xargs:cannot fork?

[Ali]

Hi

I am running a database search, where I run the .mzXML files against
the database. However, it is complaining of 'cannot fork'. This is
the full message:

run_in c:/Inetpub/wwwroot/ISB/data/All_7_strains; runsearch -pc:/
Inetpub/wwwroot/ISB/data/parameters/cbot.params -P15 A1_10.mzXML

RUNSEARCH
Written by J.Eng (c) 2000

mkdir A1_10; chmod g+w A1_10; cp c:\Inetpub\wwwroot\ISB\data\parameters
\cbot.params A1_10/
msxml2other -dta A1_10.mzXML
Converting A1_10.mzXML to thermofinnigan dta
cd A1_10; dtafilter -A -P15
cd A1_10; find . -maxdepth 1 -depth -name "A1_10*.dta" -print0 | xargs
-0 -n 500 sequest27.exe -Pc:\Inetpub\wwwroot\ISB\data\parameters
\cbot.params -S
xargs: cannot fork

command 'C:\Inetpub\ipp-bin\cmd.exe /C C:\Inetpub\ipp-bin\find.exe . -
maxdepth 1 -depth -name "A1_10*.dta" -print0 | xargs -0 -n 500
sequest27.exe -Pc:\Inetpub\wwwroot\ISB\data\parameters\cbot.params -S'
failed with code 1: Operation not permitted
cd A1_10; out2summary . > ../A1_10.html

Command Successful

Any ideas?

Ali

[Brian Pratt]

It appears you're running IPP ("C:\Inetpub\ipp-bin\cmd.exe")- I'd start by
getting the latest TPP and see if the problem hasn't already been addressed.

Brian

[user1]

Hello! 

I am running the sequest search. I have read that the search can be really long, but I cannot see any progress in the command line since few hours (attached below), but it is mentioned that: "this command is still running" and there is no error that command failed. Is it as it suppose to be? 

thank you

RUNSEARCH
Written by J.Eng (c) 2000

TPP v4.6 OCCUPY rev 3, Build 201307241109 (MinGW)

MzXML2Search -dta -P15 Bladder-cancer-side-wall-BCa09.mzML

output mode selected: SEQUEST DTA format
MzXML2Search - SEQUEST DTA format

Reading Bladder-cancer-side-wall-BCa09.mzML
Getting the index offset
Reading the index
Scan 1 000% 2 000% 3 000% 4 
000% ......
Done.

mod g+w Bladder-cancer-side-wall-BCa09; cp 
c:/Inetpub/wwwroot/ISB/data/parameters/sequest.params 
Bladder-cancer-side-wall-BCa09
cd Bladder-cancer-side-wall-BCa09; find . -maxdepth 1 -depth -name 
"Bladder-cancer-side-wall-BCa09*.dta" -print | xargs --max-args=50 
c:/xcalibur/system/programs/bioworksbrowser/sequest.exe 
-Pc:/Inetpub/wwwroot/ISB/data/parameters/sequest.params
xargs: cannot fork

[Joseph Slagel]

It sounds like a resource problem, you might be exceeding the capabilities of the system you are on.  Do you have a lot of applications/processes running?  How many spectrum files are in the directory Bladder-cancer-side-wall-BCa09 and what kind of run is this?  And what version of Windows/TPP are you using?

-Joe

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Joe Slagel
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(206) 732-1362

[user1]

Hi Joe!

Thank you for the prompt reply. Yes, indeed there is a problem with the run. 

"This command was deemed to have timed-out on the server as per user input. "

I was running two files in the same time, however, before I have started the second one, the status from the first was exactly as I have sent. 

I have the WIndows 7 and the latest version of TPP: 4.6.3. I have run previousy this data with Proteome Discoverer (sequest) and  I have around 52 000 spectra. This was the LC-MS/MS run, 8 hours gradient. 

Thank you in advance!

W dniu środa, 8 lipca 2009 19:26:18 UTC+3 użytkownik Ali napisał: