bug jflow workflow failed
* for symlink : trying to connect with ssh, but errors in keys in knownhosts. Deleting keys regarding ng6-slurm and 147.99.107.64 solved the problem
* for url : tries to open in the ...can select data to download bug jflow workflow failed
* for symlink : trying to connect with ssh, but errors in keys in knownhosts. Deleting keys regarding ng6-slurm and 147.99.107.64 solved the problem
* for url : tries to open in the browser a url prefix with http instead of httpsV3.2.1https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/84no template for BasicAnalyse2018-10-22T12:59:26+02:00Gerald Salingerald.salin@inra.frno template for BasicAnalysecf Maria.
The template does not exist
copy from BasicAnalysis.tplcf Maria.
The template does not exist
copy from BasicAnalysis.tplV3.2.1https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/56no output for methylationExtractor2018-10-16T17:19:32+02:00Gerald Salingerald.salin@inra.frno output for methylationExtractorseems removeduplicate component generates a truncated bam fil :
`Summarising genome-wide cytosine methylation report parameters:
===============================================================
Generating comprehensive genome-wide cytosi...seems removeduplicate component generates a truncated bam fil :
`Summarising genome-wide cytosine methylation report parameters:
===============================================================
Generating comprehensive genome-wide cytosine report
(output format: <Chromosome> <Position> <Strand> <count methylated> <count non-methylated> <C-context> <trinucleotide context> )
Reporting methylation for all cytosine contexts. Be aware that this will generate enormous files
Using zero-based start and 1-based end genomic coordinates (zero-based, half-open; user-defined)
Genome folder was specified as /work/ng6-test/jflow_gsalin/work/methylseq/wf000069/BismarkGenomePreparation_default/
Checking file >>/work/ng6-test/jflow_gsalin/work/methylseq/wf000069/RemoveDuplicate_paired/Histone-1-3_clean.bam<< for signs of file truncation...
Captured error message: '[E::bgzf_read] Read block operation failed with error -1 after 0 of 4 bytes'
[ERROR] The file appears to be truncated, please ensure that there were no errors while copying the file!!! Exiting...
`
and then, no data loaded in the database
![image](/uploads/54888793e98cfb2c0651d64e496e1a7e/image.png)https://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/80methyl_seq - template Bismark error displaying2018-10-16T17:19:32+02:00Gerald Salingerald.salin@inra.frmethyl_seq - template Bismark error displaying08-10-18 11:09 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Too few arguments to function smarty_modifier_get_description(), 1 passed in /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/templates_c/320094d0cb490e0a640ff2...08-10-18 11:09 - Core: Exception handler (WEB): Uncaught TYPO3 Exception: Too few arguments to function smarty_modifier_get_description(), 1 passed in /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/templates_c/320094d0cb490e0a640ff26100dfbb61200023b2.file.Bismark.tpl.php on line 159 and exactly 2 expected | ArgumentCountError thrown in file /save/ng6-test/src/ng6-git-gsalin/ui/nG6/res/smarty/libs/plugins/modifier.get_description.php in line 177. Requested URL: http://ng6-slurm.toulouse.inra.fr/ng6-mmanno/index.php?id=55&tx_nG6_pi1%5Banalyze_id%5D=55299&tx_nG6_pi1%5Bproject_id%5D=7&tx_nG6_pi1%5Brun_id%5D=14200
![image](/uploads/1d71ea9dd0f07714692a5d1832293e27/image.png)V3.2 - Slurmhttps://forgemia.inra.fr/genotoul-bioinfo/ng6/-/issues/79bug sending mail for purge demand while user disconnected2018-10-01T19:35:52+02:00Gerald Salingerald.salin@inra.frbug sending mail for purge demand while user disconnectedafter a while, the user is dosconnected from the interface.
we can still send mail for purge management
but the purge_deman_id is 0...after a while, the user is dosconnected from the interface.
we can still send mail for purge management
but the purge_deman_id is 0...V3.2 - SlurmGerald Salingerald.salin@inra.frGerald Salingerald.salin@inra.fr