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 On Fri, Nov 15, 2013 at 8:14 AM, user1 <[email protected]>wrote: > 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 > > > > W dniu środa, 8 lipca 2009 19:26:18 UTC+3 użytkownik Ali napisał: >> >> 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 >> > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. > -- Joe Slagel Institute for Systems Biology [email protected] (206) 732-1362 -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
