Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

While those tests are still running, I pulled out all 185 of the proteins 
that are in the 10OV pepXMLs but not in 01-09OV, figuring that maybe one of 
those is causing the error. I've uploaded that to the same folder 
everything else is in (it's called 10OV_uniq.fasta) - I don't see anything 
that jumps out immediately. (There are no individual characters unique to 
either the headers or the sequences in 10OV, so I don't think there's an 
individual character messing things up.)

On Thursday, October 22, 2020 at 3:49:18 PM UTC-4 David Shteynberg wrote:

> I just re extracted that file and I don't see the issue anymore.  Perhaps 
> this was a decompression issue.
>
> Thanks for checking.
>
> -David
>
> On Thu, Oct 22, 2020 at 12:19 PM Emily Kawaler  wrote:
>
>> Hello,
>> Thanks so much for taking a look! I think the selenocysteines ("U") are 
>> likely not the problem, since I've got those in all of my databases, 
>> including the ones that run correctly. I'm looking at 
>> 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML and I don't see 
>> anything odd in line 171821 (""), so I think our line 
>> numberings might not match up - what does your problematic line contain?
>>
>
>> When I try to run it on my end, it always sticks somewhere in the 
>> 10CPTAC_OV files. Right now I'm running a working set of spectra with a 
>> database that didn't work and vice versa, so hopefully that'll help me pin 
>> down whether it's a problem with my spectra or my database - will let you 
>> know how that turns out!
>>
>> Emily
>>
>> On Thursday, October 22, 2020 at 3:09:29 PM UTC-4 David Shteynberg wrote:
>>
>>> Hi Emily,
>>>
>>> I analyzed the search results that you sent and I am seeing some strange 
>>> things in at least one of the files you gave me.  This may be causing some 
>>> of the problems you saw.
>>> In file 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML on line 
>>> 171821 there are some strange characters (possibly binary) that are 
>>> tripping up the TPP.  I think these might be caused by a bug in an analysis 
>>> tool upstream of the TPP.  Not sure if there are other mistakes of this 
>>> sort.  Also I found some 'U' amino acids in the database which the TPP 
>>> complains about having a mass of 0.
>>>
>>> I hope this helps you somewhat.  Let me know what you find on your end.
>>>
>>> Cheers,
>>> -David
>>>
>>> On Tue, Oct 20, 2020 at 1:42 PM Emily Kawaler  wrote:
>>>
 Sure! The spectra are from the CPTAC2 ovarian propective dataset, 
 though I removed all scans that matched to a standard reference database 
 (I 
 don't think the scan removal is the issue, since I'm also having this 
 problem on a different dataset without removing any scans; I also checked 
 with xmllint and it looks like the mzML pepXML files are valid). I've been 
 running it with the philosopher pipeline, so the pepXML files were 
 generated with MSFragger as part of that pipeline. The database is a 
 customized variant database with contaminants and decoys added by 
 philosopher's database tool. Are there any other specifics you'd like? I 
 can upload my full philosopher.yml file if that would be helpful.

 On Tuesday, October 20, 2020 at 1:30:44 AM UTC-4 David Shteynberg wrote:

> Hi Emily,
>
> I got the data and now I am trying to understand how you are running 
> the analysis.  Can you please describe those steps?
>
> Thank you,
> -David
>
> On Sat, Oct 17, 2020 at 12:54 PM Emily Kawaler  
> wrote:
>
>> I've uploaded the pepXML files, the parameters I used, and the 
>> database here. 
>> 
>> Please let me know if I should be uploading anything else! Thank you!
>>
>> On Saturday, October 17, 2020 at 12:04:21 AM UTC-4 Emily Kawaler 
>> wrote:
>>
>>> Thank you! I'm working on getting it transferred to Drive, so it 
>>> might take a little while, but I'll be in touch!
>>>
>>> On Tuesday, October 13, 2020 at 3:08:44 PM UTC-4 David Shteynberg 
>>> wrote:
>>>
 Hello Emily,

 If you are able to share the dataset including the pepXML file and 
 the database I can try to replicate the issue here and try to 
 troubleshoot 
 the sticking point.

 Thanks,
 -David

 On Tue, Oct 13, 2020 at 11:15 AM Emily Kawaler  
 wrote:

> Hello, and thank you for your response! It doesn't look like the 
> process is using too much memory (I've allocated 300 GB and it's 
> maxing out 
> around 10), and I've kicked up the minprob parameter - it's still 
> getting 
> stuck, unfortunately. 
> Emily
>
> On Friday, October 9, 2020 at 2:24:37 PM UTC-4 Luis wrote:
>
>> Hello Emily,
>>
>> This is not a problem 

Re: [spctools-discuss] DIA to mzML question

[Science Gurl]

Thanks!


On Thu, 22 Oct 2020 at 17:11, Mark Athanason 
wrote:

> If you follow the link further
>
> https://skyline.ms/wiki/home/software/Skyline/page.view?name=OverlappingWindowScheme&_docid=wiki%3A41195689-d578-1036-894e-e465a393d561
>
> they explain how to actually make the isolation scheme in skyline that is
> compatible with several MS manufacturers; I believe the file is quite
> large. You may need to re-acquire your data under these circumstances.
>
> On Thu, Oct 22, 2020 at 5:08 PM Science Gurl 
> wrote:
>
>> Hi Mark,
>>
>> Thanks for the suggestion... This is what I've been doing but I get an
>> error.  I'll switch this query to the SkyLine team for some more
>> troubleshooting!
>> -jane
>>
>> On Thu, 22 Oct 2020 at 17:04, Mark Athanason 
>> wrote:
>>
>>> Jane,
>>>
>>> See this from the Skyline team:
>>>
>>> https://skyline.ms/wiki/home/software/Skyline/page.view?name=DemultiplexingOverlappingDIAWindows
>>>
>>> Best
>>> Mark
>>>
>>> On Thu, Oct 22, 2020 at 4:28 PM Science Gurl 
>>> wrote:
>>>
 Hey David!

 Yes, I'd like to know more about DISCo.  I was poking around that tool
 too and kinda got lost :)  That's what 3 years away from proteomics will do
 for you!  The MSconvert within TPP creates mzML files fine, I guess I don't
 know how to check to see if they have been demultiplexed.  Can I use them
 in DISCo or should I use the MS2 fragment extractor?

 -JN

 On Thu, 22 Oct 2020 at 16:17, 'David Shteynberg' via spctools-discuss <
 spctools-discuss@googlegroups.com> wrote:

> Dear Jane,
>
> I cannot help you with the demultiplexing, because I have not used
> that feature before in MSConvert.  But if you do manage to get a regular
> DIA mzML file out of the conversion you can use the DISCo tool available 
> in
> the TPP under Tools->DIA->Extract MS2 Fragments that will generate a new
> mzML file that you can search and analyze with DDA tools.  As DISCo has
> recently seen major improvements I can provide you with a release 
> candidate
> version if you are interested.
>
> Cheers,
> -David
>
> On Thu, Oct 22, 2020 at 1:08 PM jane n  wrote:
>
>> Hi all,
>>
>> I have acquired a bunch of files on my Eclipse to build a DIA library
>> using an 8mz window in overlap mode (ie essentially 4mz windows) and I'm
>> not clear if the Convert to MzML is demultiplexing to 4mz windows?  I've
>> tried doing it manually in MSconvert but the conversion fails.  On the
>> other hand, do I need to demulitplex?
>>
>> Cheers!
>> -Jane
>>
>> --
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>> Groups "spctools-discuss" group.
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>> send an email to spctools-discuss+unsubscr...@googlegroups.com.
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>> 
>> .
>>
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Re: [spctools-discuss] DIA to mzML question

[Mark Athanason]

If you follow the link further
https://skyline.ms/wiki/home/software/Skyline/page.view?name=OverlappingWindowScheme&_docid=wiki%3A41195689-d578-1036-894e-e465a393d561

they explain how to actually make the isolation scheme in skyline that is
compatible with several MS manufacturers; I believe the file is quite
large. You may need to re-acquire your data under these circumstances.

On Thu, Oct 22, 2020 at 5:08 PM Science Gurl  wrote:

> Hi Mark,
>
> Thanks for the suggestion... This is what I've been doing but I get an
> error.  I'll switch this query to the SkyLine team for some more
> troubleshooting!
> -jane
>
> On Thu, 22 Oct 2020 at 17:04, Mark Athanason 
> wrote:
>
>> Jane,
>>
>> See this from the Skyline team:
>>
>> https://skyline.ms/wiki/home/software/Skyline/page.view?name=DemultiplexingOverlappingDIAWindows
>>
>> Best
>> Mark
>>
>> On Thu, Oct 22, 2020 at 4:28 PM Science Gurl 
>> wrote:
>>
>>> Hey David!
>>>
>>> Yes, I'd like to know more about DISCo.  I was poking around that tool
>>> too and kinda got lost :)  That's what 3 years away from proteomics will do
>>> for you!  The MSconvert within TPP creates mzML files fine, I guess I don't
>>> know how to check to see if they have been demultiplexed.  Can I use them
>>> in DISCo or should I use the MS2 fragment extractor?
>>>
>>> -JN
>>>
>>> On Thu, 22 Oct 2020 at 16:17, 'David Shteynberg' via spctools-discuss <
>>> spctools-discuss@googlegroups.com> wrote:
>>>
 Dear Jane,

