MassChroQ issueshttps://forgemia.inra.fr/pappso/masschroq/-/issues2020-12-10T15:10:31+01:00https://forgemia.inra.fr/pappso/masschroq/-/issues/1crash on mzML files (problem getting precursor intensity)2020-12-10T15:10:31+01:00Langella Oliviercrash on mzML files (problem getting precursor intensity)Oops! an error occurred in MassChroQ. Dont Panic :
error reading masschroqML input file '/gorgone/pappso/moulon/users/Willy/PRIDE/PXD004549/MassChroq/21-24DL3-7_formula-2.masschroqml' :
Parse error at line 1335873, column 84:
ERROR in Ma...Oops! an error occurred in MassChroQ. Dont Panic :
error reading masschroqML input file '/gorgone/pappso/moulon/users/Willy/PRIDE/PXD004549/MassChroq/21-24DL3-7_formula-2.masschroqml' :
Parse error at line 1335873, column 84:
ERROR in MasschroqmlParser::startElement tag align, MCQ exception:
error aligning MSrun msruna1 with reference MSrun msruna1 :
AlignmentBase::alignTwoMsRuns mcqError error in msrun 'msruna1' (in getPrecursorIntensity method): scan (MS level >=2) number 14328 does not existLangella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/2error parsing tag "quantify"2020-12-10T15:10:13+01:00Langella Oliviererror parsing tag "quantify"An error occured when running MassChroQ on huge data amaizing file :
```
Oops! an error occurred in MassChroQ. Dont Panic :
error reading masschroqML input file '/gorgone/pappso/moulon/users/Melisande/Amaizing/reinterro_v4/avec_filtre_x...An error occured when running MassChroQ on huge data amaizing file :
```
Oops! an error occurred in MassChroQ. Dont Panic :
error reading masschroqML input file '/gorgone/pappso/moulon/users/Melisande/Amaizing/reinterro_v4/avec_filtre_xtp_sur_peptides/reinterro_amaizing_secheresse_v4.masschroqml' :
Parse error at line 6190424, column 19:
ERROR in MasschroqmlParser::endElement tag quantify, MCQ exception:
error in MassChroQ::executeQuantification q1 PappsoException :
Could not find a MSDataPtr matching the requested run id.
```Langella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/3fix library path for the debian package2020-11-25T19:25:00+01:00Langella Olivierfix library path for the debian packageinternal MassChroQ shared library must be placed in :
`/usr/lib/<triplet>/masschroq/libmasschroq.so`
CMakeLists has to be modified.internal MassChroQ shared library must be placed in :
`/usr/lib/<triplet>/masschroq/libmasschroq.so`
CMakeLists has to be modified.Langella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/4segmentation fault sur fichier fractionnement en condor2020-12-18T13:36:42+01:00Thierry Balliausegmentation fault sur fichier fractionnement en condorle fichier suivant `/gorgone/pappso/moulon/users/thierry/20201112_bourguignon_26_membrane/masschroq/20201130_bourguignon_26_membrane.masschroqml` provoque une fin en segmentation fault durant l'execution via condor avec les parametre sui...le fichier suivant `/gorgone/pappso/moulon/users/thierry/20201112_bourguignon_26_membrane/masschroq/20201130_bourguignon_26_membrane.masschroqml` provoque une fin en segmentation fault durant l'execution via condor avec les parametre suivant
```
masschroq-condor.pl -c 8 -m 20 20201130_bourguignon_26_membrane.masschroqml
```
pas d'erreur reporter dans le log d'erreur `tail -F /gorgone/pappso/tmp/temp_masschroq_condor_jobJrGi/`
mais mail avec segmentation fault mentionnéLangella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/5pb dans la sortie peptides de MassChroQ (liée avec les point mutation?)2021-02-24T13:23:53+01:00Melisande Blein-Nicolaspb dans la sortie peptides de MassChroQ (liée avec les point mutation?)Salut Olivier, j'ai regardé les résultats de masschroq obtenus à partir des xml de 2016. Avec les 1015 msrun, j'obtiens grosso modo la même chose qu'avec les xml de 2020 => j'en déduis que Xtandem et XtandemPipeline ne sont pas en cause ...Salut Olivier, j'ai regardé les résultats de masschroq obtenus à partir des xml de 2016. Avec les 1015 msrun, j'obtiens grosso modo la même chose qu'avec les xml de 2020 => j'en déduis que Xtandem et XtandemPipeline ne sont pas en cause (le nb de peptides, protéines groupés sont les mêmes entre les 2 versions 2016 et 2020 des xml)
