Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

Not a problem! In the end I decided just to remove all of the titins from 
my database - it shouldn't have a huge effect on my results - and I was 
indeed able to run all of my datasets to completion. Thanks for all of your 
help!
Emily

On Friday, November 6, 2020 at 8:25:56 PM UTC-5 David Shteynberg wrote:

> Hello again Emily,
>
> Apologies for the delay but I needed a bit more time to look into this.  
>  You are absolutely right about the titins causing this issue.  The problem 
> is the significant overlap in peptides in this very large titin group.  
>  Your database contains 343 variations of titin with different SAAPs, 
> which share large subsets of the same peptides.  Calculating this 
> enormous protein group is certainly stressing the ProteinProphet 
> algorithm, forcing it into a higher-order polynomial time complexity 
> problem.  I was looking into the code to see if there was a simple way to 
> speed it up, but unfortunately this doesn't seem to be the case.  Is there 
> any way you can reduce the number of titin entries in your database?  Have 
> you considered using PEFF?
>
> Thanks,
> -David
>
> On Sat, Oct 24, 2020 at 10:48 PM Emily Kawaler  wrote:
>
>> Another update: I've pinpointed a much smaller database that reproduces 
>> the error when run with just 10OV - uploaded to the same folder as above, 
>> named "titins_revs.fasta" (it contains a bunch of titins and some reverse 
>> decoy sequences). Something in the titins is causing this error, I think 
>> (I've run this set of titins with a few different sets of reverse decoys so 
>> I don't think it's caused by the decoys). I also think there are a couple 
>> of other sequences in the database that may have the same effect, but if we 
>> can figure out what's doing it in this set, it should be easier to know 
>> what to look for. Any thoughts?
>
>
>>
>> On Friday, October 23, 2020 at 3:45:08 PM UTC-4 Emily Kawaler wrote:
>>
>>> Okay - When I ran the working set of spectra with the database that 
>>> failed, it seems to have failed; when I ran the set of spectra that failed 
>>> with a database that worked, it ran to completion. I think we can probably 
>>> narrow the problem down to something in the database. 
>>>
>>> On Friday, October 23, 2020 at 1:56:18 AM UTC-4 Emily Kawaler wrote:
>>>
 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 

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

['David Shteynberg' via spctools-discuss]

Hello again Emily,

Apologies for the delay but I needed a bit more time to look into this.
 You are absolutely right about the titins causing this issue.  The problem
is the significant overlap in peptides in this very large titin group.
 Your database contains 343 variations of titin with different SAAPs,
which share large subsets of the same peptides.  Calculating this
enormous protein group is certainly stressing the ProteinProphet
algorithm, forcing it into a higher-order polynomial time complexity
problem.  I was looking into the code to see if there was a simple way to
speed it up, but unfortunately this doesn't seem to be the case.  Is there
any way you can reduce the number of titin entries in your database?  Have
you considered using PEFF?

Thanks,
-David

On Sat, Oct 24, 2020 at 10:48 PM Emily Kawaler  wrote:

> Another update: I've pinpointed a much smaller database that reproduces
> the error when run with just 10OV - uploaded to the same folder as above,
> named "titins_revs.fasta" (it contains a bunch of titins and some reverse
> decoy sequences). Something in the titins is causing this error, I think
> (I've run this set of titins with a few different sets of reverse decoys so
> I don't think it's caused by the decoys). I also think there are a couple
> of other sequences in the database that may have the same effect, but if we
> can figure out what's doing it in this set, it should be easier to know
> what to look for. Any thoughts?
>
> On Friday, October 23, 2020 at 3:45:08 PM UTC-4 Emily Kawaler wrote:
>
>> Okay - When I ran the working set of spectra with the database that
>> failed, it seems to have failed; when I ran the set of spectra that failed
>> with a database that worked, it ran to completion. I think we can probably
>> narrow the problem down to something in the database.
>>
>> On Friday, October 23, 2020 at 1:56:18 AM UTC-4 Emily Kawaler wrote:
>>
>>> 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 

