Hey
I am trying to run interact on 170 pepxml files. The software spits
out error 256 when I do this. If I cut the batch of files into chunks,
so say run only 50 files at a time it will work fine.
Any idea if there is a limit on the number of files I can put into
this? Or perhaps I am hitting a
Hi Oded,
Let me see if I understand you. What I did is I searched Sequest using
+28Da on K and n-terminus as fixed modification and +4Da on these two
sites as variable modification. So my Sequest .OUT files contains the
information of both versions of labeling. Now are you asking me to run
the
Yeah I just tried that. It still gave me an error, instead the 7 is
now a 9, but otherwise the same error.
On Apr 23, 2:21 pm, Luis Mendoza lmend...@systemsbiology.org wrote:
Hi Chris,
Did you try:
xinteract '*.pep.xml' -Ninteract.pep.xml -p0.05 -l9 -OAp
-X-m0.15-nR,10-nK,8-L
(note the
Hi Xin,
Yes - you describe my suggestion correctly - just pay attention that
you'll have 2 different files (and names) for your mzXML,out, pepXML
and so on.
I don't have full explanation for what you see - only my experience
with TPP usage, maybe Jimmy or David can answer form the developers
The globbing command doesn't seem to work for me.
When I enter the command
xinteract '*.pep.xml'
the command line returns
error, cannot parse input file '*.pep.xml'
However, the command
xinteract *.pep.xml
works with 120 input files.
On Apr 23, 11:21 am, Luis Mendoza
well the globbing command is meant to be actual quotes I believe. As
when I do '*.pep.xml' I get the same error as you. However when I use
either *.pep.xml or *.pep.xml it lists out all my files in command
prompt for that directory then errors out.
On Apr 23, 3:05 pm, Kristian
There it goes.
Is there any difference in the analysis or output with or without
globbing?
On Apr 23, 12:09 pm, Brian Pratt brian.pr...@insilicos.com wrote:
On windows those need to be double quotes, *.pep.xml.
-Original Message-
From: spctools-discuss@googlegroups.com
Only if *.pep.xml accidentally picks up something you didn't mean it to -
like maybe an interact.pep.xml file from a previous run.
-Original Message-
From: spctools-discuss@googlegroups.com
[mailto:spctools-disc...@googlegroups.com] On Behalf Of Kristian
Sent: Thursday, April 23, 2009
Hi guys,
I am having a difficulty again with the TPP funtions. This time the
ProteinProphet would not work when I tried on the Tutorial data.
Here is the failure message:
ProteinProphet c:/Inetpub/wwwroot/ISB/data/Tutorial/raft.pep.xml c:/
Inetpub/wwwroot/ISB/data/Tutorial/raft.prot.xml
