Let me start by asking what version of Mascot you have, and whether you have yet made any modifications to any of the Mascot .pl files.

I know I had to make a minor modification to one of the .pl files to get this working at FHCRC. This should not be necessary with the very latest version(s) of Mascot, but certainly is with versions even 6 months old.

This is the Mascot info:
Version: 2.1.04 - Licensed to: Memorial Sloan-Kettering Cancer Center (KA253-1350), (2 processors).
4 logical, 2 physical Intel processors (hyper-threading enabled, single core). CPUs: 0 1 2 3 available, using: 0 1 2 3 .

And we have done no modifications to the .pl files.

-- john

Hi John,

Sorry to have been MIA. Error 112 means Missing END IONS statement in your mascot generic file.

Do you mind to post 120506_Urotsa_20ug_3C.mgf here (or send it to my mail box if it is sensitive)?

You might want want to try out a small .mzXML file (attached here) to see if it can work out.

*Chee-Hong.

Hi Chee-Hong,

I was using an mzXML file to search. I think CPAS converts that to MGF to send to mascot. Here is the mzXML file I used to search.

http://ftsext.mskcc.org/FileExchange/FileList.aspx?id=ad5b5af2-65b0-47dd-82ed-9353e98eebe9

That link is valid for 7 days. Please get the file ASAP.

john

I tried a smaller mzXML file and got the following error:
21 Dec 2006 15:38:52,890 INFO : Mascot search for 120506_Urotsa_20ug_3C_2.mzXML
21 Dec 2006 15:38:52,890 INFO : =======================================
21 Dec 2006 15:46:20,046 INFO : MzXML2Search output
21 Dec 2006 15:46:20,046 INFO : =======================================
21 Dec 2006 15:46:35,015 INFO : running: MzXML2Search -mgf 120506_Urotsa_20ug_3C_2.mzXML
21 Dec 2006 15:46:35,093 INFO :
21 Dec 2006 15:46:35,093 INFO : MzXML2Search - Mascot Generic Format
21 Dec 2006 15:46:35,093 INFO :
21 Dec 2006 15:46:35,093 INFO : Reading 120506_Urotsa_20ug_3C_2.mzXML
21 Dec 2006 15:46:35,093 INFO : Getting the index offset
21 Dec 2006 15:46:35,109 INFO : Reading the index
21 Dec 2006 15:46:41,734 INFO : scan: 1 000% 2 000% 3 000% 4 000% 5 000% 6 000% 7 000% 8 000% 9 000% ... 099% 5676 099% 5677 100%
21 Dec 2006 15:46:41,750 INFO : Done.
21 Dec 2006 15:46:41,750 INFO :
21 Dec 2006 15:46:41,750 INFO : mascot client output
21 Dec 2006 15:46:41,765 INFO : =======================================
21 Dec 2006 15:46:41,765 INFO : Creating Mascot session...
21 Dec 2006 15:46:42,062 INFO : Creating Mascot search task...
21 Dec 2006 15:46:42,328 INFO : Submitting search to Mascot server...
21 Dec 2006 15:47:14,562 INFO : Mascot search task status: query upload completed
21 Dec 2006 15:47:45,750 INFO : Mascot search status: 0%
21 Dec 2006 15:48:16,015 INFO : Mascot search task status error: (-1)
21 Dec 2006 15:48:16,015 INFO : Mascot search status: error=-1

21 Dec 2006 15:48:16,265 INFO : Mascot session ended.
21 Dec 2006 15:48:16,265 ERROR: Failed running Mascot.

-------
What is error = -1?

The file is here:

http://ftsext.mskcc.org/FileExchange/FileList.aspx?id=f17dd5bd-a89b-4c3f-92b1-8534ecd13d75

Again you have 7 days before the link expires.

john

Hi John,

Positive error codes are reserved by Mascot. -1 indicate that we did not received any error code from Mascot.

I tried the smaller file but did not experience the same problem. I have had some trouble downloading the full 300+MB file. Will test out the file tomorrow.

There are 2 potential causes here. Do you mind to run the Mascot search against CAexample_mini.mzXML which is very small. Let us know how it goes.

