Thanks a lot.
These days, I tested all of my sample data as you told me.
ALL of them worked well.
Thank you for helping me.
---One more thing:
I use idconvert to change mzid file to pepXML fomat.
The scan information in changed pepXML is not equal to real scan
information.
I checked the file, and found that the scan information in changed PepXML
file is same as the 'index" of MGF file.
Am I right?
I just want to confirm it.
Honglan Li.
2016년 4월 19일 화요일 오전 2시 44분 21초 UTC+9, David Shteynberg 님의 말:
>
> Hello Honglan,
>
>
> It appears that the paths to your data contain some restricted
> characters. The only allowed characters when naming paths that are
> compatible with the TPP are alpha-numeric and '_' (underscore) ('.' and
> whitespace are disallowed.) That doesn't mean that it won't work sometimes
> when the paths contain restricted character, but it can be hit or miss.
> Please rename the directories and redo analysis.
>
> -David
>
>
>
> On Wed, Apr 13, 2016 at 7:40 AM, David Shteynberg <
> [email protected] <javascript:>> wrote:
>
>> Hi Honglan,
>>
>> I am on vacation this week. I did fix another processing issue with MSGF+
>> earlier, but I was still testing. I will get back to you once I'm back
>> next week.
>>
>> David
>> On Apr 13, 2016 12:14 AM, "Honglan Li" <[email protected] <javascript:>>
>> wrote:
>>
>>> Hi David
>>>
>>> It's me again.
>>>
>>> Thanks for giving me new PeptideProphet file to run MS_GF+ results.
>>>
>>> But it still has problem to execute new test file.
>>>
>>> Would you please tell me the reason?
>>>
>>>
>>> Thanks a lot.
>>>
>>> Honglan Li
>>>
>>>
>>> XML file:
>>> https://drive.google.com/file/d/0B5i2NDdAgrJ3bDY4ZFR0M2VOUlU/view?usp=sharing
>>>
>>> Recieved msg:
>>>
>>> ----
>>> 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
>>> ----
>>>
>>> Thanks a lot.
>>>
>>> Honglan Li
>>>
>>>
>>> 2016년 3월 30일 수요일 오후 8시 30분 5초 UTC+9, Honglan Li 님의 말:
>>>>
>>>>
>>>> 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>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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>>>>>>
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