Not able to install in Discoverer 2.4

[ncarrut]

Hi, I'm trying to use MSFragger with Discoverer 2.4. I think I've followed all the directions but the processing nodes don't appear. The MagellanServer log is attached. It seems like there is a problem with the .net framework. Ours is version 4.0.30319. Do you have any suggestions?
Regards, Nick Carruthers, Wayne State MagellanServer.log

[huiyinc]

Hi Nick,

I notice that you have .NET Framework 4.0 installed in your computer. Could you please install .Net Framework 4.7 (or above) and try it again? Here is the link for downloading .Net Framework 4.7: https://dotnet.microsoft.com/download/visual-studio-sdks?utm_source=getdotnetsdk&utm_medium=referral Please feel free to contact me if you have any question. Thank you.

Huiyin

ncarrut notifications@github.com 於 2020年2月18日 週二 下午3:11寫道：

Hi, I'm trying to use MSFragger with Discoverer 2.4. I think I've followed all the directions but the processing nodes don't appear. The MagellanServer log is attached. It seems like there is a problem with the .net framework. Ours is version 4.0.30319. Do you have any suggestions? Regards, Nick Carruthers, Wayne State MagellanServer.log https://github.com/Nesvilab/MSFragger/files/4221446/MagellanServer.log

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/59?email_source=notifications&email_token=ALAWWA4PAEAYZMEHJT2N77TRDQ6FRA5CNFSM4KXLUF72YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IONXCXQ, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA5AU5SGMN56NV5YDZTRDQ6FRANCNFSM4KXLUF7Q .

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[ncarrut]

Huiyin, Thanks for your advice. I upgraded .NET and got Discoverer to import the nodes. But I still can't get a search to finish. It starts OK but then gets stuck. I attached a screen shot. Can you suggest anything else? Is there anything else I can send you? Regards, Nick

PS I used the workflow you provided in the PD download.

[huiyinc]

Hi Nick,

Thanks for reaching out. Could you please convert the RAW files to mzML files and try it again? Thank you.

Huiyin

ncarrut notifications@github.com 於 2020年2月24日 週一 上午9:38寫道：

Huiyin, Thanks for your advice. I upgraded .NET and got Discoverer to import the nodes. But I still can't get a search to finish. It starts OK but then gets stuck. I attached a screen shot. Can you suggest anything else? Is there anything else I can send you? Regards, Nick

[image: image] https://user-images.githubusercontent.com/7575597/75160784-aa6ea200-56e8-11ea-9e5f-6b9b98c66c7e.png

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/59?email_source=notifications&email_token=ALAWWAYZKUHABW5GQLPGIPTREPLUPA5CNFSM4KXLUF72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMYAXDA#issuecomment-590351244, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA2OSQNPHZEOKZG7UTLREPLUPANCNFSM4KXLUF7Q .

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[ncarrut]

Huiyin, Thanks for your continued attention to this. I converted to mzML and re-ran but there was not much impact. Do you have any other suggestions? Regards, Nick

[ncarrut]

Huiyin, The same search as my previous comment (using mzML) eventually failed and generated some additional messages:

[huiyinc]

Hi Nick,

Based on your log, there is 0 PSMs stored in msf file, meaning there is no pepXML file generated by MSFragger. Could you please send me the full log messages by copying and pasting the logs in a text file? Thank you.

Huiyin

ncarrut notifications@github.com 於 2020年2月25日 週二 下午12:36寫道：

Huiyin, The same search as my previous comment (using mzML) eventually failed and generated some additional messages:

[image: image] https://user-images.githubusercontent.com/7575597/75270700-fd1f8b00-57c8-11ea-9c80-4635261adb25.png

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/59?email_source=notifications&email_token=ALAWWA4WDWYZYACSVCALU6LREVJJ3A5CNFSM4KXLUF72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM4YR5Y#issuecomment-590973175, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAZI2P7YMMHCJJWM7I3REVJJ3ANCNFSM4KXLUF7Q .

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[ncarrut]

Huiyin, Here are the messages. Regards, Nick errorLot.txt

[huiyinc]

Hi Nick,

I notice that you are using a very old version of MSFragger, MSFragger version MSFragger-20171106. You might have to download the latest version of MSFragger to run the MSFragger-PD node. Thank you.

Huiyin

ncarrut notifications@github.com 於 2020年2月25日 週二 下午2:37寫道：

Huiyin, Here are the messages. Regards, Nick errorLot.txt https://github.com/Nesvilab/MSFragger/files/4251814/errorLot.txt

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/59?email_source=notifications&email_token=ALAWWA7WOYUAPJOF7FNNEY3REVXQZA5CNFSM4KXLUF72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM5GUAA#issuecomment-591030784, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA4KIJFH2GXHFERJZYDREVXQZANCNFSM4KXLUF7Q .

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan

[ncarrut]

Huiyin, Thanks for your help. Updating MSFragger fixed the problem. Regards, Nick

[huiyinc]

Hi Nick,

Glad to hear that. Please feel free to ask if you have any question Best wishes,

Huiyin

ncarrut notifications@github.com 於 2020年3月2日 週一 下午1:03寫道：

Huiyin, Thanks for your help. Updating MSFragger fixed the problem. Regards, Nick

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/MSFragger/issues/59?email_source=notifications&email_token=ALAWWA5HPJJEZLFW7QAIUQTRFPYGBA5CNFSM4KXLUF72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENQKDOY#issuecomment-593535419, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA65TOESH22HCYDHIK3RFPYGBANCNFSM4KXLUF7Q .

-- Hui-Yin Chang, 張彙音 Research Fellow Department of Pathology University of Michigan