Re: [spctools-discuss] Analyze peptides- error

[Darya Laptanovich]

Hello David!

I have the same problem. After running the command I've got this info 
message:

C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 
(Windows_NT-x86_64))
 PPM mode in Accurate Mass Model ...
C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a04048\': File exists

command "C:\TPP\bin\mkdir.exe -p "/tmp/a04048/"" failed: Operation not permitted
could not create temp dir /tmp/a04048/, working in data directory
running: "C:/TPP/bin/InteractParser "interact.pep.xml" "search.pep.xml" -L"7"" 



And after this there is new file interact.pep.xml.tmp.a04100 created in 
directory C:\tmp\a05484 while my data directory is C:\TPP\data
 

понедельник, 20 ноября 2017 г., 8:38:59 UTC+3 пользователь David Shteynberg 
написал:
>
> Looks like this is not an error message but some information.  It seems 
> that the process actually got past this point.  Are you certain that the 
> command dies here?  Can you see the output file interact.pep.xml in your 
> working directory?  You can try deleting the directory C: /tmp/a04316/ to 
> seeing this particular message.
>
> -David
>
> On Sun, Nov 19, 2017 at 6:17 PM, Elkan Dong  > wrote:
>
>> Hi David,
>>
>> Still encountered the problem.
>>
>> C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 
>> (Windows_NT-x86_64))
>>  PPM mode in Accurate Mass Model ...
>> C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a04316\': File exists
>>
>> command "C:\TPP\bin\mkdir.exe -p "/tmp/a04316/"" failed: Operation not 
>> permitted
>> could not create temp dir /tmp/a04316/, working in data directory
>>
>> running: "C:/TPP/bin/InteractParser "interact.pep.xml" 
>> "I17F1SAX.decoy.pep.xml" "I17F1SAX.pep.xml" "I17F1SCX.decoy.pep.xml" 
>> "I17F1SCX.pep.xml" "I17F2SAX.decoy.pep.xml" "I17F2SAX.pep.xml" 
>> "I17F2SCX.decoy.pep.xml" "I17F2SCX.pep.xml" "I17F3SAX.decoy.pep.xml" 
>> "I17F3SAX.pep.xml" "I17F3SCX.decoy.pep.xml" "I17F3SCX.pep.xml" 
>> "I17F4SAX.decoy.pep.xml" "I17F4SAX.pep.xml" "I17F4SCX.decoy.pep.xml" 
>> "I17F4SCX.pep.xml" "I17F5SAX.decoy.pep.xml" "I17F5SAX.pep.xml" 
>> "I17F5SCX.decoy.pep.xml" "I17F5SCX.pep.xml" "I17F6SAX.decoy.pep.xml" 
>> "I17F6SAX.pep.xml" "I17F6SCX.decoy.pep.xml" "I17F6SCX.pep.xml" 
>> "I17F7SAX.decoy.pep.xml" "I17F7SAX.pep.xml" "I17F7SCX.decoy.pep.xml" 
>> "I17F7SCX.pep.xml" "I17F8SAX.decoy.pep.xml" "I17F8SAX.pep.xml" 
>> "I17F8SCX.decoy.pep.xml" "I17F8SCX.pep.xml" -L"5""
>>
>>
>> Regards,
>>
>> Elkan
>>
>>
>> 在 2017年11月17日星期五 UTC+8下午10:47:29，David Shteynberg写道：
>>>
>>> Hello Elkan,
>>>
>>> Although unlikely, the dashes in your filename could be the issue.  In 
>>> my email on this thread I mentioned that only alphanumerics and underscores 
>>> "_" should be utilized.  If that fails there is a problem with the pep.xml 
>>> file itself, that you would need to troubleshoot.  How was the file 
>>> generated? 
>>>
>>> -David   
>>>
>>> On Fri, Nov 17, 2017 at 12:46 AM, Elkan Dong  wrote:
>>>
 I'm using the newest version of TPP, but encountered the same error 
 when using PeptideProphet. The file name I used looks like 
 I08-F4-SAX1.pep.xml
 Any solution?

 Thanks.

