poky builder crashes during preprocess

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Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

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From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Tuesday, August 10, 2021 at 5:19 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] poky builder crashes during preprocess

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Jun Yang

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Aug 11, 2021, 12:03:33 PM8/11/21

to NMR POKY/SPARKY USER GROUP

Yes, I have full privilege on the working folder. In fact, I can see a bunch of peak list files are created during poky builder process. I'm so close to actually get a taste of this powerful program!

Jun

Lee, Woonghee

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Aug 11, 2021, 12:06:58 PM8/11/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

Would you check the following?

H_completeness.txt in the working folder
oxiCys.txt in the working folder
cisPro.txt in the working folder
.list files in the working folder
packed_inputs.txt file in the working folder
failed.txt in the working folder

Please let me know the existence of those files.

Thanks,

Woonghee

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Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>

Date: Wednesday, August 11, 2021 at 10:03 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>

Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

[External Email - Use Caution]Yes, I have full privilege on the working folder. In fact, I can see a bunch of peak list files are created during poky builder process. I'm so close to actually get a taste of this powerful program!

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/074a619a-9e75-4871-bf66-c17c872c2ea1n%40googlegroups.com.

Jun Yang

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Aug 11, 2021, 12:37:40 PM8/11/21

to NMR POKY/SPARKY USER GROUP

I put answers after each question.

On Wednesday, August 11, 2021 at 12:06:58 PM UTC-4 Lee, Woonghee wrote:

Hi Jun,

Would you check the following?

H_completeness.txt in the working folder: " 80.436608 %" in H_completeness.txt
oxiCys.txt in the working folder: no such file because no cys in the sequence
cisPro.txt in the working folder: no such file because no known Pro
.list files in the working folder: n-noesy.list; c-noesy.list; n-hsqc.list; c-hsqc.list, all look fine to me. by the way, does the assignment format matter because I use %a3-%a2 for noesy and %a2 for hsqc.
packed_inputs.txt file in the working folder: no such file
failed.txt in the working folder: no such file

Lee, Woonghee

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Aug 11, 2021, 12:50:08 PM8/11/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

Would you compress the working folder and send me not copying the user group email?

Thanks,

Woonghee

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Wednesday, August 11, 2021 at 10:37 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

[External Email - Use Caution]I put answers after each question.

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Lee, Woonghee

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Aug 11, 2021, 2:03:18 PM8/11/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

Do you include c-hsqc.list and n-hsqc.list as inputs? They are not NMR thru-space data.

Best,

Woonghee

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Wednesday, August 11, 2021 at 10:37 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

[External Email - Use Caution]I put answers after each question.

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Jun Yang

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Aug 11, 2021, 2:59:01 PM8/11/21

to NMR POKY/SPARKY USER GROUP

I didn't input the two hsqc lists. I re-created the two noesy list files with assignment format %a1-%a2-%a3 and open them in poky builder instead of the dataset itself, and again I got the core dumped error as follow:

Copy /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/protein.seq to /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/protein.seq.bak.
ReadSequenceFromFile()
Copy /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/protein.seq to /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/protein.seq.bak.
ReadSequenceFromFile()
Copy /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/n-noesy_assgin.list to /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/n-noesy_assgin.list.bak.
Copy /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/c-noesy_assign.list to /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/c-noesy_assign.list.bak.

ReadSequence()
Copy /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/pokybuilder.prot to /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/pokybuilder.prot.
CreateSequence()
FixWinPathSeparators
ReadChemicalShift
Reading /home-lri/yangj2/Transfer/Poky/Structure/Poky_Builder/work1_initial/pokybuilder.prot...
1785 lines loaded.
FindCisProlines
Done with Build Parameters
GetCompleteness: Completeness - 80.436608

free(): invalid pointer
Aborted (core dumped)

The files in the work folder are:

c-noesy_assign.list H_completeness.txt n-noesy_assgin.list pokybuilder.prot protein.seq
c-noesy_assign.list.bak H_missing.txt n-noesy_assgin.list.bak pokybuilder.seq protein.seq.bak

Anything else I need to check?

Bests,

Jun

Lee, Woonghee

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Aug 11, 2021, 4:14:15 PM8/11/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun, your assignment format is incorrect in your noesy data. Clear them all (pa, aD) and do it again.

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/2ff4b2ac-4256-4107-9465-bccf1b2872a9n%40googlegroups.com.