Please also get the following information after the search on CAexample_mini.mzXML:
1) Both cpas.log and cpas-error.log in apache directory on your CPAS server.
2) The mascot error log at your Mascot server. (found at /mascot/logs/errorlog.txt)
3) If possible, please confirm the session time-out of the web server on your Mascot server.
4) The operating system which your Mascot server is running on.
5) Can I also confirm that you are running CPAS on MacOS X?

Thanks,
Chee-Hong.

I ran the CAexample file.

1. Attached are the cpas.log and cpas-error.log files.
2. Attached is the error log of the mascot server
3. How do I find out the session time-out?
4. Mascot is running in Windows 2003 Enterprise server.
5. CPAS is running in Windows XP. I would like to get it running on a mac but haven't the time. I have Tandem running on a mac so far.

thanks,
john

Hi John,

Thanks for the information.

Here are the findings:
1. From the log, you CPAS machine seem to have run out of disk space. Consequently, the run on CAexample_mini.mzXML was not conclusive.
2. There has not been any successful MS2 search recorded since the upgrade to v1.7 for both X! Tandem and Mascot.
3. Thus, the run on 120506_Urotsa_20ug_3C_2.mzXML (smaller file) could have failed due to the disk space.
4. I was able to reproduce the Error code 112. I need to confirm if the constraint is coming from Mascot server.
5. Your mzXML file is converted with mzStar in 'profile' mode, which generate a lot of scans that have over 10,000 m/z values.

I will like to suggest the followings:
a) Free up some disk space on CPAS server.
b) Confirm that the MS2 search is working with X! Tandem. Try this with CAexample_mini.mzXML first.
c) When step b) works out, perform MS2 search with Mascot on CAexample_mini.mzXML. Please note that you need to download a copy of the fasta database from Mascot server into "FASTA root" for result conversion to pepXML.
d) When step c) works out, we can re-try Mascot search on 120506_Urotsa_20ug_3C_2.mzXML
e) When step d) works, let's discuss finding #5.

Time out setting is dependent on the web server used by the Mascot server. Assuming that apache is installed, you can locate this as a setting "Timeout" in <apache directory>/conf/httpd.conf

*Chee-Hong.

Hi,

It took me a little while to do these steps.
a. Freed up 9.4 GB.
b. MS2 works with XTandem with both CAexample and 120506Urotsa20ug3C2.mzXML
c. Mascot on CAexample failed. Error given below.
d. Didn't bother since step c failed.

09 Jan 2007 15:42:22,421 INFO : Mascot search for CAexample_mini.mzXML
09 Jan 2007 15:42:22,421 INFO : =======================================
09 Jan 2007 15:42:22,578 INFO : MzXML2Search output
09 Jan 2007 15:42:22,578 INFO : =======================================
09 Jan 2007 15:42:22,625 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML
09 Jan 2007 15:42:23,031 INFO :
09 Jan 2007 15:42:23,031 INFO : MzXML2Search - Mascot Generic Format
09 Jan 2007 15:42:23,046 INFO :
09 Jan 2007 15:42:23,046 INFO : Reading CAexample_mini.mzXML
09 Jan 2007 15:42:23,046 INFO : Getting the index offset
09 Jan 2007 15:42:23,046 INFO : Reading the index
09 Jan 2007 15:42:23,109 INFO : scan: 1 000% 2 001% 3 001% 4 002% 5 002% 6 003% 7 003% 8 004% 9 004% 10 005% ....... 099% 200 100%
09 Jan 2007 15:42:23,109 INFO : Done.
09 Jan 2007 15:42:23,109 INFO :
09 Jan 2007 15:42:23,109 INFO : mascot client output
09 Jan 2007 15:42:23,125 INFO : =======================================
09 Jan 2007 15:42:23,125 INFO : Creating Mascot session...
09 Jan 2007 15:42:23,375 INFO : Creating Mascot search task...
09 Jan 2007 15:42:23,640 INFO : Submitting search to Mascot server...
09 Jan 2007 15:42:24,359 INFO : Mascot search task status: query upload completed
09 Jan 2007 15:42:55,312 INFO : Mascot search status: 21%
09 Jan 2007 15:43:25,562 INFO : Mascot search status: 43%
09 Jan 2007 15:43:55,828 INFO : Mascot search task status error: (-1)
09 Jan 2007 15:43:55,828 INFO : Mascot search status: error=-1

09 Jan 2007 15:43:56,078 INFO : Mascot session ended.
09 Jan 2007 15:43:56,078 ERROR: Failed running Mascot.

______________

I have mascot installed on Windows 2003 Enterprise server. So I am using IIS not Apache.

john

Hi John,

Thanks for taking the time to help to narrow down the issues.