 Elkan


 在 2017年6月20日星期二 UTC+8上午1:28:34，David Shteynberg写道：
>
> Hello Ada,
>
> One immediate problem I notice is that your files contain parenthesis 
> character.  Please name your files using only alphanumeric and underscore 
> character, please no special characters or whitespace.  Also, you might 
> consider using comet search engine, support for which is more streamlined 
> in the TPP.
>
> Cheers,
> -David
>
> On Mon, Jun 19, 2017 at 9:46 AM, Ada A  wrote:
>
>> Hello, 
>>
>> I was trying to run peptide analysis with PeptideProphet but it keeps 
>> showig me error... 
>> I was using dimethyl labeling technique and peptides were identified 
>> using Mascot. I exported all data from Mascot, uploaded here and it 
>> fails 
>> to do anything. I was wondering whether anyone could advice me what 
>> should 
>> I do with it? I would be grateful for some help.
>>
>> Here is what it shows me: 
>>
>> C:/TPP/bin/xinteract (TPP v5.0.0 Typhoon, Build 201610111222-7423 
>> (Windows_NT-x86_64))
>>  PPM mode in Accurate Mass Model ...
>> C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a09964\': File exists
>>
>> command "C:\TPP\bin\mkdir.exe -p "/tmp/a09964/"" failed: Operation not 
>> permitted
>> could not create temp dir /tmp/a09964/, working in data directory
>> running: "C:/TPP/bin/InteractParser "interact.pep.xml" "H7(3).pep.xml" 
>> "h7(3).xml" -L"7"" file 1: H7(3).pep.xmlWARNING: empty raw_data in 
>> msms_run_summary tag ... trying mzML ...
>> Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data 
>> file c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
>> Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot 

Re: [spctools-discuss] Analyze peptides- error

[David Shteynberg]

Looks like this is not an error message but some information.  It seems
that the process actually got past this point.  Are you certain that the
command dies here?  Can you see the output file interact.pep.xml in your
working directory?  You can try deleting the directory C: /tmp/a04316/ to
seeing this particular message.

-David

On Sun, Nov 19, 2017 at 6:17 PM, Elkan Dong  wrote:

> Hi David,
>
> Still encountered the problem.
>
> C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 
> (Windows_NT-x86_64))
>  PPM mode in Accurate Mass Model ...
> C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a04316\': File exists
>
> command "C:\TPP\bin\mkdir.exe -p "/tmp/a04316/"" failed: Operation not 
> permitted
> could not create temp dir /tmp/a04316/, working in data directory
>
> running: "C:/TPP/bin/InteractParser "interact.pep.xml" 
> "I17F1SAX.decoy.pep.xml" "I17F1SAX.pep.xml" "I17F1SCX.decoy.pep.xml" 
> "I17F1SCX.pep.xml" "I17F2SAX.decoy.pep.xml" "I17F2SAX.pep.xml" 
> "I17F2SCX.decoy.pep.xml" "I17F2SCX.pep.xml" "I17F3SAX.decoy.pep.xml" 
> "I17F3SAX.pep.xml" "I17F3SCX.decoy.pep.xml" "I17F3SCX.pep.xml" 
> "I17F4SAX.decoy.pep.xml" "I17F4SAX.pep.xml" "I17F4SCX.decoy.pep.xml" 
> "I17F4SCX.pep.xml" "I17F5SAX.decoy.pep.xml" "I17F5SAX.pep.xml" 
> "I17F5SCX.decoy.pep.xml" "I17F5SCX.pep.xml" "I17F6SAX.decoy.pep.xml" 
> "I17F6SAX.pep.xml" "I17F6SCX.decoy.pep.xml" "I17F6SCX.pep.xml" 
> "I17F7SAX.decoy.pep.xml" "I17F7SAX.pep.xml" "I17F7SCX.decoy.pep.xml" 
> "I17F7SCX.pep.xml" "I17F8SAX.decoy.pep.xml" "I17F8SAX.pep.xml" 
> "I17F8SCX.decoy.pep.xml" "I17F8SCX.pep.xml" -L"5""
>
>
> Regards,
>
> Elkan
>
>
> 在 2017年11月17日星期五 UTC+8下午10:47:29，David Shteynberg写道：
>>
>> Hello Elkan,
>>
>> Although unlikely, the dashes in your filename could be the issue.  In my
>> email on this thread I mentioned that only alphanumerics and underscores
>> "_" should be utilized.  If that fails there is a problem with the pep.xml
>> file itself, that you would need to troubleshoot.  How was the file
>> generated?
>>
>> -David
>>
>> On Fri, Nov 17, 2017 at 12:46 AM, Elkan Dong  wrote:
>>
>>> I'm using the newest version of TPP, but encountered the same error when
>>> using PeptideProphet. The file name I used looks like
>>> I08-F4-SAX1.pep.xml
>>> Any solution?
>>>
>>> Thanks.
>>>
>>> Elkan
>>>
>>>
>>> 在 2017年6月20日星期二 UTC+8上午1:28:34，David Shteynberg写道：

 Hello Ada,

 One immediate problem I notice is that your files contain parenthesis
 character.  Please name your files using only alphanumeric and underscore
 character, please no special characters or whitespace.  Also, you might
 consider using comet search engine, support for which is more streamlined
 in the TPP.