 I cannot help you with the demultiplexing, because I have not used that
 feature before in MSConvert.  But if you do manage to get a regular DIA
 mzML file out of the conversion you can use the DISCo tool available in the
 TPP under Tools->DIA->Extract MS2 Fragments that will generate a new mzML
 file that you can search and analyze with DDA tools.  As DISCo has recently
 seen major improvements I can provide you with a release candidate version
 if you are interested.

 Cheers,
 -David

 On Thu, Oct 22, 2020 at 1:08 PM jane n  wrote:

> Hi all,
>
> I have acquired a bunch of files on my Eclipse to build a DIA library
> using an 8mz window in overlap mode (ie essentially 4mz windows) and I'm
> not clear if the Convert to MzML is demultiplexing to 4mz windows?  I've
> tried doing it manually in MSconvert but the conversion fails.  On the
> other hand, do I need to demulitplex?
>
> Cheers!
> -Jane
>
> --
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> 
> .
>
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Re: [spctools-discuss] DIA to mzML question

[Science Gurl]

Hi Mark,

Thanks for the suggestion... This is what I've been doing but I get an
error.  I'll switch this query to the SkyLine team for some more
troubleshooting!
-jane

On Thu, 22 Oct 2020 at 17:04, Mark Athanason 
wrote:

> Jane,
>
> See this from the Skyline team:
>
> https://skyline.ms/wiki/home/software/Skyline/page.view?name=DemultiplexingOverlappingDIAWindows
>
> Best
> Mark
>
> On Thu, Oct 22, 2020 at 4:28 PM Science Gurl 
> wrote:
>
>> Hey David!
>>
>> Yes, I'd like to know more about DISCo.  I was poking around that tool
>> too and kinda got lost :)  That's what 3 years away from proteomics will do
>> for you!  The MSconvert within TPP creates mzML files fine, I guess I don't
>> know how to check to see if they have been demultiplexed.  Can I use them
>> in DISCo or should I use the MS2 fragment extractor?
>>
>> -JN
>>
>> On Thu, 22 Oct 2020 at 16:17, 'David Shteynberg' via spctools-discuss <
>> spctools-discuss@googlegroups.com> wrote:
>>
>>> Dear Jane,
>>>
>>> I cannot help you with the demultiplexing, because I have not used that
>>> feature before in MSConvert.  But if you do manage to get a regular DIA
>>> mzML file out of the conversion you can use the DISCo tool available in the
>>> TPP under Tools->DIA->Extract MS2 Fragments that will generate a new mzML
>>> file that you can search and analyze with DDA tools.  As DISCo has recently
>>> seen major improvements I can provide you with a release candidate version
>>> if you are interested.
>>>
>>> Cheers,
>>> -David
>>>
>>> On Thu, Oct 22, 2020 at 1:08 PM jane n  wrote:
>>>
 Hi all,

 I have acquired a bunch of files on my Eclipse to build a DIA library
 using an 8mz window in overlap mode (ie essentially 4mz windows) and I'm
 not clear if the Convert to MzML is demultiplexing to 4mz windows?  I've
 tried doing it manually in MSconvert but the conversion fails.  On the
 other hand, do I need to demulitplex?

 Cheers!
 -Jane

 --
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 .

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>>> .
>>>
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>>
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Re: [spctools-discuss] DIA to mzML question

[Mark Athanason]

Jane,

See this from the Skyline team:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=DemultiplexingOverlappingDIAWindows

Best
Mark

On Thu, Oct 22, 2020 at 4:28 PM Science Gurl  wrote:

