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Nesvilab / PD-Nodes

The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes
http://www.nesvilab.org/PD-Nodes/
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Error with PD2.5 node? #29

Closed Alemarcohen closed 1 year ago

Alemarcohen commented 2 years ago

Hi MSFragger folks,

I'm running the MSFragger3.5 node within PD 2.5 on data acquired on a Fusion Lumos with FAIMS source on. I get the following errors, any ideas? Screenshot 2022-09-01 162600 Screenshot 2022-09-01 163116

Thanks!

Alejandro

huiyinc commented 2 years ago

Hi Alejandro,

The Java SE Runtime Environment 8 (or above) is required to be installed prior to use MSFragger-PD node. Have you installed it? If not, you may download the JRE here: https://www.oracle.com/java/technologies/downloads/#java8

Best,

Huiyin

Alemarcohen @.***> 於 2022年9月2日 上午3:33 寫道：



Hi MSFragger folks,

I'm running the MSFragger3.5 node within PD 2.5 on data acquired on a Fusion Lumos with FAIMS source on. I get the following errors, any ideas? [image: Screenshot 2022-09-01 162600] https://user-images.githubusercontent.com/29800323/187997157-d6c33a49-ac8e-4814-b2e6-fee3195465c9.gif [image: Screenshot 2022-09-01 163116] https://user-images.githubusercontent.com/29800323/187997161-db0a8043-0e3b-412b-944b-0a2e996b51e1.gif

Thanks!

Alejandro

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/29, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA7645UT47VI256WJY3V4EAJ3ANCNFSM6AAAAAAQCU75PM . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Alemarcohen commented 2 years ago

Dear Huiyin, thanks for the quick response!

Yes, I do have Java installed. Interestingly, when I run MSFragger from Fragpipe, it works fine, hence, I suppose something wrong with the PD setup? Any suggestions?

Alejandro

huiyinc commented 2 years ago

Hi Alejandro,

I notice that there is an error message: invalid maximum heap size -Xmx116G. Do you specify the RAM or use the default value (i.e., -1)? If you use the default value, I am guessing maybe the RAM is insufficient because you are using two search engines. Maybe you could specify the RAM as 60GB to ensure that the RAM is sufficient for the two search engines. Please feel free to let me know if it works for you.

Best,

Huiyin

Alemarcohen @.***> 於 2022年9月3日 上午4:59 寫道：



Dear Huiyin, thanks for the quick response!

Yes, I do have Java installed. Interestingly, when I run MSFragger from Fragpipe, it works fine, hence, I suppose something wrong with the PD setup? Any suggestions?

Alejandro

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/29#issuecomment-1235890440, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA3HQYOSDBQWWM4RJH3V4JTCHANCNFSM6AAAAAAQCU75PM . You are receiving this because you commented.Message ID: @.***>