 Cheers,
 -David

 On Mon, Jun 19, 2017 at 9:46 AM, Ada A  wrote:

> Hello,
>
> I was trying to run peptide analysis with PeptideProphet but it keeps
> showig me error...
> I was using dimethyl labeling technique and peptides were identified
> using Mascot. I exported all data from Mascot, uploaded here and it fails
> to do anything. I was wondering whether anyone could advice me what should
> I do with it? I would be grateful for some help.
>
> Here is what it shows me:
>
> C:/TPP/bin/xinteract (TPP v5.0.0 Typhoon, Build 201610111222-7423 
> (Windows_NT-x86_64))
>  PPM mode in Accurate Mass Model ...
> C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a09964\': File exists
>
> command "C:\TPP\bin\mkdir.exe -p "/tmp/a09964/"" failed: Operation not 
> permitted
> could not create temp dir /tmp/a09964/, working in data directory
> running: "C:/TPP/bin/InteractParser "interact.pep.xml" "H7(3).pep.xml" 
> "h7(3).xml" -L"7"" file 1: H7(3).pep.xmlWARNING: empty raw_data in 
> msms_run_summary tag ... trying mzML ...
> Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data 
> file c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
> Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT 
> data file c:/TPP/data/.mzXML in msms_run_summary tag ...WARNING: empty 
> raw_data in msms_run_summary tag ... trying mzML ...
> Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data 
> file c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
> Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT 
> data file c:/TPP/data/.mzXML in msms_run_summary tag ...
>
>
>
> Kind Regards,
>
> Ada
>
> --
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> an email to spctools-discu...@googlegroups.com.
> To post to this group, send email to spctools...@googlegroups.com.
> Visit this 

Re: [spctools-discuss] Analyze peptides- error

[Elkan Dong]

Hi David,

Still encountered the problem.

C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 
(Windows_NT-x86_64))
 PPM mode in Accurate Mass Model ...
C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a04316\': File exists

command "C:\TPP\bin\mkdir.exe -p "/tmp/a04316/"" failed: Operation not permitted
could not create temp dir /tmp/a04316/, working in data directory

running: "C:/TPP/bin/InteractParser "interact.pep.xml" "I17F1SAX.decoy.pep.xml" 
"I17F1SAX.pep.xml" "I17F1SCX.decoy.pep.xml" "I17F1SCX.pep.xml" 
"I17F2SAX.decoy.pep.xml" "I17F2SAX.pep.xml" "I17F2SCX.decoy.pep.xml" 
"I17F2SCX.pep.xml" "I17F3SAX.decoy.pep.xml" "I17F3SAX.pep.xml" 
"I17F3SCX.decoy.pep.xml" "I17F3SCX.pep.xml" "I17F4SAX.decoy.pep.xml" 
"I17F4SAX.pep.xml" "I17F4SCX.decoy.pep.xml" "I17F4SCX.pep.xml" 
"I17F5SAX.decoy.pep.xml" "I17F5SAX.pep.xml" "I17F5SCX.decoy.pep.xml" 
"I17F5SCX.pep.xml" "I17F6SAX.decoy.pep.xml" "I17F6SAX.pep.xml" 
"I17F6SCX.decoy.pep.xml" "I17F6SCX.pep.xml" "I17F7SAX.decoy.pep.xml" 
"I17F7SAX.pep.xml" "I17F7SCX.decoy.pep.xml" "I17F7SCX.pep.xml" 
"I17F8SAX.decoy.pep.xml" "I17F8SAX.pep.xml" "I17F8SCX.decoy.pep.xml" 
"I17F8SCX.pep.xml" -L"5""


