Hi David.
It's me again.
Last time, you gave me the s/w and cmd.
It's works well when I use the sample I gave you, and some other XML files.
But for some XML files, it still do not work well.
XML
file:
https://drive.google.com/file/d/0B5i2NDdAgrJ3bDY4ZFR0M2VOUlU/view?usp=sharing
When I executed this test sample (test2.pep.xml.xml) with the cmd you told
me
"PeptideProphetParser.exe test2.pep.xml.xml NONPARAM
DECOY=XXX DECOYPROBS MINPROB=0 CLEVEL=2 ACCMASS PPM"
I received msg as follows: (detail: I added captured error msg file)
----
KDModel.cpp, Line 144
Expression: idx < posprobs_ -> size()
This application has requested the Runtime to terminate it in an unusual
way.
Please contact the application's support team for more information
----
Would you please tell me what happened to this XML file?
Thanks a lot.
Honglan Li
2016년 3월 28일 월요일 오전 8시 52분 13초 UTC+9, Honglan Li 님의 말:
>
> Thank you very much for your help, David.
>
> It works well now.
>
> Best wishes,
> Honglan Li
>
>
> 2016년 3월 26일 토요일 오전 2시 33분 59초 UTC+9, David Shteynberg 님의 말:
>>
>> Hello Honglan,
>>
>> I was unable to replicate the error on my system, however, I have tested
>> that this command works on a more recently compiled version of
>> PeptideProphet. You can download the binary here
>> https://dl.dropboxusercontent.com/u/21286225/PeptideProphetParser.exe
>> and run as follows
>>
>> PeptideProphetParser.exe test.pep.xml NONPARAM DECOY=XXX DECOYPROBS
>> MINPROB=0 CLEVEL=2 ACCMASS PPM
>>
>>
>> I had to set a fairly high CLEVEL value on this data since MSGF+ suffers
>> from scoring highly of some decoys and is not always accurate at the
>> critical 1% error. The WARNING message in the new code has been updated to
>> reflect this problem.
>>
>> Cheers,
>> -David
>>
>>
>> On Thu, Mar 24, 2016 at 8:21 PM, Honglan Li <[email protected]> wrote:
>>
>>> Thanks for your quick reply.
>>>>
>>>
>>> I tried the command you told me, but it stll didn't work well.
>>>
>>> The warning msg is "*The discriminant function for MSGFPL is not yet
>>> complete" *
>>>
>>> How to fix it ?
>>>
>>>
>>> *cmd*:
>>>
>>> xinteract -OPd -p0 -dXXX_ *.xml
>>>
>>>
>>>
>>> *Error msg I received*
>>>
>>> ----
>>> running: "/usr/local/tpp/bin/DatabaseParser 'interact.pep.xml'"
>>> command completed in 0 sec
>>>
>>> running: "/usr/local/tpp/bin/RefreshParser 'interact.pep.xml'
>>> 'C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1.
>>> CYH\uniprot_C+H+Y+48.revCat.fasta'"
>>> - Building Commentz-Walter keyword tree... - Searching the
>>> tree...opening "C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1.
>>> CYH\uniprot_C+H+Y+48.revCat.fasta" as
>>> "/home/mllab/hllee/uniprot_C+H+Y+48.revCat.fasta"
>>>
>>> - Linking duplicate entries... - Printing results...
>>>
>>> command completed in 11 sec
>>>
>>> running: "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'
>>> NONPARAM DECOYPROBS MINPROB=0 DECOY=XXX_"
>>> Using Decoy Label "XXX_".
>>> Decoy Probabilities will be reported.
>>> Using non-parametric distributions
>>> (MS-GF+) (minprob 0)
>>> WARNING!! *The discriminant function for MSGFPL is not yet complete.*
>>> It is presented here to help facilitate trial and discussion. Reliance on
>>> this code for publishable scientific results is not recommended.
>>> init with MS-GF+ trypsin
>>> Segmentation fault (core dumped)
>>>
>>> command "/usr/local/tpp/bin/PeptideProphetParser 'interact.pep.xml'
>>> NONPARAM DECOYPROBS MINPROB=0 DECOY=XXX_" exited with non-zero exit code:
>>> 35584
>>> QUIT - the job is incomplete
>>>
>>> -----
>>>
>>> *XML format per PSM: (file: *
>>> https://drive.google.com/file/d/0B5i2NDdAgrJ3Y2diWDAzVHBQSm8/view?usp=sharing
>>> )
>>>
>>> <spectrum_query
>>> spectrum="C:\Users\JONGHUN\Desktop\MSGFPlus\C-25fmol\C-25fmol-R1\1.
>>> CYH\C-25fmol-R1_QEx2_000090.51174.51174.4" spectrumNativeID="index=51174"
>>> start_scan="51174" end_scan="51174"
>>> precursor_neutral_mass="3972.990669523105" assumed_charge="4" index="1">
>>> <search_result>
>>> <search_hit hit_rank="1"
>>> peptide="VGNVGEDDAIPEVSHAGDVSTTLQVVNELLKDETVAPR" peptide_prev_aa="R"
>>> peptide_next_aa="F" protein="sp|P16521|EF3A_YEAST" num_tot_proteins="1"
>>> calc_neutral_pep_mass="3972.99140194498" massdiff="7.32421875e-04"
>>> protein_descr="sp|P16521|EF3A_YEAST Elongation factor 3A OS=Saccharomyces
>>> cerevisiae (strain ATCC 204508 / S288c) GN=YEF3 PE=1 SV=4" num_tol_term="2"
>>> num_missed_cleavages="1">
>>> <search_score name="raw" value="269"/>
>>> <search_score name="denovo" value="289"/>
>>> <search_score name="SpecEValue"
>>> value="2.8337685502588284E-39"/>
>>> <search_score name="EValue" value="1.2856572993111488E-31"/>
>>> <search_score name="IsotopeError" value="0"/>
>>> </search_hit>
>>> </search_result>
>>> </spectrum_query>
>>>
>>>
>>>
>>>
>>>
>>> --
>>> 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 [email protected].
>>> To post to this group, send email to [email protected].
>>> Visit this group at https://groups.google.com/group/spctools-discuss.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>
--
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 [email protected].
To post to this group, send email to [email protected].
Visit this group at https://groups.google.com/group/spctools-discuss.
For more options, visit https://groups.google.com/d/optout.