> Hey David!
>
> Yes, I'd like to know more about DISCo.  I was poking around that tool too
> and kinda got lost :)  That's what 3 years away from proteomics will do for
> you!  The MSconvert within TPP creates mzML files fine, I guess I don't
> know how to check to see if they have been demultiplexed.  Can I use them
> in DISCo or should I use the MS2 fragment extractor?
>
> -JN
>
> On Thu, 22 Oct 2020 at 16:17, 'David Shteynberg' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> Dear Jane,
>>
>> I cannot help you with the demultiplexing, because I have not used that
>> feature before in MSConvert.  But if you do manage to get a regular DIA
>> mzML file out of the conversion you can use the DISCo tool available in the
>> TPP under Tools->DIA->Extract MS2 Fragments that will generate a new mzML
>> file that you can search and analyze with DDA tools.  As DISCo has recently
>> seen major improvements I can provide you with a release candidate version
>> if you are interested.
>>
>> Cheers,
>> -David
>>
>> On Thu, Oct 22, 2020 at 1:08 PM jane n  wrote:
>>
>>> Hi all,
>>>
>>> I have acquired a bunch of files on my Eclipse to build a DIA library
>>> using an 8mz window in overlap mode (ie essentially 4mz windows) and I'm
>>> not clear if the Convert to MzML is demultiplexing to 4mz windows?  I've
>>> tried doing it manually in MSconvert but the conversion fails.  On the
>>> other hand, do I need to demulitplex?
>>>
>>> Cheers!
>>> -Jane
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discuss+unsubscr...@googlegroups.com.
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>>> https://groups.google.com/d/msgid/spctools-discuss/af9c2037-59d0-478e-bcfc-d0d09adabd29n%40googlegroups.com
>>> 
>>> .
>>>
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>> 
>> .
>>
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Re: [spctools-discuss] DIA to mzML question

[Science Gurl]

Hey David!

Yes, I'd like to know more about DISCo.  I was poking around that tool too
and kinda got lost :)  That's what 3 years away from proteomics will do for
you!  The MSconvert within TPP creates mzML files fine, I guess I don't
know how to check to see if they have been demultiplexed.  Can I use them
in DISCo or should I use the MS2 fragment extractor?

-JN

On Thu, 22 Oct 2020 at 16:17, 'David Shteynberg' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

> Dear Jane,
>
> I cannot help you with the demultiplexing, because I have not used that
> feature before in MSConvert.  But if you do manage to get a regular DIA
> mzML file out of the conversion you can use the DISCo tool available in the
> TPP under Tools->DIA->Extract MS2 Fragments that will generate a new mzML
> file that you can search and analyze with DDA tools.  As DISCo has recently
> seen major improvements I can provide you with a release candidate version
> if you are interested.
>
> Cheers,
> -David
>
> On Thu, Oct 22, 2020 at 1:08 PM jane n  wrote:
>
>> Hi all,
>>
>> I have acquired a bunch of files on my Eclipse to build a DIA library
>> using an 8mz window in overlap mode (ie essentially 4mz windows) and I'm
>> not clear if the Convert to MzML is demultiplexing to 4mz windows?  I've
>> tried doing it manually in MSconvert but the conversion fails.  On the
>> other hand, do I need to demulitplex?
>>
>> Cheers!
>> -Jane
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to spctools-discuss+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/af9c2037-59d0-478e-bcfc-d0d09adabd29n%40googlegroups.com
>> 
>> .
>>
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> 
> .
>

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Re: [spctools-discuss] DIA to mzML question

['David Shteynberg' via spctools-discuss]

Dear Jane,

I cannot help you with the demultiplexing, because I have not used that
feature before in MSConvert.  But if you do manage to get a regular DIA
mzML file out of the conversion you can use the DISCo tool available in the
TPP under Tools->DIA->Extract MS2 Fragments that will generate a new mzML
file that you can search and analyze with DDA tools.  As DISCo has recently
seen major improvements I can provide you with a release candidate version
if you are interested.

Cheers,
-David

On Thu, Oct 22, 2020 at 1:08 PM jane n  wrote:

> Hi all,
>
> I have acquired a bunch of files on my Eclipse to build a DIA library
> using an 8mz window in overlap mode (ie essentially 4mz windows) and I'm
> not clear if the Convert to MzML is demultiplexing to 4mz windows?  I've
> tried doing it manually in MSconvert but the conversion fails.  On the
> other hand, do I need to demulitplex?
>
> Cheers!
> -Jane
>
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> 
> .
>

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[spctools-discuss] DIA to mzML question

[jane n]

Hi all,

I have acquired a bunch of files on my Eclipse to build a DIA library using 
an 8mz window in overlap mode (ie essentially 4mz windows) and I'm not 
clear if the Convert to MzML is demultiplexing to 4mz windows?  I've tried 
doing it manually in MSconvert but the conversion fails.  On the other 
hand, do I need to demulitplex?

