still have a problem viewing spectra

[CH]

I've recently posted this with no response.

-----
The problem I had earlier with view spectra temporarily solved itself,
but has now returned.

I have searched a single .mzXML file twice with the TPP GUI. The run
I searched last week had links to spectra, ions, and ASAPRAtio/XPRESS
ratios. The run I searched yesterday did have slightly different
search parameters but resulted in links that showed none of the
spectra I need to see. In the past however (see previous posts) the
different parameters for searching was not related to whether I could
see the spectra/ratios or not.

The errors I see
1. When clicking on ions: Error - Cannot read spectrum; tried
direct .dta, from mzXML/mzData and from .tgz
2. When clicking on ASAPRatio: Could not open input file
filename.mzXML. Error in reading filename.mzXML.
3. When clicking on XPRESS ratio: Error - cannot open file
"filename.mzXML."
4. When clicking on spectrum in Peptide/ProteinProphet: just lines of
text show up, no images.

I'm not sure if it makes a difference, but the mzXML file is in the
same folder that the .xml files are in for viewing the results.

Not sure why I'm the only one with this issue. Perhaps you can help
me figure out if I'm doing something wrong...

Thanks
-----

I'm at a loss and I absolutely don't know where to go from here. I
don't know what I'm doing wrong or how to figure out if I'm doing
something to cause this problem. Please, please help.

[Jimmy Eng]

None of the tools appear to be able to read their respective data from
the mzXML file. The answer to your problem is to figure out why.

For the ms/ms spectrum viewer, it looks for the location of the mzXML
file using the value specified in the "Dta=<full_path_to_dta_file>" in
the URL. Can you reply with:

1) the full path directory+name of your mzXML file
2) there are two "base_name=" attributes in your interact.xml file; what
are their values (should be the same)?
3) what is the <full_path_to_dta_file> string from the "Dta=" variable
in the ms/ms spectrum viewer cgi URL?
4) did you run the search/tools through the TPP GUI?

- Jimmy

[CH]

1) the full path directory+name of your mzXML file

C:\Inetpub\wwwroot\ISB\data\tpp_newversiontest
\3_4_1\cn109_silac_jl_rh_01.mzxml

2) there are two "base_name=" attributes in your interact.xml file;
what
are their values (should be the same)?

How do I find these values? Do I open up the interact.xml file? And
look where?

3) what is the <full_path_to_dta_file> string from the "Dta=" variable
in the ms/ms spectrum viewer cgi URL?

Again, I'm not sure of where to find this...sorry, thanks for your
patience.

4) did you run the search/tools through the TPP GUI

Yes, I did run the search/tools through the GUI.

If it helps, Brian Pratt tried to help in a previous post but I never
got a response.
http://groups.google.com/group/spctools-discuss/browse_thread/thread/4d3a1c12db447344#

Thanks for you help.

[Jimmy Eng]

Is your mzXML file explicitly named cn109_silac_jl_rh_01.mzxml or is it
named cn109_silac_jl_rh_01.mzXML? Case will matter.

CH wrote:
> 1) the full path directory+name of your mzXML file
> C:\Inetpub\wwwroot\ISB\data\tpp_newversiontest
> \3_4_1\cn109_silac_jl_rh_01.mzxml
>
> 2) there are two "base_name=" attributes in your interact.xml file;
> what
> are their values (should be the same)?
> How do I find these values? Do I open up the interact.xml file? And
> look where?

If you need to, open up the interact.xml file in some text editor (like
Word) and do a search for "base_name=". Report back what the value is.

> 3) what is the <full_path_to_dta_file> string from the "Dta=" variable
> in the ms/ms spectrum viewer cgi URL?
> Again, I'm not sure of where to find this...sorry, thanks for your
> patience.

When you click on the link under the ions column to pull up the ms/ms
spectrum view, there is a long text string in your browser's address bar
starting with "http://". This is the URL (uniform resource locator).
Look in that string, you have to use your mouse cursor to scroll to the
right, and report back what the value of "Dta=" is. Report the text
right after "Dta=" and end at the first "&" which is a delimiter character.

[CH]

It's named cn109_silac_jl_rh_01.mzXML

> >http://groups.google.com/group/spctools-discuss/browse_thread/thread/...

[Jimmy Eng]

Can you also answer the other 2 questions I had in that response?

To, repeat, what's the value of the 'base_name' attribute in the
interact.xml file and the value of the 'Dta' variable in the ms/ms
spectrum view URL?

[CH]

I had responded to your original message by saying that I'm not sure
where to find this information. Do I have to open up an interact.xml
file? Where do I look in the interact.xml file?