Avec les 1103 msrun, la sortie de masschroq est toute buggée: MCQR n'arrive pas à charger le résultat de masschroq car le nb de colonnes n'est pas le même à toutes les lignes. J'ai eu le message d'erreur suivant avec MCQR: Warning message:
```
In fread(pepFile, header = TRUE, sep = "\t", dec = ".", quote = "", :
Stopped early on line 8492674. Expected 18 fields but found 11. Consider fill=TRUE and comment.char=. First discarded non-empty line: <<q1 All msrunc641 20130607_ GDIPTYVVGVNADQYNPDEPIISNASCTTNCLAPFVK 3 [C 173 H 268 O 60 N 45 S 2] 27C:57.02 31C:57.02 34P:pmP=>G|[C 173 H 268 O 60 N 45 S 2] 20P:pmP=>G 27C:57.02 31C:57.02 2 1 0.239637807531>>
```
Effectivement, la ligne 8492674 est pourrie à cause de l'affichage des modifs. J'ai supprimé cette ligne du fichier peptide avec une commande sed en bash et jai rechargé dans mcqr. Encore un message d'erreur:
```
In fread(pepFile, header = TRUE, sep = "\t", dec = ".", quote = "", :
Stopped early on line 8492680. Expected 18 fields but found 21. Consider fill=TRUE and comment.char=. First discarded non-empty line: <<q1 All msrunc641 20130607_blein_amaizing_1_C08_836 1348.94993123 2730.83805765 25669042 484006218.689 2708.86845417 2770.92555155 pepa9c477 YLGPFSEQTPSYLTGEFPGDYGWDTAGLSADPETFAR 3 [C 185 H 257 O 61 N 42 S 0] 2 1 0.24399 11 0.286594135744>>In fread(pepFile, header = TRUE, sep = "\t", dec = ".", quote = "", :
```
là encore, la ligne 8492680 est pourrie: il y a trop de colonnes après la colonnes mods.
si tu veux aller voir les fichiers, c'est dans
```
/gorgone/pappso/moulon/users/Melisande/Amaizing/reinterro_v4_061120/avec_v2_ancienne_interro/masschroq/result_xtp2016_1103.d
```
J'ai renommé la sortie initiale de masschroq peptides_q1_All_original.tsv. Le fichier peptides_q1_All_original.tsv est celui que j'ai modifié avec sed. Il ne contient pas la ligne 8492674. Le fichier peptides_q1_All.tsvori est le backup de la fonction sed.
3:25 PM
D'après Thierry, ce n'est pas un problème lié à la fonction fread dans R.Langella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/6amelioration du fichier Informations2022-04-25T11:35:38+02:00Thierry Balliauamelioration du fichier Informationspour mieux tracer ce qu'on fait est qu'il serait possible d'ajouter les parametres utilisés das masschroq dans le fichier masschroq information
le fichier pourrait etre sous forme de fichier tabulés
* champ \t valeur
* ms2_tendency_halfw...pour mieux tracer ce qu'on fait est qu'il serait possible d'ajouter les parametres utilisés das masschroq dans le fichier masschroq information
le fichier pourrait etre sous forme de fichier tabulés
* champ \t valeur
* ms2_tendency_halfwindow \t 10
* ms2_smoothing_halfwindow \t 15
* ms1_smoothing_halfwindow \t 0
* ppm_range min \t 10
* ppm range max \t 10
* anti_spike half \t 5
* mean_filter_half_edge \t 2
* minmax_half_edge \t 4
* maxmin_half_edge \t 3
* detection_threshold_on_max \t 50000
* detection_threshold_on_min \t 30000
* mode \t post_matching
* ni_min_abundance \t 0.8
.....
il pourrait aussi etre interessant d'avoir la reference pour l'alignement
ET est qu'il serait aussi possible de changer le nom pour enelver les espaces.
Mon idée est de potentiellement utilsier ce fichier pour les rapport de resultat via scripting et il sera plus facile a lire si il n'y a pas d'espace
merciLangella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/7The user manual does not build when creating the Debian package...2021-02-10T11:28:38+01:00Rusconi FilippoThe user manual does not build when creating the Debian package...J'ai l'impression qu'au moment de la fabrication du manuel, il ne se trouve pas là où on pense. De ce fait, il ne trouve pas les images. J'ai mis les extensions aux noms de fichiers image dans le .tex. Les fichiers graphiques PDF sont bi...J'ai l'impression qu'au moment de la fabrication du manuel, il ne se trouve pas là où on pense. De ce fait, il ne trouve pas les images. J'ai mis les extensions aux noms de fichiers image dans le .tex. Les fichiers graphiques PDF sont bien générés, mais à la compilation du LaTeX il ne les trouve pas...