Can I also trouble you with both cpas.log and cpas-error.log?

*Chee-Hong

Here they are.

Hi John,

If you are using IIS 4.0 or later, Mascot installation will have set the time out to 1 day. Failing even on CAexample_mini.mzXML rules out 'time out' as potential factor.

I need your help to replace a jar file to tell us what Mascot returns:
1) stop tomcat
2) make a backup copy of <cpaswebapp dir>\WEB-INF\lib\api.jar (this copy contains the non-verbose copy of Mascot Client)
3) copy the attached api.jar to same location
4) start tomcat
5) perform MS2 search with Mascot on CAexample_mini.mzXML and provide the search log file, cpas.log and cpas-error.log

Thanks for staying with us on this issue.

*Chee-Hong.

Done. Here are the logs.

Hi John,
Please post the search log for the 2 searches (via the pipeline tab). Thanks.
*Chee-Hong.

Search 1:
12 Jan 2007 16:28:44,859 INFO : Mascot search for CAexample_mini2.mzXML
12 Jan 2007 16:28:44,859 INFO : =======================================
12 Jan 2007 16:30:37,953 INFO : MzXML2Search output
12 Jan 2007 16:30:37,953 INFO : =======================================
12 Jan 2007 16:30:37,968 INFO : running: MzXML2Search -mgf CAexample_mini2.mzXML
12 Jan 2007 16:30:38,000 INFO :
12 Jan 2007 16:30:38,000 INFO : MzXML2Search - Mascot Generic Format
12 Jan 2007 16:30:38,000 INFO :
12 Jan 2007 16:30:38,000 INFO : Reading CAexample_mini2.mzXML
12 Jan 2007 16:30:38,000 INFO : Getting the index offset
12 Jan 2007 16:30:38,015 INFO : Reading the index
12 Jan 2007 16:30:38,062 INFO : scan: 1 000% ..... 099% 200 100%
12 Jan 2007 16:30:38,062 INFO : Done.
12 Jan 2007 16:30:38,062 INFO :
12 Jan 2007 16:30:38,062 INFO : mascot client output
12 Jan 2007 16:30:38,062 INFO : =======================================
12 Jan 2007 16:30:38,078 INFO : Creating Mascot session...
12 Jan 2007 16:30:38,328 INFO : Creating Mascot search task...
12 Jan 2007 16:30:38,593 INFO : Submitting search to Mascot server...
12 Jan 2007 16:30:39,046 INFO : Mascot search task status: query upload completed
12 Jan 2007 16:30:39,046 INFO : Mascot search status verbose reporting on
12 Jan 2007 16:31:10,031 INFO : Mascot search status: 21%
12 Jan 2007 16:31:40,281 INFO : Mascot search task status error: (-1)
12 Jan 2007 16:31:40,296 INFO : Full Mascot response: (error=-1
)
12 Jan 2007 16:31:40,296 INFO : Mascot search status: error=-1