[Jimmy Eng]

If you read my full response, I gave you instructions on where/how to
find the information.

[CH]

Sorry, I'm really slow and inept when it comes to this stuff. Thanks
for your patience.

2) cn109_silac_c_jl_rh_01 for both of them

3) cn109_silac_c_jl_rh_01/cn109_silac_c_jl_rh_01.00341.00341.2.dta

[Jimmy Eng]

Thanks. That at least defines what the problem is. For whatever
reason, the full path is not being written out in the base_name
attribute of the pep.xml and interact.xml files. That's why all of the
tools can't find the data because they don't know where to look.

Now that I'm reading through the old thread, I see Brian on 1/29 had
already noted that the path information was not being written out. I
was looking through the thread to see what search engine you were using
but I don't see that mentioned anywhere. I'll assume you're using
X!Tandem. If so, just make sure that you always specify the full path
reference to the input spectra you are searching.

Do this
<note type="input" label="spectrum, path">c:\my\path\my.mzXML</note>
instead of
<note type="input" label="spectrum, path">my.mzXML</note>

I'm assuming that if you run searched through the TPP GUI, you would not
have this problem.

For your existing results below, you can hopefully salvage them by
editing your interact.xml file. In the two occurrences of

base_name=cn109_silac_c_jl_rh_01

change them to

base_name=c:\Inetpub\wwwroot\ISB\data\tpp_newversiontest\3_4_1\cn109_silac_c_jl_rh_01

using a text editor. My only concern at this point is that you'll need
to use cygwin paths (/cygdrive/c/Inetpub/wwwroot/ISB/data/...) instead
of Windows paths. Other developers can chime in if they know the answer
to this concern.

Good luck.

- Jimmy

[Oded]

Hi all,
I'm having similar problems using X!Tandem or Sequest with ASAPratio
or Libra through the GUI. In my case it seem to be reIated to the TPP
version: on TPP 3.4.0a the links work fine while on machines with TPP
3.4.1a (got it with too) and TPP 3.5.1 the image links are broken.
Since I'm using the GUI the base_name path is the full path but still
I tried to play with it following Jimmy's suggestion and changing it
in tandem.pep.xml from /cygdrive/c/Inetpub.... to c:\Inetpub.....and
vise versa but that didn't do the trick.
Any help will be appreciated.
Thanks,
Oded

[Brian Pratt]

Hi Oded,

If you can zip up some representative files and drop them on the Insilicos
ftp site (ftp://insilicos.serveftp.net/pub) I'll have a look.

Brian

[Davis, Darryl [CNTUS]]

Hi,
After upgrading to 3.5 (Windows XP machine). GUI is spitting

Output
c:\Inetpub\wwwroot\ISB\data\07Aug07a1.mzXML (file not found: not created or deleted?)

but

Command
/usr/bin/readw "c:\Inetpub\wwwroot\ISB\data\07Aug07a1.RAW" c
--------------------------------------------------------------------------------

Xcalibur 2.0 interface initialized.
(Thermo lib opened file c:\Inetpub\wwwroot\ISB\data\07Aug07a1.RAW)
file version is 62, interface version is 2.0 or greater
file should contain scan numbers 1 through 2395
(got computer name: WCNTUSRDLB0576)
Calculating sha1-sum of mzXML
--done (mzXML sha1):e4c2dad7bc8c8a1922729b4a5a26da7d7cf2dc3a
Command Successful

looks OK. No mzXML file is there however.

Also DB search from GUI spits

FIND: Parameter format not correct
params file here: yw7112705/sequest.params
FIND: Parameter format not correct

Then sequest27.exe debugging popups start. Error is related to signature.

Command line works fine for both. Noted command line does not work w/ -c but does w/ --centroid. Also noted notes for readw.exe ref system1 folder should be system folder.

DD
Darryl L. Davis, Ph.D.
Senior Research Scientist
Centocor, PD Analytical Development
145 King of Prussia Rd.
Radnor, PA 19087
610 240-8286
Fax 610 651-6986
MailStopR-1-1
CONFIDENTIALITY NOTICE : The information in this email may be confidential and/or privileged. This email is intended to be reviewed by only the individual or organization named above. If you are not the intended recipient or an authorized representative of the intended recipient, you are hereby notified that any review, dissemination or copying of this email and its attachments, if any, or the information contained herein is prohibited. If you have received this email in error, please immediately notify the sender by return email and delete this email from your system. Thank You

[Joshua Tasman]

Hi Darryl,

Sorry to hear you've having trouble. Could you please give a little more detail about what steps you're running when you get these errors?

