It would be useful to have the output just above what you sent. What you sent says:
- ProteinProphet failed for some reason.
- Unable to move the ProteinProphet output (probably not there, since it failed)
- Failed to set ERROR status on CPAS. This is strange. Not sure why.

But, clearly the interesting thing, is why did ProteinProphet.pl fail to complete successfully. Did everything else run okay? Seems unlikely to me that this is either a problem with the X! Tandem parameters or a permissions error.

<!-- Nonsecific cleavage search --> <note type="input" label="protein, cleavage
site">[X]|[X]</note>


18 Nov 2006 06:30:39,843 INFO : X! Tandem search for KRL01-092906-TZ-0145-GEL-FT-01.mzXML
18 Nov 2006 06:30:39,848 INFO : =======================================
18 Nov 2006 06:30:39,898 INFO : tandem.exe output
18 Nov 2006 06:30:39,901 INFO : =======================================
18 Nov 2006 06:30:39,907 INFO : running: tandem.exe input.xml
18 Nov 2006 06:30:40,098 INFO :
18 Nov 2006 06:30:40,102 INFO : X! TANDEM 2 (2006.09.15.1)
18 Nov 2006 06:30:40,105 INFO :
18 Nov 2006 06:30:46,002 INFO : Loading spectra ...... loaded.
18 Nov 2006 06:30:46,008 INFO : Spectra matching criteria = 10337
18 Nov 2006 06:30:46,012 INFO : Pluggable scoring enabled.
18 Nov 2006 06:30:46,017 INFO : Starting threads . started.
18 Nov 2006 06:30:46,022 INFO : Computing models:
18 Nov 2006 06:30:46,037 INFO :
18 Nov 2006 06:30:47,450 INFO : Spectrum-to-sequence matching process in progress | 50 ks
18 Nov 2006 06:30:48,386 INFO : Spectrum-to-sequence matching process in progress | 100 ks
18 Nov 2006 06:30:48,694 INFO : Spectrum-to-
18 Nov 2006 06:30:48,697 INFO :
18 Nov 2006 06:30:48,703 INFO : kilosequences modelled = 111
18 Nov 2006 06:30:48,704 INFO : Model refinement:
18 Nov 2006 06:30:48,709 INFO : Creating report:
18 Nov 2006 06:30:48,746 INFO :     initial calculations ..... done.
18 Nov 2006 06:30:48,749 INFO :     sorting ..... done.
18 Nov 2006 06:30:48,752 INFO :     finding repeats ..... done.
18 Nov 2006 06:30:48,756 INFO :     evaluating results ..... done.
18 Nov 2006 06:30:48,759 INFO :     calculating expectations ..... done.
18 Nov 2006 06:30:51,176 INFO :     writing results ..... done.
18 Nov 2006 06:30:51,191 INFO :
18 Nov 2006 06:30:51,196 INFO : Valid models = 0
18 Nov 2006 06:30:51,200 INFO :
18 Nov 2006 06:30:51,204 INFO :
18 Nov 2006 06:30:51,218 INFO : Tandem2XML output
18 Nov 2006 06:30:51,219 INFO : =======================================
18 Nov 2006 06:30:51,223 INFO : running: Tandem2XML /proteomics/Duffy/CPASPiplineRoot/primigravid_and_multigravid/TZ_0145_GEL/xtandem/Non/KRL01-092906-TZ-0145-GEL-FT-01.work/KRL01-092906-TZ-0145-GEL-FT-01.xtan.xml /proteomics/Duffy/CPASPiplineRoot/primigravid_and_multigravid/TZ_0145_GEL/xtandem/Non/KRL01-092906-TZ-0145-GEL-FT-01.work/KRL01-092906-TZ-0145-GEL-FT-01-raw.pep.xml
18 Nov 2006 06:30:52,214 INFO : xinteract output
18 Nov 2006 06:30:52,217 INFO : =======================================
18 Nov 2006 06:30:52,220 INFO : running: xinteract -p0 -Opt -nR -NKRL01-092906-TZ-0145-GEL-FT-01.pep.xml /proteomics/Duffy/CPASPiplineRoot/primigravid_and_multigravid/TZ_0145_GEL/xtandem/Non/KRL01-092906-TZ-0145-GEL-FT-01.work/KRL01-092906-TZ-0145-GEL-FT-01-raw.pep.xml
18 Nov 2006 06:30:52,293 INFO :
18 Nov 2006 06:30:52,298 INFO : /usr/local/tpp/bin/xinteract (TPP v2.9 GALE rev.3, Build 200610171545)
18 Nov 2006 06:30:52,302 INFO :
18 Nov 2006 06:30:52,304 INFO : running: "InteractParser KRL01-092906-TZ-0145-GEL-FT-01.pep.xml '/proteomics/Duffy/CPASPiplineRoot/primigravid_and_multigravid/TZ_0145_GEL/xtandem/Non/KRL01-092906-TZ-0145-GEL-FT-01.work/KRL01-092906-TZ-0145-GEL-FT-01-raw.pep.xml'"
18 Nov 2006 06:30:52,321 INFO : file 1: /proteomics/Duffy/CPASPiplineRoot/primigravid_and_multigravid/TZ_0145_GEL/xtandem/Non/KRL01-092906-TZ-0145-GEL-FT-01.work/KRL01-092906-TZ-0145-GEL-FT-01-raw.pep.xml
18 Nov 2006 06:30:52,329 INFO : processed altogether 0 results
18 Nov 2006 06:30:52,360 INFO : command completed in 0 sec
18 Nov 2006 06:30:52,364 INFO :
18 Nov 2006 06:30:52,367 INFO : running: "PeptideProphetParser KRL01-092906-TZ-0145-GEL-FT-01.pep.xml MINPROB=0"
18 Nov 2006 06:30:52,392 INFO : (X! Tandem) (minprob 0)
18 Nov 2006 06:30:52,395 INFO : init with X! Tandem nonspecific
18 Nov 2006 06:30:52,397 INFO : MS Instrument info: Manufacturer: ThermoFinnigan, Model: LTQ, Ionization: ESI, Analyzer: Ion Trap, Detector: EMT
18 Nov 2006 06:30:52,402 INFO :
18 Nov 2006 06:30:52,403 INFO : PeptideProphet v3.0 April 1, 2004 (TPP v2.9 GALE rev.3, Build 200610171545) AKeller@ISB
18 Nov 2006 06:30:52,406 INFO : read in 0 1+, 0 2+, and 0 3+ spectra
18 Nov 2006 06:30:52,407 INFO : read in no data
18 Nov 2006 06:30:52,408 INFO :
18 Nov 2006 06:30:52,410 INFO : command "PeptideProphetParser KRL01-092906-TZ-0145-GEL-FT-01.pep.xml MINPROB=0" exited with non-zero exit code: 256
18 Nov 2006 06:30:52,412 INFO : QUIT - the job is incomplete
18 Nov 2006 06:30:52,436 ERROR: Failed to move /proteomics/Duffy/CPASPiplineRoot/primigravid_and_multigravid/TZ_0145_GEL/xtandem/Non/KRL01-092906-TZ-0145-GEL-FT-01.work/KRL01-092906-TZ-0145-GEL-FT-01.pep-prot.xml to /proteomics/Duffy/CPASPiplineRoot/primigravid_and_multigravid/TZ_0145_GEL/xtandem/Non/KRL01-092906-TZ-0145-GEL-FT-01.prot.xml
18 Nov 2006 06:30:52,449 ERROR: Failed to set status to 'ERROR' for '/proteomics/Duffy/CPASPiplineRoot/primigravid_and_multigravid/TZ_0145_GEL/xtandem/Non/KRL01-092906-TZ-0145-GEL-FT-01.log'.
org.postgresql.util.PSQLException: ERROR: value too long for type character varying(255)
    at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1525)
    at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1309)
    at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:452)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:354)
    at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:347)
    at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.execute(DelegatingPreparedStatement.java:168)
    at org.fhcrc.cpas.data.Table._execute(Table.java:116)
    at org.fhcrc.cpas.data.Table.update(Table.java:931)
    at org.fhcrc.cpas.pipeline.PipelineStatusManager.setStatusFile(PipelineStatusManager.java:155)
    at org.fhcrc.cpas.pipeline.PipelineJob.setStatus(PipelineJob.java:220)
    at org.fhcrc.cpas.pipeline.PipelineJob.error(PipelineJob.java:356)
    at org.fhcrc.cpas.pipeline.PipelineJob.error(PipelineJob.java:349)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.search(XTandemPipelineJob.java:553)
    at org.fhcrc.cpas.ms2.pipeline.XTandemPipelineJob.run(XTandemPipelineJob.java:189)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
    at java.util.concurrent.FutureTask.run(FutureTask.java:123)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:168)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
    at java.lang.Thread.run(Thread.java:595)