Cheers!
-Jane

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Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

['David Shteynberg' via spctools-discuss]

I just re extracted that file and I don't see the issue anymore.  Perhaps
this was a decompression issue.

Thanks for checking.

-David

On Thu, Oct 22, 2020 at 12:19 PM Emily Kawaler  wrote:

> Hello,
> Thanks so much for taking a look! I think the selenocysteines ("U") are
> likely not the problem, since I've got those in all of my databases,
> including the ones that run correctly. I'm looking at
> 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML and I don't see
> anything odd in line 171821 (""), so I think our line
> numberings might not match up - what does your problematic line contain?
>
> When I try to run it on my end, it always sticks somewhere in the
> 10CPTAC_OV files. Right now I'm running a working set of spectra with a
> database that didn't work and vice versa, so hopefully that'll help me pin
> down whether it's a problem with my spectra or my database - will let you
> know how that turns out!
>
> Emily
>
> On Thursday, October 22, 2020 at 3:09:29 PM UTC-4 David Shteynberg wrote:
>
>> Hi Emily,
>>
>> I analyzed the search results that you sent and I am seeing some strange
>> things in at least one of the files you gave me.  This may be causing some
>> of the problems you saw.
>> In file 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML on line
>> 171821 there are some strange characters (possibly binary) that are
>> tripping up the TPP.  I think these might be caused by a bug in an analysis
>> tool upstream of the TPP.  Not sure if there are other mistakes of this
>> sort.  Also I found some 'U' amino acids in the database which the TPP
>> complains about having a mass of 0.
>>
>> I hope this helps you somewhat.  Let me know what you find on your end.
>>
>> Cheers,
>> -David
>>
>> On Tue, Oct 20, 2020 at 1:42 PM Emily Kawaler  wrote:
>>
>>> Sure! The spectra are from the CPTAC2 ovarian propective dataset, though
>>> I removed all scans that matched to a standard reference database (I don't
>>> think the scan removal is the issue, since I'm also having this problem on
>>> a different dataset without removing any scans; I also checked with xmllint
>>> and it looks like the mzML pepXML files are valid). I've been running it
>>> with the philosopher pipeline, so the pepXML files were generated with
>>> MSFragger as part of that pipeline. The database is a customized variant
>>> database with contaminants and decoys added by philosopher's database tool.
>>> Are there any other specifics you'd like? I can upload my full
>>> philosopher.yml file if that would be helpful.
>>>
>>> On Tuesday, October 20, 2020 at 1:30:44 AM UTC-4 David Shteynberg wrote:
>>>
 Hi Emily,

 I got the data and now I am trying to understand how you are running
 the analysis.  Can you please describe those steps?

 Thank you,
 -David

 On Sat, Oct 17, 2020 at 12:54 PM Emily Kawaler 
 wrote:

> I've uploaded the pepXML files, the parameters I used, and the
> database here.
> 
> Please let me know if I should be uploading anything else! Thank you!
>
> On Saturday, October 17, 2020 at 12:04:21 AM UTC-4 Emily Kawaler wrote:
>
>> Thank you! I'm working on getting it transferred to Drive, so it
>> might take a little while, but I'll be in touch!
>>
>> On Tuesday, October 13, 2020 at 3:08:44 PM UTC-4 David Shteynberg
>> wrote:
>>
>>> Hello Emily,
>>>
>>> If you are able to share the dataset including the pepXML file and
>>> the database I can try to replicate the issue here and try to 
>>> troubleshoot
>>> the sticking point.
>>>
>>> Thanks,
>>> -David
>>>
>>> On Tue, Oct 13, 2020 at 11:15 AM Emily Kawaler 
>>> wrote:
>>>
 Hello, and thank you for your response! It doesn't look like the
 process is using too much memory (I've allocated 300 GB and it's 
 maxing out
 around 10), and I've kicked up the minprob parameter - it's still 
 getting
 stuck, unfortunately.
 Emily

 On Friday, October 9, 2020 at 2:24:37 PM UTC-4 Luis wrote:

> Hello Emily,
>
> This is not a problem that we have seen much of.  Do you know
> which version of ProteinProphet / TPP you are using?
>
> One potential issue is the large number of proteins (and peptides)
> that it is trying to process -- can you either monitor the memory 
> usage of
> the machine when you run this dataset, and/or try on one with more 
> memory?
>
> Hope this helps,
> --Luis
>
>
> On Tue, Oct 6, 2020 at 6:32 PM Emily Kawaler 
> wrote:
>
>> Hello! I've been running ProteinProphet as part of the
>> Philosopher pipeline for a while now with no problems. However, one 
>> of my
>> datasets seems to 

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

Hello,
Thanks so much for taking a look! I think the selenocysteines ("U") are 
likely not the problem, since I've got those in all of my databases, 
including the ones that run correctly. I'm looking at 
03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML and I don't see 
anything odd in line 171821 (""), so I think our line numberings might not match up - 
what does your problematic line contain?