Pourtant si je construis le paquet en faisant make pdf, alors là le manuel est correct. Il est généré dans
./share/doc/masschroq-doc/masschroq_manual.pdf, ce qui est un peu inattendu, franchement.
Ensuite, je me suis rendu compte qu'en faisant deux fois le paquet (dpkg-buildpackage -nc), le manuel était bien fabriqué...
Il est trois heures du mat, je vais me coucher...
```
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Chapter 1.
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[]\T1/cmtt/m/n/12 libmasschroq\T1/cmr/m/n/12 , a li-brary for in-te-gra-tion in
other soft-ware or pro-teomic pipelines;
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{MassChroQ Studio}, a graphical interface allowing the user
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Chapter 3.
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Chapter 5.
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Appendix A.
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)
(see the transcript file for additional information)
[snip]
Output written on masschroq_manual.pdf (70 pages, 637079 bytes).
Transcript written on masschroq_manual.log.
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```Langella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/8Error in MasschroqmlParser needs the creation of directory 'results.d'2021-10-20T17:43:42+02:00Aaron Millan-Oropezaaaron.millan-oropeza@inra.frError in MasschroqmlParser needs the creation of directory 'results.d'When running masschroq there is the need to create in advance a directory named **'results.d'** in order to export the peaks integration obtained by MassChroq.
I send the error message that can be fixed just by creating the so called d...When running masschroq there is the need to create in advance a directory named **'results.d'** in order to export the peaks integration obtained by MassChroq.
I send the error message that can be fixed just by creating the so called directory as a quick solution. But in the future probably this directory might be created automatically when launching MassChroQ.
Here the error message:
```
Parse error at line 269421, column 62:
ERROR in MasschroqmlParser::startElement tag ms2, MCQ exception:
error the output directory :
/gorgone/pappso/jouy/users/Aaron/2021_RD/2021_01_21_47_Gruss/xml/masschroq/results.d
to write time values does not exists.
```https://forgemia.inra.fr/pappso/masschroq/-/issues/9Uniformisation du nom des fichiers dans les données de sortie2021-09-23T16:50:29+02:00BIENVENUT WillyUniformisation du nom des fichiers dans les données de sortieBonjour,
Serait-il possible d'avoir une uniformité dans l'identification des fichiers sources au niveau des différentes sorties...
Par exemple, si les fichiers raw initiaux sont par exemples
20201126_WIB_Zm_F6_15N_terre_t1-1.xml et 2020...Bonjour,
Serait-il possible d'avoir une uniformité dans l'identification des fichiers sources au niveau des différentes sorties...
Par exemple, si les fichiers raw initiaux sont par exemples
20201126_WIB_Zm_F6_15N_terre_t1-1.xml et 20201126_WIB_Zm_F6_15N_terre_t1-2.xml
Ils deviennent identa0 et identa1 au niveau de la colonne "Indentification Run ID)
Mais lors de l'export des peptide trace (par exemples) cela devient msruna1 et msruna2
Serait-il donc possible d'avoir une seule façon d'identifier le fichier d'origine à tous les niveaux si l'on ne conserve pas le nom complet d'origine. J'ai personnellement une préférence pour msruna1, msruna2...
Merci
WillyLangella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/10execution en erreur sur un fichier particulier2021-02-19T12:12:44+01:00Thierry Balliauexecution en erreur sur un fichier particuliertballiau@proteus1:/gorgone/pappso/tmp/xtpcpp.Nlatbq$ tail -F masschroq.0.error
Oops! an error occurred in MassChroQ. Dont Panic :
error reading masschroqML input file '/gorgone/pappso/moulon/users/thierry/20210202_bourguignon_26_cytosol/...tballiau@proteus1:/gorgone/pappso/tmp/xtpcpp.Nlatbq$ tail -F masschroq.0.error
Oops! an error occurred in MassChroQ. Dont Panic :
error reading masschroqML input file '/gorgone/pappso/moulon/users/thierry/20210202_bourguignon_26_cytosol/export/QC.masschroqml' :
Parse error at line 80, column 175:
problem creating msrun msrunb76:
problem creating msrun msrunb76:
error reading xml input file '/gorgone/pappso/moulon/raw/20210129_Bourguignon_26_cytosol/20201203_bourguignon_26_cytosol_Ns1_F1.mzXML' :
Pwiz spectrum index 0 not found in MS file std::runtime_error :
[SpectrumList_mzXML::spectrum()] Error seeking to <scan>.