Yep. You have to read the log, and look at your files closely.

The first indicator that something is going wrong is that you get "Valid models = 0" from X! Tandem. With 10337 spectra, and 111K sequences this would indicate a real problem with your data, or some totally bogus FASTA file. Or just that you messed up the unspecified cleavage spec. My best guess is that you for got to also include the line:

  <note type="input" label="scoring, maximum missed cleavage sites">50</note>

The default is 2, which would mean you searched only all 2 amino acid peptides. Not surprising you found nothing. If you read default_input.xml this is all explained.

Please send your tandem.xml and your default_input.xml. Something is really wrong with your search.

Further down the line, if you look at your .xtan.xml you will see that it has no "protein" tags, meaning that it made absolutely no matches, and subsequently, and more obvious, the .pep.xml is just a stub of a file with no matches in it. Of course everything goes south from there.

Anyway look to your search definition. It is clearly bogus in some way. Sorry we don't do a better job of calling this out for you, but you also need to start looking a little deeper.

Here're xml files

tandem.xml
default_input.xml

When I did just a default X! tendem search, it worked.
but when I did non-specific search, I had error
I replaced <!-- Override default parameters here. --> with
<note type="input" label="protein, cleavage site">[X]|[X]</note>

Thank you for your considerations.

As I indicated above you need to also add the line:

  <note type="input" label="scoring, maximum missed cleavage sites">50</note>

This is clearly missing from your tandem.xml.

The default is 2, which would means you searched only all 2 amino acid peptides with unspecified cleavage. Not surprising you found nothing. If you read default_input.xml this is all explained.