When I try to run it on my end, it always sticks somewhere in the 
10CPTAC_OV files. Right now I'm running a working set of spectra with a 
database that didn't work and vice versa, so hopefully that'll help me pin 
down whether it's a problem with my spectra or my database - will let you 
know how that turns out!

Emily


On Thursday, October 22, 2020 at 3:09:29 PM UTC-4 David Shteynberg wrote:

> Hi Emily,
>
> I analyzed the search results that you sent and I am seeing some strange 
> things in at least one of the files you gave me.  This may be causing some 
> of the problems you saw.
> In file 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML on line 
> 171821 there are some strange characters (possibly binary) that are 
> tripping up the TPP.  I think these might be caused by a bug in an analysis 
> tool upstream of the TPP.  Not sure if there are other mistakes of this 
> sort.  Also I found some 'U' amino acids in the database which the TPP 
> complains about having a mass of 0.
>
> I hope this helps you somewhat.  Let me know what you find on your end.
>
> Cheers,
> -David
>
> On Tue, Oct 20, 2020 at 1:42 PM Emily Kawaler  wrote:
>
>> Sure! The spectra are from the CPTAC2 ovarian propective dataset, though 
>> I removed all scans that matched to a standard reference database (I don't 
>> think the scan removal is the issue, since I'm also having this problem on 
>> a different dataset without removing any scans; I also checked with xmllint 
>> and it looks like the mzML pepXML files are valid). I've been running it 
>> with the philosopher pipeline, so the pepXML files were generated with 
>> MSFragger as part of that pipeline. The database is a customized variant 
>> database with contaminants and decoys added by philosopher's database tool. 
>> Are there any other specifics you'd like? I can upload my full 
>> philosopher.yml file if that would be helpful.
>>
>> On Tuesday, October 20, 2020 at 1:30:44 AM UTC-4 David Shteynberg wrote:
>>
>>> Hi Emily,
>>>
>>> I got the data and now I am trying to understand how you are running the 
>>> analysis.  Can you please describe those steps?
>>>
>>> Thank you,
>>> -David
>>>
>>> On Sat, Oct 17, 2020 at 12:54 PM Emily Kawaler  
>>> wrote:
>>>
 I've uploaded the pepXML files, the parameters I used, and the database 
 here. 
 
 Please let me know if I should be uploading anything else! Thank you!

 On Saturday, October 17, 2020 at 12:04:21 AM UTC-4 Emily Kawaler wrote:

> Thank you! I'm working on getting it transferred to Drive, so it might 
> take a little while, but I'll be in touch!
>
> On Tuesday, October 13, 2020 at 3:08:44 PM UTC-4 David Shteynberg 
> wrote:
>
>> Hello Emily,
>>
>> If you are able to share the dataset including the pepXML file and 
>> the database I can try to replicate the issue here and try to 
>> troubleshoot 
>> the sticking point.
>>
>> Thanks,
>> -David
>>
>> On Tue, Oct 13, 2020 at 11:15 AM Emily Kawaler  
>> wrote:
>>
>>> Hello, and thank you for your response! It doesn't look like the 
>>> process is using too much memory (I've allocated 300 GB and it's maxing 
>>> out 
>>> around 10), and I've kicked up the minprob parameter - it's still 
>>> getting 
>>> stuck, unfortunately. 
>>> Emily
>>>
>>> On Friday, October 9, 2020 at 2:24:37 PM UTC-4 Luis wrote:
>>>
 Hello Emily,

 This is not a problem that we have seen much of.  Do you know which 
 version of ProteinProphet / TPP you are using?

 One potential issue is the large number of proteins (and peptides) 
 that it is trying to process -- can you either monitor the memory 
 usage of 
 the machine when you run this dataset, and/or try on one with more 
 memory?