>Also noted notes for readw.exe ref s System1 folder should be system folder.

Could you please explain what you mean here?

Thanks,

Josh

[Davis, Darryl [CNTUS]]

Hi Josh,
No worries like to have issues since you (at least me) often learn alot. Seems like the mzXML conversion from RAW files referenced first is now working although a restart (2nd) and registering dll did not help but after starting Xcalibur and opening some files the GUI now works.

The second ref. is
When doing database search (Sequest)

> FIND: Parameter format not correct
> params file here: yw7112705/sequest.params
> FIND: Parameter format not correct

Running the command in TPP command line

MzXML2Search -dta -P15 07Aug07a1.mzXML
chmod g+w 07Aug07a1; cp c:/Inetpub/wwwroot/ISB/data/sequest.params 07Aug07a1/
cd 07Aug07a1; tar --wildcards -xzf ../07Aug07a1.tgz '*.out'
cd 07Aug07a1; find . -maxdepth 1 -depth -name "07Aug07a1*.dta" -print | xargs --max-args=50 /cygdrive/c/xcalibur/system/programs/bioworksbrowser/sequest27.exe -Pc:/Inetpub/wwwroot/ISB/data/sequest.params
Out2XML 07Aug07a1 1

gives correct output

This is still not working. Attached is error log.

Going to wiki.

http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW

regsvr32 "C:\Xcalibur2\system\programs\XRawfile2.dll" should read Xcalibur not Xcalibur2 but i guess one may install there (sorry I said system1 earlier).

Hi Darryl,

Sorry to hear you've having trouble. Could you please give a little more detail about what steps you're running when you get these errors?

>Also noted notes for readw.exe ref s System1 folder should be system folder.

Could you please explain what you mean here?

Thanks,

Josh

Davis, Darryl [CNTUS] wrote:
> Hi,
> After upgrading to 3.5 (Windows XP machine).

When doing mzXML conversion

[Chee-Hong WONG]

Hi Darry,

The message on the command "FIND" comes from the copy distributed in
Windows (<windows dir>\system32\find.exe). The copy that should be run
is the Cygwin copy of /usr/bin/find but is not 'cos the the environment
variable PATH having windows and windows system directory before the
path to Cygwin's related path. (If you searched the mailing list
archive, I think there are some related postings.)

You can use http://localhost:1441/tpp-bin/check_env.pl to check for the
exact value that your CGI program will see.

You can override this with "SetEnv PATH" directive with the correct path
order in your apache configuration.

Cheers,
Chee-Hong.

[Davis, Darryl [CNTUS]]

Thanks Chee-Hong that indeed did the trick. Actually turns out that the path for sys var had a truncated cygwin path (guess there is a charac max)and placing cygwin path in beg. now DB search is fine. As for the mzXML conv. it turns out win cmd is fine TPP cmd is not and GUI works on some folders but not all. strange. Thanks again to you and Josh.
DD

[Davis, Darryl [CNTUS]]

To close this out the mzXML conv (readw) works from TPP cmd if the output file is explicitly stated. From GUI if mzXML file of same name as raw file exists it will update (save) the conv. If not then it generally does not produce any conv. file. Strangely enough in two circumstances it produced files w/out any extensions. These files are valid mzXML files (opened w/ Insilicos viewer after giving mzXML ext.)
Thanks again,
DD

Darryl L. Davis, Ph.D.
Senior Research Scientist
Centocor, PD Analytical Development
145 King of Prussia Rd.
Radnor, PA 19087
610 240-8286
Fax 610 651-6986
MailStopR-1-1
CONFIDENTIALITY NOTICE : The information in this email may be confidential and/or privileged. This email is intended to be reviewed by only the individual or organization named above. If you are not the intended recipient or an authorized representative of the intended recipient, you are hereby notified that any review, dissemination or copying of this email and its attachments, if any, or the information contained herein is prohibited. If you have received this email in error, please immediately notify the sender by return email and delete this email from your system. Thank You

[Joshua Tasman]

Thanks, Darryl; we'll try to get a fix into the next release.

[CH]

I'm having (somewhat) similar issues with readw. I'm getting the same
output file message as Darryl after installing the latest version
(v3.5.1)

c:\Inetpub\wwwroot\ISB\data\eric\bjab\020608_march8_arg
\031008_bjab_march8_arg_01.mzXML (file not found: not created or
deleted?)

Command
/usr/bin/readw -v "c:\Inetpub\wwwroot\ISB\data\eric\bjab
\020608_march8_arg\031008_bjab_march8_arg_01.RAW"

However, the result from the command is "Command FAILED" with no other
message.