le fichier mzxml semble ok mais pwiz semble ne pas reussir a le lire (il ne posep as de probleme a xtandem)https://forgemia.inra.fr/pappso/masschroq/-/issues/11erreur de segmentation quanti big problem2021-09-18T08:01:10+02:00Marlene Davantureerreur de segmentation quanti big problem```
mdavanture@proteus1:/gorgone/pappso/moulon/users/Marlene/20210819_Domergue_48/masschroq$ /usr/bin/masschroq -c 8 -t /tmp 20210819_Domergue_48.masschroqml
8 CPUs used
Running MassChroQ 2.4.0 with XML file '20210819_Domergue_48.masschr...```
mdavanture@proteus1:/gorgone/pappso/moulon/users/Marlene/20210819_Domergue_48/masschroq$ /usr/bin/masschroq -c 8 -t /tmp 20210819_Domergue_48.masschroqml
8 CPUs used
Running MassChroQ 2.4.0 with XML file '20210819_Domergue_48.masschroqml'
validating MassChroqML file /gorgone/pappso/moulon/users/Marlene/20210819_Domergue_48/masschroq/20210819_Domergue_48.masschroqml...
Parsing XML input file '/gorgone/pappso/moulon/users/Marlene/20210819_Domergue_48/masschroq/20210819_Domergue_48.masschroqml'
MS run 'msruna1' file '/gorgone/pappso/moulon/raw/20210819_Domergue_48/20210826_Domergue_48_52H.mzXML' : parsing begin
MS run 'msruna1' : xml file '/gorgone/pappso/moulon/raw/20210819_Domergue_48/20210826_Domergue_48_52H.mzXML' : parsing OK
MS run 'msruna1' : added
MS run 'msruna2' file '/gorgone/pappso/moulon/raw/20210819_Domergue_48/20210826_Domergue_48_IMB.mzXML' : parsing begin
MS run 'msruna2' : xml file '/gorgone/pappso/moulon/raw/20210819_Domergue_48/20210826_Domergue_48_IMB.mzXML' : parsing OKmdavanture@proteus1:/gorgone/pappso/moulon/users/Marlene/20210819_Domergue_48/masschroq$ /usr/bin/masschroq -c 8 -t /tmp 20210819_Domergue_48.masschroqml
8 CPUs used
Running MassChroQ 2.4.0 with XML file '20210819_Domergue_48.masschroqml'
validating MassChroqML file /gorgone/pappso/moulon/users/Marlene/20210819_Domergue_48/masschroq/20210819_Domergue_48.masschroqml...
Parsing XML input file '/gorgone/pappso/moulon/users/Marlene/20210819_Domergue_48/masschroq/20210819_Domergue_48.masschroqml'
MS run 'msruna1' file '/gorgone/pappso/moulon/raw/20210819_Domergue_48/20210826_Domergue_48_52H.mzXML' : parsing begin
MS run 'msruna1' : xml file '/gorgone/pappso/moulon/raw/20210819_Domergue_48/20210826_Domergue_48_52H.mzXML' : parsing OK
MS run 'msruna1' : added
MS run 'msruna2' file '/gorgone/pappso/moulon/raw/20210819_Domergue_48/20210826_Domergue_48_IMB.mzXML' : parsing begin
MS run 'msruna2' : xml file '/gorgone/pappso/moulon/raw/20210819_Domergue_48/20210826_Domergue_48_IMB.mzXML' : parsing OK
MS run 'msruna2' : added
MS run group 'all_msrun' = (msruna1, msruna2) : defined
Alignment method 'my_ms2' : added
MS run group 'all_msrun': alignment method 'my_ms2', reference msrun 'msruna1': alignment begin
MS2 alignment parameters :
ms2_tendency_halfwindow = 10
ms2_smoothing_halfwindow = 15
ms1_smoothing_halfwindow = 0
Aligning MS run 'msruna1' : shared peptides 4242
Aligning MS run 'msruna2' : shared peptides 2258
MS run group 'all_msrun' : alignment method 'my_ms2', reference msrun 'msruna1' : alignment finished
Quantification method 'quant1' : added
MS run group 'all_msrun': quantification method 'quant1': quantification begin
Quantification method 'quant1' parameters :
xic type : 'max' second chance:0
Quantification 'q1' : preparing MS run 'msruna1' to extract and quantify 15963 XICs
quantifying MS run 'msruna1' : 1/2 in group 'all_msrun'
Erreur de segmentation
`
MS run 'msruna2' : added
MS run group 'all_msrun' = (msruna1, msruna2) : defined
Alignment method 'my_ms2' : added
MS run group 'all_msrun': alignment method 'my_ms2', reference msrun 'msruna1': alignment begin
MS2 alignment parameters :
ms2_tendency_halfwindow = 10
ms2_smoothing_halfwindow = 15
ms1_smoothing_halfwindow = 0
Aligning MS run 'msruna1' : shared peptides 4242
Aligning MS run 'msruna2' : shared peptides 2258
MS run group 'all_msrun' : alignment method 'my_ms2', reference msrun 'msruna1' : alignment finished
Quantification method 'quant1' : added