 Hope this helps,
 --Luis


 On Tue, Oct 6, 2020 at 6:32 PM Emily Kawaler  
 wrote:

> Hello! I've been running ProteinProphet as part of the Philosopher 
> pipeline for a while now with no problems. However, one of my 
> datasets 
> seems to be getting stuck in the middle of this function. It doesn't 
> throw 
> an error or anything - just stops advancing (the last 
> line of the output is "Computing degenerate peptides for 69919 
> proteins: 0%...10%...20%...30%...40%...50%"). Has 

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

Hello,
Thanks so much for taking a look! I think the selenocysteines ("U") are 
likely not the problem, since I've got those in all of my databases, 
including the ones that run correctly. I'm looking at 
03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML and I don't see 
anything odd in line 171821 (""), so I think our line 
numberings might not match up - what does your problematic line contain?

When I try to run it on my end, it always sticks somewhere in the 
10CPTAC_OV files. Right now I'm running a working set of spectra with a 
database that didn't work and vice versa, so hopefully that'll help me pin 
down whether it's a problem with my spectra or my database - will let you 
know how that turns out!

Emily

On Thursday, October 22, 2020 at 3:09:29 PM UTC-4 David Shteynberg wrote:

> Hi Emily,
>
> I analyzed the search results that you sent and I am seeing some strange 
> things in at least one of the files you gave me.  This may be causing some 
> of the problems you saw.
> In file 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML on line 
> 171821 there are some strange characters (possibly binary) that are 
> tripping up the TPP.  I think these might be caused by a bug in an analysis 
> tool upstream of the TPP.  Not sure if there are other mistakes of this 
> sort.  Also I found some 'U' amino acids in the database which the TPP 
> complains about having a mass of 0.
>
> I hope this helps you somewhat.  Let me know what you find on your end.
>
> Cheers,
> -David
>
> On Tue, Oct 20, 2020 at 1:42 PM Emily Kawaler  wrote:
>
>> Sure! The spectra are from the CPTAC2 ovarian propective dataset, though 
>> I removed all scans that matched to a standard reference database (I don't 
>> think the scan removal is the issue, since I'm also having this problem on 
>> a different dataset without removing any scans; I also checked with xmllint 
>> and it looks like the mzML pepXML files are valid). I've been running it 
>> with the philosopher pipeline, so the pepXML files were generated with 
>> MSFragger as part of that pipeline. The database is a customized variant 
>> database with contaminants and decoys added by philosopher's database tool. 
>> Are there any other specifics you'd like? I can upload my full 
>> philosopher.yml file if that would be helpful.
>>
>> On Tuesday, October 20, 2020 at 1:30:44 AM UTC-4 David Shteynberg wrote:
>>
>>> Hi Emily,
>>>
>>> I got the data and now I am trying to understand how you are running the 
>>> analysis.  Can you please describe those steps?
>>>
>>> Thank you,
>>> -David
>>>
>>> On Sat, Oct 17, 2020 at 12:54 PM Emily Kawaler  
>>> wrote:
>>>
 I've uploaded the pepXML files, the parameters I used, and the database 
 here. 
 
 Please let me know if I should be uploading anything else! Thank you!

 On Saturday, October 17, 2020 at 12:04:21 AM UTC-4 Emily Kawaler wrote:

> Thank you! I'm working on getting it transferred to Drive, so it might 
> take a little while, but I'll be in touch!
>
> On Tuesday, October 13, 2020 at 3:08:44 PM UTC-4 David Shteynberg 
> wrote:
>
>> Hello Emily,
>>
>> If you are able to share the dataset including the pepXML file and 
>> the database I can try to replicate the issue here and try to 
>> troubleshoot 
>> the sticking point.
>>
>> Thanks,
>> -David
>>
>> On Tue, Oct 13, 2020 at 11:15 AM Emily Kawaler  
>> wrote:
>>
>>> Hello, and thank you for your response! It doesn't look like the 
>>> process is using too much memory (I've allocated 300 GB and it's maxing 
>>> out 
>>> around 10), and I've kicked up the minprob parameter - it's still 
>>> getting 
>>> stuck, unfortunately. 
>>> Emily
>>>
>>> On Friday, October 9, 2020 at 2:24:37 PM UTC-4 Luis wrote:
>>>
 Hello Emily,

 This is not a problem that we have seen much of.  Do you know which 
 version of ProteinProphet / TPP you are using?

 One potential issue is the large number of proteins (and peptides) 
 that it is trying to process -- can you either monitor the memory 
 usage of 
 the machine when you run this dataset, and/or try on one with more 
 memory?