Regards,

Elkan


在 2017年11月17日星期五 UTC+8下午10:47:29，David Shteynberg写道：
>
> Hello Elkan,
>
> Although unlikely, the dashes in your filename could be the issue.  In my 
> email on this thread I mentioned that only alphanumerics and underscores 
> "_" should be utilized.  If that fails there is a problem with the pep.xml 
> file itself, that you would need to troubleshoot.  How was the file 
> generated? 
>
> -David   
>
> On Fri, Nov 17, 2017 at 12:46 AM, Elkan Dong  > wrote:
>
>> I'm using the newest version of TPP, but encountered the same error when 
>> using PeptideProphet. The file name I used looks like 
>> I08-F4-SAX1.pep.xml
>> Any solution?
>>
>> Thanks.
>>
>> Elkan
>>
>>
>> 在 2017年6月20日星期二 UTC+8上午1:28:34，David Shteynberg写道：
>>>
>>> Hello Ada,
>>>
>>> One immediate problem I notice is that your files contain parenthesis 
>>> character.  Please name your files using only alphanumeric and underscore 
>>> character, please no special characters or whitespace.  Also, you might 
>>> consider using comet search engine, support for which is more streamlined 
>>> in the TPP.
>>>
>>> Cheers,
>>> -David
>>>
>>> On Mon, Jun 19, 2017 at 9:46 AM, Ada A  wrote:
>>>
 Hello, 

 I was trying to run peptide analysis with PeptideProphet but it keeps 
 showig me error... 
 I was using dimethyl labeling technique and peptides were identified 
 using Mascot. I exported all data from Mascot, uploaded here and it fails 
 to do anything. I was wondering whether anyone could advice me what should 
 I do with it? I would be grateful for some help.

 Here is what it shows me: 

 C:/TPP/bin/xinteract (TPP v5.0.0 Typhoon, Build 201610111222-7423 
 (Windows_NT-x86_64))
  PPM mode in Accurate Mass Model ...
 C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a09964\': File exists

 command "C:\TPP\bin\mkdir.exe -p "/tmp/a09964/"" failed: Operation not 
 permitted
 could not create temp dir /tmp/a09964/, working in data directory
 running: "C:/TPP/bin/InteractParser "interact.pep.xml" "H7(3).pep.xml" 
 "h7(3).xml" -L"7"" file 1: H7(3).pep.xmlWARNING: empty raw_data in 
 msms_run_summary tag ... trying mzML ...
 Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data 
 file c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
 Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT 
 data file c:/TPP/data/.mzXML in msms_run_summary tag ...WARNING: empty 
 raw_data in msms_run_summary tag ... trying mzML ...
 Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data 
 file c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
 Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT 
 data file c:/TPP/data/.mzXML in msms_run_summary tag ...



 Kind Regards, 

 Ada

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>>>
>>> -- 
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Re: [spctools-discuss] Analyze peptides- error

[np . dong572]

Hi David,

All the xml files are generated by Comet search in command line. Ok, I will 
revise the file names to meet the requirements and run PeptideProphet again. 
Wish everything go right.

Thanks.

Regards,
Elkan

发自我的 iPad

> 在 2017年11月17日，22:47，David Shteynberg  写道：
> 
> Hello Elkan,
> 
> Although unlikely, the dashes in your filename could be the issue.  In my 
> email on this thread I mentioned that only alphanumerics and underscores "_" 
> should be utilized.  If that fails there is a problem with the pep.xml file 
> itself, that you would need to troubleshoot.  How was the file generated? 
> 
> -David   
> 
>> On Fri, Nov 17, 2017 at 12:46 AM, Elkan Dong  wrote:
>> I'm using the newest version of TPP, but encountered the same error when 
>> using PeptideProphet. The file name I used looks like 
>> I08-F4-SAX1.pep.xml
>> Any solution?
>> 
>> Thanks.
>> 
>> Elkan
>> 
>> 
>> 在 2017年6月20日星期二 UTC+8上午1:28:34，David Shteynberg写道：
>>> 
>>> Hello Ada,
>>> 
>>> One immediate problem I notice is that your files contain parenthesis 
>>> character.  Please name your files using only alphanumeric and underscore 
>>> character, please no special characters or whitespace.  Also, you might 
>>> consider using comet search engine, support for which is more streamlined 
>>> in the TPP.
>>> 
>>> Cheers,
>>> -David
>>> 
 On Mon, Jun 19, 2017 at 9:46 AM, Ada A  wrote:
 Hello, 
 
 I was trying to run peptide analysis with PeptideProphet but it keeps 
 showig me error... 
 I was using dimethyl labeling technique and peptides were identified using 
 Mascot. I exported all data from Mascot, uploaded here and it fails to do 
 anything. I was wondering whether anyone could advice me what should I do 
 with it? I would be grateful for some help.
 