12 Jan 2007 16:31:40,531 INFO : Mascot session ended.
12 Jan 2007 16:31:40,546 ERROR: Failed running Mascot.


Search 2:
12 Jan 2007 16:28:44,734 INFO : Mascot search for 120506Urotsa20ug3C2.mzXML
12 Jan 2007 16:28:44,734 INFO : =======================================
12 Jan 2007 16:28:44,953 INFO : MzXML2Search output
12 Jan 2007 16:28:44,953 INFO : =======================================
12 Jan 2007 16:28:54,656 INFO : running: MzXML2Search -mgf 120506Urotsa20ug3C2.mzXML
12 Jan 2007 16:28:56,156 INFO :
12 Jan 2007 16:28:56,156 INFO : MzXML2Search - Mascot Generic Format
12 Jan 2007 16:28:56,156 INFO :
12 Jan 2007 16:28:56,156 INFO : Reading 120506Urotsa20ug3C2.mzXML
12 Jan 2007 16:28:56,156 INFO : Getting the index offset
12 Jan 2007 16:28:56,171 INFO : Reading the index
12 Jan 2007 16:29:02,843 INFO : scan: 1 000% 2 000% 3 000% 4 000% 5 000% 6 000% 7 000% 8 000% 9 000% 10 000% .... 099% 5677 100%
12 Jan 2007 16:29:02,859 INFO : Done.
12 Jan 2007 16:29:02,859 INFO :
12 Jan 2007 16:29:02,859 INFO : mascot client output
12 Jan 2007 16:29:02,859 INFO : =======================================
12 Jan 2007 16:29:02,875 INFO : Creating Mascot session...
12 Jan 2007 16:29:03,125 INFO : Creating Mascot search task...
12 Jan 2007 16:29:03,390 INFO : Submitting search to Mascot server...
12 Jan 2007 16:29:36,125 INFO : Mascot search task status: query upload completed
12 Jan 2007 16:29:36,125 INFO : Mascot search status verbose reporting on
12 Jan 2007 16:30:07,328 INFO : Mascot search status: 0%
12 Jan 2007 16:30:37,593 INFO : Mascot search task status error: (-1)
12 Jan 2007 16:30:37,609 INFO : Full Mascot response: (error=-1
)
12 Jan 2007 16:30:37,609 INFO : Mascot search status: error=-1

12 Jan 2007 16:30:37,843 INFO : Mascot session ended.
12 Jan 2007 16:30:37,843 ERROR: Failed running Mascot.



Mascot.xml for both searchs:
<?xml version="1.0" encoding="UTF-8"?>
<bioml>
  <!-- Override default parameters here. -->
  <note label="pipeline, protocol name" type="input">mascot</note>
  <note label="pipeline, protocol description" type="input"/>
  <note label="pipeline, database" type="input">NCBInr</note>
  <note label="pipeline, email address" type="input">j-philip@mskcc.org</note>
  <note label="pipeline, mascot server" type="input">mascot.mskcc.org</note>
  <note label="pipeline, mascot http proxy" type="input"/>
</bioml>

It looks like you are now having the exact same issue that I started a thread on yesterday. Your searches seem to be getting killed after 1 minute.

Hi Greg and John,

I will like to summarise the findings so far, althought I am still working on the exact cause.

1. Error Code 112 indicates Missing END IONS statement in the submitted mgf file. This is usually caused by partial upload if not incorrectly formatted file. John's file is intact and correctly formatted. Looking thru' his mascot search log, it has a number of "more than 10,000 m/z value per spectrum" warning. To resolve this, you need to turn on the centroid in mzStar convertor. But you will need the a version that uses Analyst centroid algorithm.

2. The large search seems to 'time out' in 90 secs. John has helped to test with small file "CAexample_mini.mzXML". This however seems to 'time out' in 30 secs. This is the default status checking interval. This suggests that there are other issue than time out.

3. The error code -1 indicates other issue. It is used indicate no response content from MascotServer to the status query. The list of mascot error code and message can be retrieved by pointing your browser to your Mascot server (e.g. http://mascotserver/mascot/cgi/ms-geterror.exe?ALL)

4. Thinking that the response could be unexpected, a new api.jar which has verbose logging turn on for the search log is posted. The search log indicated the response "12 Jan 2007 16:30:37,609 INFO : Full Mascot response: (error=-1<\n>)" which is puzzling.

I am still trying to re-construct what could have caused this response.

*Chee-Hong.

Hi John,

Please pick up the new api.jar from the thread https://cpas.fhcrc.org/announcements/home/support/thread.view?rowId=1178

Thanks.

*Chee-Hong.

Hi John,

Thanks for testing out the new api.jar.

Attached is the new Mascot2XML which will resolve 2 potential crashes that have been reported and fixed in the past 2.5 months.

Let's know how it goes.

*Chee-Hong.