Any help would be appreciated.

Thanks.

> > You can usehttp://localhost:1441/tpp-bin/check_env.plto check for the

> >>> Also noted notes forreadw.exe ref s System1 folder should be system folder.

> >>> Command line works fine for both. Noted command line does not work w/ -c but does w/ --centroid. Also noted notes forreadw.exe ref system1 folder should be system folder.
>
> >>> DD

[Davis, Darryl [CNTUS]]

Command failed is same outcome for me on new install. Sep. thread (RE: Permissions issue w/ 3.5rev1 on Windows XP machine (GUI)). In that thread (not that I am suggesting you do this as a fix) if you re-install and choose ver 3.4 for ISB tools the issues are not there.
DD

Darryl L. Davis, Ph.D.
Senior Research Scientist
Centocor, PD Analytical Development
145 King of Prussia Rd.
Radnor, PA 19087
610 240-8286
Fax 610 651-6986
MailStopR-1-1
CONFIDENTIALITY NOTICE : The information in this email may be confidential and/or privileged. This email is intended to be reviewed by only the individual or organization named above. If you are not the intended recipient or an authorized representative of the intended recipient, you are hereby notified that any review, dissemination or copying of this email and its attachments, if any, or the information contained herein is prohibited. If you have received this email in error, please immediately notify the sender by return email and delete this email from your system. Thank You

-----Original Message-----
From: spctools...@googlegroups.com
[mailto:spctools...@googlegroups.com]On Behalf Of CH
Sent: Thursday, March 13, 2008 11:54 AM
To: spctools-discuss

[Joshua Tasman]

Hi all,

Sorry to hear about the GUI issues. Perhaps the GUI isn't calling the new version of readw (which has different options formats than that last version) correctly. I will try to track this down. As Darryl found, I believe, an alternate route is to use the command-line to run readw instead of the GUI. I recommend using the newest readw rather than the 3.4 version, if possible.

[CH]

As expected, success with the 3.4 version. Would prefer using the 3.5
version if possible. Let us know if there's a readw fix for TPP v3.5.

> >>> You can usehttp://localhost:1441/tpp-bin/check_env.pltocheck for the

[Davis, Darryl [CNTUS]]

Note there is another thread (Permissions issue w/ 3.5rev1 on Windows XP machine (GUI)) detailing issues.

Unfortunately if other user has same issue as me then the command line will not work (from either win cmd or TPP, try to run it and generic application configuration incorrect pops up).

The command line works for machine that was upgrade but not for fresh install. Seems to be tied to permissions (bash: usr/bin/readw/: permission denied). Maybe Cygwin issue, here is shell which is not seen on other platforms (guess the machine it is not as Unix like as hoped). Files do exist though.

Your group is currently "mkpasswd". This indicates that
the /etc/passwd (and possibly /etc/group) files should be rebuilt.
See the man pages for mkpasswd and mkgroup then, for example, run
mkpasswd -l [-d] > /etc/passwd
mkgroup -l [-d] > /etc/group
Note that the -d switch is necessary for domain users.

Tried it w/out domain but each restart the message is still there.

[Davis, Darryl [CNTUS]]

Following link (as detailed by Chee-Hong) previously allows raw file conv. So in the end I re-installed 3.5 then placed dll and exe in cyqwin/bin. Sidenote mzwiff not func. before this so must have been the dll as Chee-Hong mentioned prev.
http://tools.proteomecenter.org/wiki/index.php?title=Software:ReAdW

DD
Darryl L. Davis, Ph.D.
Senior Research Scientist
Centocor, PD Analytical Development
145 King of Prussia Rd.
Radnor, PA 19087
610 240-8286
Fax 610 651-6986
MailStopR-1-1
CONFIDENTIALITY NOTICE : The information in this email may be confidential and/or privileged. This email is intended to be reviewed by only the individual or organization named above. If you are not the intended recipient or an authorized representative of the intended recipient, you are hereby notified that any review, dissemination or copying of this email and its attachments, if any, or the information contained herein is prohibited. If you have received this email in error, please immediately notify the sender by return email and delete this email from your system. Thank You

-----Original Message-----
From: spctools...@googlegroups.com
[mailto:spctools...@googlegroups.com]On Behalf Of CH
Sent: Thursday, March 13, 2008 1:39 PM
To: spctools-discuss
Subject: Re: 3.5rev1 GUI

As expected, success with the 3.4 version. Would prefer using the 3.5
version if possible. Let us know if there's a readw fix for TPP v3.5.

> >>> You can usehttp://localhost:1441/tpp-bin/check_env.pltocheck for the