 Here is what it shows me: 
 
 C:/TPP/bin/xinteract (TPP v5.0.0 Typhoon, Build 201610111222-7423 
 (Windows_NT-x86_64))
  PPM mode in Accurate Mass Model ...
 C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a09964\': File exists
 
 command "C:\TPP\bin\mkdir.exe -p "/tmp/a09964/"" failed: Operation not 
 permitted
 could not create temp dir /tmp/a09964/, working in data directory
 
 running: "C:/TPP/bin/InteractParser "interact.pep.xml" "H7(3).pep.xml" 
 "h7(3).xml" -L"7""
  file 1: H7(3).pep.xml
 WARNING: empty raw_data in msms_run_summary tag ... trying mzML ...
 Failed to open input file 'c:/TPP/data/.mzML'.
 WARNING: cannot open data file c:/TPP/data/.mzML in msms_run_summary tag 
 .. trying .mzXML ...
 Failed to open input file 'c:/TPP/data/.mzXML'.
 WARNING: cannot CORRECT data file c:/TPP/data/.mzXML in msms_run_summary 
 tag ...
 WARNING: empty raw_data in msms_run_summary tag ... trying mzML ...
 Failed to open input file 'c:/TPP/data/.mzML'.
 WARNING: cannot open data file c:/TPP/data/.mzML in msms_run_summary tag 
 .. trying .mzXML ...
 Failed to open input file 'c:/TPP/data/.mzXML'.
 WARNING: cannot CORRECT data file c:/TPP/data/.mzXML in msms_run_summary 
 tag ...
 
 
 
 Kind Regards, 
 
 Ada
 -- 
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 "spctools-discuss" group.
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 email to spctools-discu...@googlegroups.com.
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 Visit this group at https://groups.google.com/group/spctools-discuss.
 For more options, visit https://groups.google.com/d/optout.
>>> 
>> 
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> 
> -- 
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Re: [spctools-discuss] Analyze peptides- error

[David Shteynberg]

Hello Elkan,

Although unlikely, the dashes in your filename could be the issue.  In my
email on this thread I mentioned that only alphanumerics and underscores
"_" should be utilized.  If that fails there is a problem with the pep.xml
file itself, that you would need to troubleshoot.  How was the file
generated?

-David

On Fri, Nov 17, 2017 at 12:46 AM, Elkan Dong  wrote:

> I'm using the newest version of TPP, but encountered the same error when
> using PeptideProphet. The file name I used looks like
> I08-F4-SAX1.pep.xml
> Any solution?
>
> Thanks.
>
> Elkan
>
>
> 在 2017年6月20日星期二 UTC+8上午1:28:34，David Shteynberg写道：
>>
>> Hello Ada,
>>
>> One immediate problem I notice is that your files contain parenthesis
>> character.  Please name your files using only alphanumeric and underscore
>> character, please no special characters or whitespace.  Also, you might
>> consider using comet search engine, support for which is more streamlined
>> in the TPP.
>>
>> Cheers,
>> -David
>>
>> On Mon, Jun 19, 2017 at 9:46 AM, Ada A  wrote:
>>
>>> Hello,
>>>
>>> I was trying to run peptide analysis with PeptideProphet but it keeps
>>> showig me error...
>>> I was using dimethyl labeling technique and peptides were identified
>>> using Mascot. I exported all data from Mascot, uploaded here and it fails
>>> to do anything. I was wondering whether anyone could advice me what should
>>> I do with it? I would be grateful for some help.
>>>
>>> Here is what it shows me:
>>>
>>> C:/TPP/bin/xinteract (TPP v5.0.0 Typhoon, Build 201610111222-7423 
>>> (Windows_NT-x86_64))
>>>  PPM mode in Accurate Mass Model ...
>>> C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a09964\': File exists
>>>
>>> command "C:\TPP\bin\mkdir.exe -p "/tmp/a09964/"" failed: Operation not 
>>> permitted
>>> could not create temp dir /tmp/a09964/, working in data directory
>>> running: "C:/TPP/bin/InteractParser "interact.pep.xml" "H7(3).pep.xml" 
>>> "h7(3).xml" -L"7"" file 1: H7(3).pep.xmlWARNING: empty raw_data in 
>>> msms_run_summary tag ... trying mzML ...
>>> Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data 
>>> file c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
>>> Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT data 
>>> file c:/TPP/data/.mzXML in msms_run_summary tag ...WARNING: empty raw_data 
>>> in msms_run_summary tag ... trying mzML ...
>>> Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data 
>>> file c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
>>> Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT data 
>>> file c:/TPP/data/.mzXML in msms_run_summary tag ...
>>>
>>>
>>>
>>> Kind Regards,
>>>
>>> Ada
>>>
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>>
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Re: [spctools-discuss] Analyze peptides- error

[Elkan Dong]

I'm using the newest version of TPP, but encountered the same error when 
using PeptideProphet. The file name I used looks like 
I08-F4-SAX1.pep.xml
Any solution?