MS run group 'all_msrun': quantification method 'quant1': quantification begin
Quantification method 'quant1' parameters :
xic type : 'max' second chance:0
Quantification 'q1' : preparing MS run 'msruna1' to extract and quantify 15963 XICs
quantifying MS run 'msruna1' : 1/2 in group 'all_msrun'
Erreur de segmentation
```Langella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/12bug lors de la quantiificatino de données issue de different spectro2021-11-17T09:13:31+01:00Thierry Balliaubug lors de la quantiificatino de données issue de different spectroMasschroq plante si on quantifie des données issue de differente machine meme si les quantification des machine sont faite dans different groupes
fichier masschroqml
`/gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_massc...Masschroq plante si on quantifie des données issue de differente machine meme si les quantification des machine sont faite dans different groupes
fichier masschroqml
`/gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_masschroq/test_masschroq.masschroqml`
debug message
```
tballiau@proteus1:/gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_masschroq$ tail -F /gorgone/pappso/tmp/temp_masschroq_condor_job7uch/masschroq.error
Oops! an error occurred in MassChroQ. Dont Panic :
error reading masschroqML input file '/gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_masschroq/test_masschroq.masschroqml' :
Parse error at line 1423452, column 19:
ERROR in MasschroqmlParser::endElement tag quantify, MCQ exception:
error in MassChroQ::executeQuantification q1 PappsoException :
XicCoord to add is of a different type
```Langella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/13erreur lors de la quantification de données de timstof2021-09-21T14:53:40+02:00Thierry Balliauerreur lors de la quantification de données de timstofmasschroq lors de la quantificatino de données de tims tof avec l'erreur suivante
```
> tballiau@proteus1:/gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_masschroq$ tail -F /gorgone/pappso/tmp/temp_masschroq_condor_jobJpf...masschroq lors de la quantificatino de données de tims tof avec l'erreur suivante
```
> tballiau@proteus1:/gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_masschroq$ tail -F /gorgone/pappso/tmp/temp_masschroq_condor_jobJpfL/masschroq.error
Oops! an error occurred in MassChroQ. Dont Panic :
error reading masschroqML input file '/gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_masschroq/test_masschroq_ttp_seul.masschroqml' :
Parse error at line 1359351, column 19:
ERROR in MasschroqmlParser::endElement tag quantify, MCQ exception:
error in MassChroQ::executeQuantification q1 PappsoException :
Invalid scan number : scanNum927 > m_scanNumber
```
fichier d'origine
> /gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_masschroq/test_masschroq_ttp_seul.masschroqmlLangella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/14wrong retention time alignement computation in the 2.2.0 branch2022-07-08T13:56:29+02:00Langella Olivierwrong retention time alignement computation in the 2.2.0 brancha severe problem was introduced in e7c05996564b7bd75c63c122dea0902c158b96f8 version 2.2.0-7.
The retention time target that is computed for each peptide from observed MS2 retention times was not corrected using alignment informations.
T...a severe problem was introduced in e7c05996564b7bd75c63c122dea0902c158b96f8 version 2.2.0-7.
The retention time target that is computed for each peptide from observed MS2 retention times was not corrected using alignment informations.
This is a cause of wrong retention time references and a source of error in match between run.
This problem has been partly compensated by the post matching mecanism that can retreive good peaks if they were not found, but this certainly introduce a lot of noise since 21 06 2016.
This problem should have been fixed in 42f3bae8f346ed58cf57fa9aa4cd11b2a556cc30.
After a severe refactoring, that simplifies the code and make it more efficient, this bug was found and fixed.