Jun Yang

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Aug 11, 2021, 4:52:09 PM8/11/21

to NMR POKY/SPARKY USER GROUP

I've sent you another compressed file. The assignment is in the format of %a1-%a2-%a3. Jun

Jun Yang

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Aug 12, 2021, 1:01:58 AM8/12/21

to NMR POKY/SPARKY USER GROUP

I've installed poky in July under win10 but I don't remember the version. The program only shows "20210310". Anyway, I created a working folder and copied the sequence file, resonance list, and two noesy lists. I opened the poky builder, set the working folder and load all 4 files and use default setting for everything else. After I click "preprocess", it runs for a couple seconds and the whole program then exit by itself. I looked at the cmd window, and here is the message:

Running Poky

Copy C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial/protein.seq to C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial/protein.seq.bak.

ReadSequenceFromFile()

Copy C:\Users\yangj2\Downloads\poky_win\Poky\PokyBuild\work1_initial\protein.seq to C:\Users\yangj2\Downloads\poky_win\Poky\PokyBuild\work1_initial\protein.seq.bak.

ReadSequenceFromFile()

Copy C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial/resonance.prot to C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial/resonance.prot.bak.

Copy C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial/c-noesy_assign.list to C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial/c-noesy_assign.list.bak.

Copy C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial/n-noesy_assgin.list to C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial/n-noesy_assgin.list.bak.

ReadSequence()

Copy C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial\pokybuilder.prot to C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial\pokybuilder.prot.

CreateSequence()

FixWinPathSeparators

ReadChemicalShift

Reading C:/Users/yangj2/Downloads/poky_win/Poky/PokyBuild/work1_initial/pokybuilder.prot...

1785 lines loaded.

FindCisProlines

Done with Build Parameters

GetCompleteness: Completeness - 80.352645

Finished

Is this normal? If so, what should I do next, reload everything and click "calculate"?

Bests,

Jun

Lee, Woonghee

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Aug 12, 2021, 2:10:30 AM8/12/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

You don't coy files into the working folder. They will be automatically copied from somewhere else. Once preprocess is done, you can click calculate.

Woonghee

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From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Sent: Wednesday, August 11, 2021 11:01:58 PM

To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

[External Email - Use Caution]I've installed poky in July under win10 but I don't remember the version. The program only shows "20210310". Anyway, I created a working folder and copied the sequence file, resonance list, and two noesy lists. I opened the poky builder, set the working folder and load all 4 files and use default setting for everything else. After I click "preprocess", it runs for a couple seconds and the whole program then exit by itself. I looked at the cmd window, and here is the message:

To view this discussion on the web visit https://groups.google.com/d/msgid/nmr-sparky/94853a3b-44e6-47a1-bac9-706b344ffd8an%40googlegroups.com.

Jun Yang

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Aug 12, 2021, 8:49:47 AM8/12/21

to NMR POKY/SPARKY USER GROUP

Hi Woonghee,

I tried to load data files from other folders, or import data from current project, but both approaches end with the same result where the program just exit itself and the outputs are also the same. Anything else I should try?

Bests

Jun

Lee, Woonghee

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Aug 12, 2021, 12:07:34 PM8/12/21

to NMR POKY/SPARKY USER GROUP

Do you have packed_inputs.txt in the folder? Then, it is ready to go. Just click calculate.

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

https://youtu.be/OiKSm6mubEM

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: "Lee, Woonghee" <WOONGH...@UCDENVER.EDU>
Date: Thursday, August 12, 2021 at 7:51 AM
To: Jun Yang <yangj...@gmail.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

Do you have packed_inputs.txt in the folder? Then, it is ready to go. Just click calculate.

Get Outlook for Android

From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Sent: Thursday, August 12, 2021 6:49:46 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

[External Email - Use Caution]Hi Woonghee,

I tried to load data files from other folders, or import data from current project, but both approaches end with the same result where the program just exit itself and the outputs are also the same. Anything else I should try?

Bests

Jun

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Jun Yang

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Aug 12, 2021, 12:25:21 PM8/12/21

to NMR POKY/SPARKY USER GROUP

No I don't have that file. The only files in the working folders are: H_completeness.txt, H_missing.txt, n-noesy.list, c-noesy.list, pokybuilder.prot, pokybuilder.seq.

It would be great if you have time to set up a zoom meeting, then I can share my screen and you may be able to find out the issue. I just hope this won't be the step that prevents us from taking advantage of your wonderful work.

