search

OpenMS / OpenMS

The codebase of the OpenMS project
https://www.openms.de
Other
478 stars 318 forks source link

questions about TOPP command line for openswathworkflow #4656

Open Clovernana opened 4 years ago

Clovernana commented 4 years ago

Hi there， I have used the training data set from the web set http://www.peptideatlas.org/PASS/PASS00779.I'm new to openswath,I have followed the tutorial of openswath and my operation seems always wrong.I have met a confusing problem.I have put the interface picture here. 图片1 And what's wrong ?

jpfeuffer commented 4 years ago

Hi!

Did you make any progress on this already? Your command looks very weird. Maybe there were some copy/paste issues when trying to execute the command?

Clovernana commented 4 years ago

Hi， I‘ve got a F drive in my laptop.And I did't make any progress about this .It's very confusing.And I have another problem. image image And this is all my data that is saved in F .And I can only use windows system.Or alse ,could you tell me how to write the code.I've tried many times but all failed.

Clovernana commented 4 years ago

Hi， I have met this problem shown below： C:\Program Files\OpenMS-2.5.0\bin>OpenSwathWorkflow -in F:/openswathdata/olgas_K121026_001_SW_Wayne_R1_d00-Mtb_Wayne_01.mzML -tr F:/openswathdata/library.tsv -tr_irt F:/openswathdata/iRTassays.TraML -swath_windows_file F:/openswathdata/SWATHwindows_analysis.tsv -sort_swath_maps -batchSize 1000 -readOptions cache -out_features F:/openswathdata/output.featureXML Validate provided Swath windows file: Read Swath window header: 'start end' Read Swath window file with 32 SWATH windows. Progress of 'Load TSV file': Warning: The peptide sequence GIDEQSHASWFVFQIDALR and the full peptide name DAQILGVSIDSEFAHFQWR are not equal. Please check your input. (use force_invalid_mods to override) Warning: The peptide sequence EEVTQQIALNNVDYR and the full peptide name DAQINEVQEVLTNYR are not equal. Please check your input.

occurred 2 times Warning: The peptide sequence IAVPAQITAAQPEVPCSADR and the full peptide name DAQPAQIVIAVPAAPESTC(Carbamidomethyl)R are not equal. Please check your input. occurred 2 times Warning: The peptide sequence IANVQLDALLDASPIER and the full peptide name DAQSVLAAIDNLLPEIR are not equal. Please check your input. occurred 2 times Warning: The peptide sequence LFALPQFTAPATDPR and the full peptide name DAQTPTLLFPFAAPR are not equal. Please check your input. occurred 2 times Warning: The peptide sequence GDSLMAFATALLAR and the full peptide name AAMFAGLADSTLLR are not equal. Please check your input. Warning: The peptide sequence GADAQLVIAR and the full peptide name DAQVAALIGR are not equal. Please check your input. Warning: The peptide sequence VGAVGTQAVFPAFESDK and the full peptide name DAQVFEFGTAPGSAVVK are not equal. Please check your input. occurred 2 times Warning: The peptide sequence IGVNPQTVAGHCEYVADLQTDEVHAAVDR and the full peptide name DAQVPTIETGVGNC(Carbamidomethyl)HVYVHQAADLDVAER are not equal. Please check your input. occurred 2 times Warning: The peptide sequence QARPDVGER and the full peptide name DARPGEVQR are not equal. Please check your input. Warning: The peptide sequence DQRPGGIDEAAQSDDPS and the full peptide name DARPIEQDDDQGAGSPS are not equal. Please check your input. Warning: The peptide sequence AAHFGSEGHEAGGEDSPVGQHHR and the full peptide name DASAGGEAGHQEHHHVPESGFGR are not equal. Please check your input. occurred 2 times Warning: The peptide sequence GVLLILMPTAIAR and the full peptide name AAMGLTIPVLLIR are not equal. Please check your input. Warning: The peptide sequence AVFQSVGADIR and the full peptide name DASGIAQVVFR are not equal. Please check your input. Warning: The peptide sequence AANQKPSGLTTTDAGTLAIR and the full peptide name DASGKPQIAATLNGTLATTR are not equal. Please check your input. occurred 2 times Warning: The peptide sequence GGSPAAPPDPR and the full peptide name DASPGAPPGPR are not equal. Please check your input. Warning: The peptide sequence VADQSTQK and the full peptide name DASQQVTK are not equal. Please check your input. Warning: The peptide sequence SIHTAVSDDVR and the full peptide name DASSTDVIVHR are not equal. Please check your input. occurred 2 times Warning: The peptide sequence IANHLKPSGESVSLTAAAMPSPCPSALDR and the full peptide name DASTLKPMLAAGNC(Carbamidomethyl)VAIESPHPSPLSASR are not equal. Please check your input. Error: Unexpected internal error (the value 'UniMod:4' was used but is not valid; Modification not found: ) <(use force_invalid_mods to override)> occurred 28 times Could you help me check it out? On 4/23/2020 01:39，jpfeuffer wrote： Hi! Did you make any progress on this already? Your command looks very weird. Maybe there were some copy/paste issues when trying to execute the command? The first input file looks truncated from the beginning AND the end. There is also a space missing between the first file and the second. And I am not sure about the "f" folder you are trying to use. If this is supposed to be a drive letter in Windows, unless you are in Git or MinGW bash, I don't know if you can use the Linux style (e.g. /c/ instead of C:). And if you did not intentionally store the library.tsv in the OpenMS bin folder, you probably have to additionally specify full path for library.tsv as well. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.
Clovernana commented 4 years ago