Thanks.

Elkan


在 2017年6月20日星期二 UTC+8上午1:28:34，David Shteynberg写道：
>
> Hello Ada,
>
> One immediate problem I notice is that your files contain parenthesis 
> character.  Please name your files using only alphanumeric and underscore 
> character, please no special characters or whitespace.  Also, you might 
> consider using comet search engine, support for which is more streamlined 
> in the TPP.
>
> Cheers,
> -David
>
> On Mon, Jun 19, 2017 at 9:46 AM, Ada A  
> wrote:
>
>> Hello, 
>>
>> I was trying to run peptide analysis with PeptideProphet but it keeps 
>> showig me error... 
>> I was using dimethyl labeling technique and peptides were identified 
>> using Mascot. I exported all data from Mascot, uploaded here and it fails 
>> to do anything. I was wondering whether anyone could advice me what should 
>> I do with it? I would be grateful for some help.
>>
>> Here is what it shows me: 
>>
>> C:/TPP/bin/xinteract (TPP v5.0.0 Typhoon, Build 201610111222-7423 
>> (Windows_NT-x86_64))
>>  PPM mode in Accurate Mass Model ...
>> C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a09964\': File exists
>>
>> command "C:\TPP\bin\mkdir.exe -p "/tmp/a09964/"" failed: Operation not 
>> permitted
>> could not create temp dir /tmp/a09964/, working in data directory
>> running: "C:/TPP/bin/InteractParser "interact.pep.xml" "H7(3).pep.xml" 
>> "h7(3).xml" -L"7"" file 1: H7(3).pep.xmlWARNING: empty raw_data in 
>> msms_run_summary tag ... trying mzML ...
>> Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data file 
>> c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
>> Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT data 
>> file c:/TPP/data/.mzXML in msms_run_summary tag ...WARNING: empty raw_data 
>> in msms_run_summary tag ... trying mzML ...
>> Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data file 
>> c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
>> Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT data 
>> file c:/TPP/data/.mzXML in msms_run_summary tag ...
>>
>>
>>
>> Kind Regards, 
>>
>> Ada
>>
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>
>

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[spctools-discuss] Analyze peptides- error

[Ada A]

Hello, 

I was trying to run peptide analysis with PeptideProphet but it keeps 
showig me error... 
I was using dimethyl labeling technique and peptides were identified using 
Mascot. I exported all data from Mascot, uploaded here and it fails to do 
anything. I was wondering whether anyone could advice me what should I do 
with it? I would be grateful for some help.

Here is what it shows me: 

C:/TPP/bin/xinteract (TPP v5.0.0 Typhoon, Build 201610111222-7423 
(Windows_NT-x86_64))
 PPM mode in Accurate Mass Model ...
C:\TPP\bin\mkdir.exe: cannot create directory `/tmp\a09964\': File exists

command "C:\TPP\bin\mkdir.exe -p "/tmp/a09964/"" failed: Operation not permitted
could not create temp dir /tmp/a09964/, working in data directory
running: "C:/TPP/bin/InteractParser "interact.pep.xml" "H7(3).pep.xml" 
"h7(3).xml" -L"7"" file 1: H7(3).pep.xmlWARNING: empty raw_data in 
msms_run_summary tag ... trying mzML ...
Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data file 
c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT data 
file c:/TPP/data/.mzXML in msms_run_summary tag ...WARNING: empty raw_data in 
msms_run_summary tag ... trying mzML ...
Failed to open input file 'c:/TPP/data/.mzML'.WARNING: cannot open data file 
c:/TPP/data/.mzML in msms_run_summary tag .. trying .mzXML ...
Failed to open input file 'c:/TPP/data/.mzXML'.WARNING: cannot CORRECT data 
file c:/TPP/data/.mzXML in msms_run_summary tag ...



Kind Regards, 

Ada

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