We have to check it.Langella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/15pas de génératino de fichier peptides avec timstof pro2021-11-17T09:11:55+01:00Thierry Balliaupas de génératino de fichier peptides avec timstof prole run s'arrette sans générer de fichier peptides et sans erreur
masschroqml /gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_masschroq/test_masschroq_ttp_seul_new.masschroqml
extrait de masschroq out
```
WARNING : alignm...le run s'arrette sans générer de fichier peptides et sans erreur
masschroqml /gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_masschroq/test_masschroq_ttp_seul_new.masschroqml
extrait de masschroq out
```
WARNING : alignment time file '/gorgone/pappso/moulon/users/thierry/20210517_robert_28/essai_masschroq/masschroq/time/5-22-2021_1_robert_28_pm3_la_1393.time' : already exists, it will be overwrited
MS run group 'all_msrun' : alignment method 'my_ms2', reference msrun 'msrunb16' : alignment finished
Quantification method 'quant1' : added
MS run group 'all_msrun': quantification method 'quant1': quantification begin
Quantification method 'quant1' parameters :
xic type : 'max' second chance:0
Quantification 'q1' : preparing MS run 'msruna1' to extract and quantify 263361 XICs
quantifying MS run 'msruna1' : 1/24 in group 'all_msrun'
extracting 263361 XICs on 16000 Tims frames
```Langella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/16Disparition des fichier .trace dans le repertorie de sauvegarde des données d...2022-07-08T13:56:09+02:00Thierry BalliauDisparition des fichier .trace dans le repertorie de sauvegarde des données d'alignement.lorsqu'on sauvegarde les données d'alignement le repertoire ne continet plus que les fichiers time.
Pour MCQR j'ai besoin des fichiers trace pour pouvoir afficher les alignements des msrunslorsqu'on sauvegarde les données d'alignement le repertoire ne continet plus que les fichiers time.
Pour MCQR j'ai besoin des fichiers trace pour pouvoir afficher les alignements des msrunshttps://forgemia.inra.fr/pappso/masschroq/-/issues/17not running on tims tof data2022-07-01T10:53:07+02:00Langella Oliviernot running on tims tof dataversion 2.4.10-1~bullseye+1 does not run using :
```
/gorgone/pappso/moulon/users/thierry/20220624_hirel_feuille_/QC/masschroq/QC.masschroqml
```version 2.4.10-1~bullseye+1 does not run using :
```
/gorgone/pappso/moulon/users/thierry/20220624_hirel_feuille_/QC/masschroq/QC.masschroqml
```Langella OlivierLangella Olivierhttps://forgemia.inra.fr/pappso/masschroq/-/issues/18Strange quantification value for tims tof data2022-12-08T09:00:13+01:00Thierry BalliauStrange quantification value for tims tof dataJ'ai observer des données quantitative tres etrange dans une manip de tims tof
les aires retourner par masschroq sont tres faible (1,16) alors que le XIC est propre en visualisation par masschroq.
j'ai extrait les ligne ne question da...J'ai observer des données quantitative tres etrange dans une manip de tims tof
les aires retourner par masschroq sont tres faible (1,16) alors que le XIC est propre en visualisation par masschroq.
j'ai extrait les ligne ne question dans le fichier de sortie de masschroq avec la commande suivante
`cat peptides_q1_All_samples.tsv| grep "ALLDDPVFRPLVEK" > verif_pepc220a1.tsv`
les fichier d'origines sont disponible dans le repertoire
/gorgone/pappso/moulon/users/Marlene/20221123_Balazadeh_41/masschroq/result_20221123_Balazadeh_41.d
le masschroqml se trouve dans le repertoire
/gorgone/pappso/moulon/users/Marlene/20221123_Balazadeh_41/masschroq
je joins une extraction du signal pour le peptide en question via i2masschroq avec d'autre msrun
le msrun impacte est le
/gorgone/pappso/moulon/raw/20221123_Balazadeh_41/11-26-2022_20221123_Balazadeh_41_BULK03_1_4129.d
![XIC_brute_pepc220a1](/uploads/9552d601250a9b438e80c84e754352f3/XIC_brute_pepc220a1.png)
les pic sont plutot joli et bien defini et ne devrai pas poser de probleme a l'extraction et les rt sont tres semblable pour l'ensemble des fichiers
Ce que je ne comprends pas c'est pourquoi on arrive a avoir une valeur si faible alors que le threshold est superieur.Langella OlivierLangella Olivier