Hi， In brief,the -tr file in the http://www.peptideatlas.org/PASS/PASS00779 seems always go wrong in my run . Here is the code I have used showing below. image The error is showned below. image

And I have tried the three files given in the data set. Mtb_TubercuList-R27_iRT_UPS_decoy_OpenMS21compatible.tsv Mtb_TubercuList-R27_iRT_UPS.tsv Mtb_TubercuList-R27_iRT_UPS_decoy.tsv All this three file are run in the TOPP command line,but all failed. Is there any error in my code or any problem with my operation or any question with the data set? It's really confusing.

oliveralka commented 4 years ago

Hi,

I tested with OpenMS-2.5.0 (windows10) and everything worked.

E:\Programming\OpenMS-2.5.0\bin\OpenSwathWorkflow.exe -in F:\OpenSWATH_test_data\PASS00779\olgas_K121026_001_SW_Wayne_R1_d00.mzML -tr F:\OpenSWATH_test_data\PASS00779\Mtb_TubercuList-R27_iRT_UPS_decoy_OpenMS21compatible.tsv -tr_irt F:\OpenSWATH_test_data\PASS00779\iRTassays.TraML -swath_windows_file F:\OpenSWATH_test_data\PASS00779\SWATHwindows_analysis.tsv -out_tsv F:\OpenSWATH_test_data\PASS00779\test_output.tsv

Could you please try it again? Which file are you using as -tr, since it is called library.tsv, which was not included in PASS00779? How did you convert the files or did you do anything else to the mzML files, since the name seems off "...-Mtb_Wayne_01.mzML".

Clovernana commented 4 years ago

Hi ， I use the same file as you .Exactly,I have tried the three libraries that provided in this data set.But all failed. I checked the command that i used .There is no big difference between the command that i used and yours.I use the -batchSize 1000 -readOptions cache than you .The library is the file that is the same as the decoy library file in the data set.I just changed the long name.But i just can't make it.I am also fingding the reasons. Best regard, Clover

On 5/6/2020 00:54，Oliver Alkanotifications@github.com wrote：

Hi,

I tested with OpenMS-2.5.0 and everything worked.

E:\Programming\OpenMS-2.5.0\bin\OpenSwathWorkflow.exe -in F:\OpenSWATH_test_data\PASS00779\olgas_K121026_001_SW_Wayne_R1_d00.mzML -tr F:\OpenSWATH_test_data\PASS00779\Mtb_TubercuList-R27_iRT_UPS_decoy_OpenMS21compatible.tsv -tr_irt F:\OpenSWATH_test_data\PASS00779\iRTassays.TraML -swath_windows_file F:\OpenSWATH_test_data\PASS00779\SWATHwindows_analysis.tsv -out_tsv F:\OpenSWATH_test_data\PASS00779\test_output.tsv

Could you please try it again? Which file are you using as -tr, since it is called library.tsv, which was not included in PASS00779?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

jpfeuffer commented 4 years ago

What about the difference in the name of the mzML file? Do you know the reason for that (e.g. which converter was used)? olgas_K121026_001_SW_Wayne_R1_d00.mzML vs olgas_K121026_001_SW_Wayne_R1_d00-Mtb_Wayne_01.mzML ?

Clovernana commented 4 years ago

Actually, I use the file that has been transformed by MS Convert .I followed the description in the openswath tutorial.And I have compared the file name that I used. "-in F:/openswathdata/olgas_K121026_007_SW_Wayne_R2_d00.mzML" Is there any difference between the file names? Here is the data set in the piptide atlas.And there is no " olgas_K121026_001_SW_Wayne_R1_d00-Mtb_Wayne_01.mzML".And i do not know the difference between the two names. On 5/8/2020 19:52，jpfeuffernotifications@github.com wrote：

What about the difference in the name of the mzML file? Do you know the reason for that (e.g. which converter was used)? olgas_K121026_001_SW_Wayne_R1_d00.mzML vs olgas_K121026_001_SW_Wayne_R1_d00-Mtb_Wayne_01.mzML ?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.