 Hope this helps,
 --Luis


 On Tue, Oct 6, 2020 at 6:32 PM Emily Kawaler  
 wrote:

> Hello! I've been running ProteinProphet as part of the Philosopher 
> pipeline for a while now with no problems. However, one of my 
> datasets 
> seems to be getting stuck in the middle of this function. It doesn't 
> throw 
> an error or anything - just stops advancing (the last 
> line of the output is "Computing degenerate peptides for 69919 
> proteins: 0%...10%...20%...30%...40%...50%"). Has 

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

['David Shteynberg' via spctools-discuss]

Hi Emily,

I analyzed the search results that you sent and I am seeing some strange
things in at least one of the files you gave me.  This may be causing some
of the problems you saw.
In file 03CPTAC_OVprospective_W_PNNL_20161212_B1S3_f13.pepXML on line
171821 there are some strange characters (possibly binary) that are
tripping up the TPP.  I think these might be caused by a bug in an analysis
tool upstream of the TPP.  Not sure if there are other mistakes of this
sort.  Also I found some 'U' amino acids in the database which the TPP
complains about having a mass of 0.

I hope this helps you somewhat.  Let me know what you find on your end.

Cheers,
-David

On Tue, Oct 20, 2020 at 1:42 PM Emily Kawaler  wrote:

> Sure! The spectra are from the CPTAC2 ovarian propective dataset, though I
> removed all scans that matched to a standard reference database (I don't
> think the scan removal is the issue, since I'm also having this problem on
> a different dataset without removing any scans; I also checked with xmllint
> and it looks like the mzML pepXML files are valid). I've been running it
> with the philosopher pipeline, so the pepXML files were generated with
> MSFragger as part of that pipeline. The database is a customized variant
> database with contaminants and decoys added by philosopher's database tool.
> Are there any other specifics you'd like? I can upload my full
> philosopher.yml file if that would be helpful.
>
> On Tuesday, October 20, 2020 at 1:30:44 AM UTC-4 David Shteynberg wrote:
>
>> Hi Emily,
>>
>> I got the data and now I am trying to understand how you are running the
>> analysis.  Can you please describe those steps?
>>
>> Thank you,
>> -David
>>
>> On Sat, Oct 17, 2020 at 12:54 PM Emily Kawaler  wrote:
>>
>>> I've uploaded the pepXML files, the parameters I used, and the database
>>> here.
>>> 
>>> Please let me know if I should be uploading anything else! Thank you!
>>>
>>> On Saturday, October 17, 2020 at 12:04:21 AM UTC-4 Emily Kawaler wrote:
>>>
 Thank you! I'm working on getting it transferred to Drive, so it might
 take a little while, but I'll be in touch!

 On Tuesday, October 13, 2020 at 3:08:44 PM UTC-4 David Shteynberg wrote:

> Hello Emily,
>
> If you are able to share the dataset including the pepXML file and the
> database I can try to replicate the issue here and try to troubleshoot the
> sticking point.
>
> Thanks,
> -David
>
> On Tue, Oct 13, 2020 at 11:15 AM Emily Kawaler 
> wrote:
>
>> Hello, and thank you for your response! It doesn't look like the
>> process is using too much memory (I've allocated 300 GB and it's maxing 
>> out
>> around 10), and I've kicked up the minprob parameter - it's still getting
>> stuck, unfortunately.
>> Emily
>>
>> On Friday, October 9, 2020 at 2:24:37 PM UTC-4 Luis wrote:
>>
>>> Hello Emily,
>>>
>>> This is not a problem that we have seen much of.  Do you know which
>>> version of ProteinProphet / TPP you are using?
>>>
>>> One potential issue is the large number of proteins (and peptides)
>>> that it is trying to process -- can you either monitor the memory usage 
>>> of
>>> the machine when you run this dataset, and/or try on one with more 
>>> memory?
>>>
>>> Hope this helps,
>>> --Luis
>>>
>>>
>>> On Tue, Oct 6, 2020 at 6:32 PM Emily Kawaler 
>>> wrote:
>>>
 Hello! I've been running ProteinProphet as part of the Philosopher
 pipeline for a while now with no problems. However, one of my datasets
 seems to be getting stuck in the middle of this function. It doesn't 
 throw
 an error or anything - just stops advancing (the last
 line of the output is "Computing degenerate peptides for 69919
 proteins: 0%...10%...20%...30%...40%...50%"). Has anyone run into this
 problem before?

 --
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 Groups "spctools-discuss" group.
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 https://groups.google.com/d/msgid/spctools-discuss/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com
 
 .

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