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

Another update: I've pinpointed a much smaller database that reproduces the 
error when run with just 10OV - uploaded to the same folder as above, named 
"titins_revs.fasta" (it contains a bunch of titins and some reverse decoy 
sequences). Something in the titins is causing this error, I think (I've 
run this set of titins with a few different sets of reverse decoys so I 
don't think it's caused by the decoys). I also think there are a couple of 
other sequences in the database that may have the same effect, but if we 
can figure out what's doing it in this set, it should be easier to know 
what to look for. Any thoughts?

On Friday, October 23, 2020 at 3:45:08 PM UTC-4 Emily Kawaler wrote:

> Okay - When I ran the working set of spectra with the database that 
> failed, it seems to have failed; when I ran the set of spectra that failed 
> with a database that worked, it ran to completion. I think we can probably 
> narrow the problem down to something in the database. 
>
> On Friday, October 23, 2020 at 1:56:18 AM UTC-4 Emily Kawaler wrote:
>
>> 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. 
 

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

Okay - When I ran the working set of spectra with the database that failed, 
it seems to have failed; when I ran the set of spectra that failed with a 
database that worked, it ran to completion. I think we can probably narrow 
the problem down to something in the database. 

On Friday, October 23, 2020 at 1:56:18 AM UTC-4 Emily Kawaler wrote:

> 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  
> 

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] 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?

 --
 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-discu...@googlegroups.com.
 To view this discussion on the web visit
 https://groups.google.com/d/msgid/spctools-discuss/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com
 
 .

>>> --
>> 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-discu...@googlegroups.com.
>>
> To view this discussion on the web visit
>> 

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

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?
>>>
>>> -- 
>>> 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-discu...@googlegroups.com.
>>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/spctools-discuss/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>> -- 
> 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-discu...@googlegroups.com.
>
 To view this discussion on the web visit 
> https://groups.google.com/d/msgid/spctools-discuss/6d28e150-40f0-4747-a8a3-02630b12379dn%40googlegroups.com
>  
> 
> .
>
 -- 
>> 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-discu...@googlegroups.com.
>>
> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/de634f4a-0057-4fc1-b135-e639c0eb77een%40googlegroups.com
>>  
>> 

Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

['David Shteynberg' via spctools-discuss]

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?
>>
>> --
>> 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-discu...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com
>> 
>> .
>>
> --
 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-discu...@googlegroups.com.

>>> To view this discussion on the web visit
 https://groups.google.com/d/msgid/spctools-discuss/6d28e150-40f0-4747-a8a3-02630b12379dn%40googlegroups.com
 
 .

>>> --
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> "spctools-discuss" group.
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> email to spctools-discuss+unsubscr...@googlegroups.com.
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> 
> .
>

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Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

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?
>
> -- 
> 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-discu...@googlegroups.com.
> To view this discussion on the web visit 
> https://groups.google.com/d/msgid/spctools-discuss/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com
>  
> 
> .
>
 -- 
>>> 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-discu...@googlegroups.com.
>>>
>> To view this discussion on the web visit 
>>> https://groups.google.com/d/msgid/spctools-discuss/6d28e150-40f0-4747-a8a3-02630b12379dn%40googlegroups.com
>>>  
>>> 
>>> .
>>>
>>

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Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

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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>> .
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Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

['David Shteynberg' via spctools-discuss]

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?
>>>
>>> --
>>> 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-discu...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/spctools-discuss/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com
>>> 
>>> .
>>>
>> --
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> 
> .
>

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Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

[Emily Kawaler]

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?
>>
>> -- 
>> 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-discu...@googlegroups.com.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/spctools-discuss/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com
>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] ProteinProphet sticking in findDegenGroups3

['Luis Mendoza' via spctools-discuss]

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?
>
> --
> 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/be33a8fb-a6ec-41b6-a988-981161f194fcn%40googlegroups.com
> 
> .
>

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