Re: [spctools-discuss] PTMProphet command failure (for larger datasets?)

['David Shteynberg' via spctools-discuss]

Hi Will,

There is a release candidate for version 6.0.0 available on sourceforge:
https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v6.0%20%28Release%20Candidates%29/

If you do end up trying it let me know if you find any issues.

Thanks!
-David

On Tue, Mar 16, 2021 at 5:14 PM Will Comstock  wrote:

> Hi David,
>
> I'll attempt to re-run PTMProphet analysis on a few problematic datasets
> with MAXTHREADS=1.
>
> I am currently using the version of PTMProphet that came with the
> installation of TPP 5.2. Is there a newer version available that I could be
> using instead?
>
> Thanks for your help!
> -Will
>
> On Tuesday, March 16, 2021 at 7:37:58 PM UTC-4 David Shteynberg wrote:
>
>> Hello Will,
>>
>> We routinely run PTMProphet on datasets containing multiple hundreds of
>> thousands of PSMs. This looks like multithreading issue
>> related MAXTHREADS=0 parameter, this should not happen if you use
>> MAXTHREADS=1.  I have corrected several bugs related to multithreading in
>> the codebase. Which version of PTMProphet are you using?
>>
>> Thanks,
>> -David
>>
>> On Tue, Mar 16, 2021 at 3:59 PM Will Comstock  wrote:
>>
>>> Hey everyone,
>>>
>>> I've run into an issue with PTMProphet where occasionally the command
>>> will fail for unknown reasons and the resulting ptm.pep.xml cannot be
>>> opened with the PepXML viewer. The command log seems to cut off abruptly,
>>> as pictured in the attached screenshot. Also attached is the page that
>>> appears upon trying to open the ptm.pep.xml.
>>>
>>> The interact.pep.xml files we're analyzing clock in at about 200 to 250
>>> megabytes. As a workaround, we currently just split the initial batch of
>>> pep.xmls into smaller groups before running PeptideProphet and PTMProphet
>>> on them again. Sometimes we end up with batches of pep.xmls as small as 3
>>> or 4 files, which is somewhat inconvenient for projects with hundreds of
>>> RAW files.
>>>
>>> Is there another way around this issue? We've tried running it through
>>> the command line as well and this problem still crops up frequently.
>>> [image: PTMproph_CommandFailed.png]
>>> [image: PTMproph_CommandFailed_xmlError.png]
>>> Thanks!
>>>
>>> --
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>>> 
>>> .
>>>
>> --
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Re: [spctools-discuss] PTMProphet command failure (for larger datasets?)

[Will Comstock]

Hi David,

I'll attempt to re-run PTMProphet analysis on a few problematic datasets 
with MAXTHREADS=1. 

I am currently using the version of PTMProphet that came with the 
installation of TPP 5.2. Is there a newer version available that I could be 
using instead?

Thanks for your help!
-Will

On Tuesday, March 16, 2021 at 7:37:58 PM UTC-4 David Shteynberg wrote:

> Hello Will, 
>
> We routinely run PTMProphet on datasets containing multiple hundreds of 
> thousands of PSMs. This looks like multithreading issue 
> related MAXTHREADS=0 parameter, this should not happen if you use 
> MAXTHREADS=1.  I have corrected several bugs related to multithreading in 
> the codebase. Which version of PTMProphet are you using? 
>
> Thanks,
> -David
>
> On Tue, Mar 16, 2021 at 3:59 PM Will Comstock  wrote:
>
>> Hey everyone,
>>
>> I've run into an issue with PTMProphet where occasionally the command 
>> will fail for unknown reasons and the resulting ptm.pep.xml cannot be 
>> opened with the PepXML viewer. The command log seems to cut off abruptly, 
>> as pictured in the attached screenshot. Also attached is the page that 
>> appears upon trying to open the ptm.pep.xml. 
>>
>> The interact.pep.xml files we're analyzing clock in at about 200 to 250 
>> megabytes. As a workaround, we currently just split the initial batch of 
>> pep.xmls into smaller groups before running PeptideProphet and PTMProphet 
>> on them again. Sometimes we end up with batches of pep.xmls as small as 3 
>> or 4 files, which is somewhat inconvenient for projects with hundreds of 
>> RAW files. 
>>
>> Is there another way around this issue? We've tried running it through 
>> the command line as well and this problem still crops up frequently.
>> [image: PTMproph_CommandFailed.png]
>> [image: PTMproph_CommandFailed_xmlError.png]
>> Thanks!
>>
>> -- 
>> 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/020c5be3-14ad-4350-9b12-dbb366fdb2c8n%40googlegroups.com
>>  
>> 
>> .
>>
>

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