Bests

Jun

Lee, Woonghee

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Aug 12, 2021, 12:45:07 PM8/12/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

I am busy preparing a new semester nowadays. Have you watched these videos?

https://youtu.be/roZxxhx_epo?t=26100

https://youtu.be/XPoEI0txsxY?t=1126

https://www.youtube.com/watch?v=BDx027l23U0&list=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfW&index=6&ab_channel=LeeGroupatCUDenver

Woonghee

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Thursday, August 12, 2021 at 10:25 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

[External Email - Use Caution]No I don't have that file. The only files in the working folders are: H_completeness.txt, H_missing.txt, n-noesy.list, c-noesy.list, pokybuilder.prot, pokybuilder.seq.

It would be great if you have time to set up a zoom meeting, then I can share my screen and you may be able to find out the issue. I just hope this won't be the step that prevents us from taking advantage of your wonderful work.

Bests

Jun

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Jun Yang

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Aug 12, 2021, 1:02:01 PM8/12/21

to NMR POKY/SPARKY USER GROUP

Hi Woonghee,

Of course I don't mean to interrupt your normal schedule. I just wish to get your help when you have time. I've followed exactly the steps in the first video. I didn't look into the rest videos because they are for Ponderosa and I thought one of the big advantage of poky is that I don't have to deal with the complicated steps in ponderosa.

Furthermore, since you said my data works fine from your end, so it's not the data themselves, but some settings in my end need to be fixed.

Hope to get your help soon. Do you think one of your group member can have time to help me out?

Bests,

Jun

Lee, Woonghee

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Aug 12, 2021, 1:06:20 PM8/12/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

If you can record your desktop what you are doing and send it to me, I can watch and troubleshoot for you when I can. You can simply use Zoom to do that. I hope I can help you out, but I couldn’t reproduce the problem at my end with your inputs. I just want to see how you do it.

Best,

Woonghee

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Thursday, August 12, 2021 at 11:02 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

[External Email - Use Caution]Hi Woonghee,

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Jun Yang

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Aug 12, 2021, 4:17:14 PM8/12/21

to NMR POKY/SPARKY USER GROUP

Hi Woonghee,

I'd be happy to do that so you can figure out the issue. How to record my operation in zoom without setting up a meeting?

Bests,

Jun

Lee, Woonghee

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Aug 12, 2021, 4:20:49 PM8/12/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Hi Jun,

Do you have your own zoom meeting room? If so, you can just join your own room, share the screen and click recording. If you have cloud recording feature, that will be a lot easier because you can just share the link to me. By the way, I have submitted a calculation job with your inputs and been waiting for the completion. It went through without any problem on my apple silicon m1 macbook pro. I will share you the result link when done.

Best,

Woonghee

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672

Shipping/Mailing Address:

Woonghee Lee

1201 5^th St. UCD CHEM-194

P.O. Box 173364 (USPS)

Denver, CO 80204, USA

From: <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>
Date: Thursday, August 12, 2021 at 2:17 PM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: Re: [NMR POKY/SPARKY] poky builder crashes during preprocess

[External Email - Use Caution]Hi Woonghee,

I'd be happy to do that so you can figure out the issue. How to record my operation in zoom without setting up a meeting?

Bests,

Jun

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Jun Yang

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Aug 12, 2021, 6:37:02 PM8/12/21

to NMR POKY/SPARKY USER GROUP

Good news! I just saw the new version (2021/03/10i) of poky available so I go ahead download and install it. And the preprocess went through without a problem!!

Thanks!

Jun

Lee, Woonghee

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Aug 12, 2021, 6:44:43 PM8/12/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Sounds great.

Get Outlook for iOS

From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Jun Yang <yangj...@gmail.com>

Sent: Thursday, August 12, 2021 4:37:02 PM

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Jun Yang

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Aug 13, 2021, 5:53:58 PM8/13/21

to NMR POKY/SPARKY USER GROUP

I got the result from the Ponderosa server. Then what's next? Jun

Lee, Woonghee

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Aug 13, 2021, 5:55:24 PM8/13/21

to Jun Yang, NMR POKY/SPARKY USER GROUP

Jun,

Please watch the videos that I shared. You need to do some restraint validation and do calculation iteratively.

Best,

Woonghee

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

Assistant Professor

Department of Chemistry

University of Colorado Denver

1151 Arapahoe St. (Science Bldg.) Rm 4128A

Denver, CO 80217-3364, USA

Office: +1-303-315-7672