I am also interested in using proteome discoverer results data with TPP. PD has an export fonction to pepxml format but the files exported are not readable with TPP... I managed to modify these files so that they can be readable but they miss some information: deltaCN and spRank, which, I suppose, are required for the peptideProphet analysis... Thus, I wonder how to import proteome discover results into TPP.
2013/11/15 <[email protected]> > Today's Topic Summary > > Group: http://groups.google.com/group/spctools-discuss/topics > > - xargs:cannot fork? <#1425d9a3358ed4af_group_thread_0> [3 Updates] > - TPP on cluster - Petunia running > remotely?<#1425d9a3358ed4af_group_thread_1>[4 Updates] > - error with installing TPP4.5.2 <#1425d9a3358ed4af_group_thread_2> [6 > Updates] > - sequest and tpp <#1425d9a3358ed4af_group_thread_3> [1 Update] > > xargs:cannot > fork?<http://groups.google.com/group/spctools-discuss/t/686c516a6011a30f> > > user1 <[email protected]> Nov 15 08:14AM -0800 > > 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: > > > > > Joseph Slagel <[email protected]> Nov 15 09:00AM -0800 > > 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 > > > > > -- > Joe Slagel > Institute for Systems Biology > [email protected] > (206) 732-1362 > > > > > user1 <[email protected]> Nov 15 09:18AM -0800 > > 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: > > > > TPP on cluster - Petunia running > remotely?<http://groups.google.com/group/spctools-discuss/t/9203bbd8bf4c6bf7> > > Joshua Dunham <[email protected]> Nov 11 08:07AM -0800 > > Hi Everyone, > > TPP has been successfully installed on my cluster and am now trying to > get Petunia up. I'd like to run petunia as a remote process, not on > the > cluster; is this possible? > > -Josh > > > > > Joseph Slagel <[email protected]> Nov 11 09:54AM -0800 > > Josh, > > Its easily possible to run it as a remote process, not on the cluster. > The > trick of course is having it actually run jobs on the cluster. And I > just > recently did some work to make this a little easier. Which clustering > software do you use? > > -Joe > > > > > -- > Joe Slagel > Institute for Systems Biology > [email protected] > (206) 732-1362 > > > > > Gary Smith <[email protected]> Nov 12 07:25AM -0800 > > We're using UNIVA Grid Engine (aka. SGE). > > --g > > > > > Joseph Slagel <[email protected]> Nov 13 02:24PM -0800 > > Gary/Josh, > > That's good to hear since we're using the last open source version of > SGE > and the commands should all be similar. Recently I've made to the > Petunia > web interface (tpp_gui.pl) that should also work for you. What I've > done > is made two simple modifications The first will prepend the "qrsh" to > the > list of commands. That way the commands are submitted to the cluster > instead of running locally on the web server. The second (and more > controversial) change does yet another prepend to the command list, > this > time using "sudo" to switch to the logged in user. Since Petunia > already > has a undocumented feature that allows you to change its authentication > mechanism (we happen to use this to use LDAP to authenticate our TPP > users) this then allows one to make sure jobs are submitted as the > appropriate user. > > I've tested this out on our development systems here at ISB and it > seems to > work pretty well. We haven't deployed it into production yet for as you > can imagine the security implications of having a CGI script using > sudo and > being tied to a cluster are significant. We do intend to eventually > roll > some solution like this but only after we can change our current system > configuration. (Our IT wants to ensure the web server node is locked > down > and strictly controlled before they'll let any program use sudo so > freely). > > If your interested I could share the code with you now -- or you can > wait > until we release 4.7 which will have said hooks in place with hopefully > some documentation. > > -Joe > > > > > -- > Joe Slagel > Institute for Systems Biology > [email protected] > (206) 732-1362 > > > > error with installing > TPP4.5.2<http://groups.google.com/group/spctools-discuss/t/4d4377eff96e8b5d> > > [email protected] Nov 10 07:44PM -0800 > > Hi, > > I am installing TPP4.5.2 on my CentOS. I got the following message > when > compiling: > > mkdir -p /software/TPP-4.5.2/src/../build/CentOS-x86_64 > make -C ../extern/xtandem/src > TANDEM_PARAMETERS_INSTALL_DIR="/usr/local/tpp/bin/" > SRC_ROOT="/software/TPP-4.5.2/src/" ARCH=CentOS-x86_64 > BUILD_DIR=/software/TPP-4.5.2/src/../build/CentOS-x86_64 > EXPAT_LIB=/software/TPP-4.5.2/src/../build/CentOS-x86_64/libexpat.a > ZLIB_INCL="" ZLIB_LIB="-lz " > > USER_OBJS="/software/TPP-4.5.2/src/../build/CentOS-x86_64/TPPVersionInfo.o" > make[1]: Entering directory `/software/TPP-4.5.2/extern/xtandem/src' > make[1]: Leaving directory `/software/TPP-4.5.2/extern/xtandem/src' > mkdir -p /software/TPP-4.5.2/src/../build/CentOS-x86_64/help > mkdir -p /software/TPP-4.5.2/src/../build/CentOS-x86_64/schema > mkdir -p /software/TPP-4.5.2/src/../build/CentOS-x86_64/images > cd perl_paths; export PERL=perl; make -f perl_paths.makefile all > make[1]: Entering directory `/software/TPP-4.5.2/src/perl_paths' > perl -pe > > "s/\/cygdrive\/c\/Inetpub\/tpp-bin\//\/usr\/local\/tpp\/cgi\-bin\//g;s/\x24\{base_dir\}users\//\/usr\/local\/tpp\/cgi-bin\/users\//g;s/\/tools\/bin\/TPP\/tpp\//\/usr\/local\/tpp\//g;s/cygpath > > \-wp > > //g;s/\"\/cygdrive\/c\/Inetpub\/wwwroot\/\"/\\x24ENV\{\'WEBSERVER_ROOT\'\}\.'\/'/g;s/\/tpp\-bin/\/tpp\/cgi\-bin/g;s/'\/usr\/bin\//'/g;s/'\/bin\//'/g > > " < ../../CGI/show_nspbin.pl > ../../build/CentOS-x86_64/show_nspbin.pl > perl -c -I ../../build/CentOS-x86_64 > ../../build/CentOS-x86_64/show_nspbin.pl > Use of ?PATTERN? without explicit operator is deprecated at > ../../build/CentOS-x86_64/show_nspbin.pl line 123. > syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 115, > near > "$head qw(bin_number nsp_range positive_freq negative_freq > positive/negative_ratio)" > syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 122, > near > "elsif" > Global symbol "$element" requires explicit package name at > ../../build/CentOS-x86_64/show_nspbin.pl line 122. > syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 146, > near "}" > Global symbol "$element" requires explicit package name at > ../../build/CentOS-x86_64/show_nspbin.pl line 148. > syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 152, > near > "$head qw(bin_number ni_range positive_freq negative_freq > positive/negative_ratio)" > syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 157, > near "}" > syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 179, > near "}" > Can't use global @_ in "my" at ../../build/CentOS-x86_64/show_nspbin.pl > line 184, near "= @_" > Global symbol "$element" requires explicit package name at > ../../build/CentOS-x86_64/show_nspbin.pl line 186. > Global symbol "$element" requires explicit package name at > ../../build/CentOS-x86_64/show_nspbin.pl line 190. > Global symbol "$element" requires explicit package name at > ../../build/CentOS-x86_64/show_nspbin.pl line 194. > syntax error at ../../build/CentOS-x86_64/show_nspbin.pl line 199, > near "}" > ../../build/CentOS-x86_64/show_nspbin.pl has too many errors. > make[1]: *** [../../build/CentOS-x86_64/show_nspbin.pl] Error 255 > make[1]: *** Deleting file `../../build/CentOS-x86_64/show_nspbin.pl' > make[1]: Leaving directory `/software/TPP-4.5.2/src/perl_paths' > make: *** [perl_paths] Error 2 > > Can someone have an idea of what to do with this? I am installing on > CentOS6.2. > Thanks a lot, > Qiaojun > > > > > chr12is <[email protected]> Nov 11 03:11AM -0800 > > Hi Qiaojun, > > I had the same errors when installing the latest version of the TPP on > my > CentOS cluster. For some reason it throws an error with the qw syntax > in > the perl files. If you go in those files where it is giving an error, > e.g. > show_nspbin.pl, and edit the the lines containing qw(variableX > variableY) > for example, to use the conventional syntax of ('variableX' , > 'variableY') > removing the qw and using quotes and commas instead it should > work...at > least it did for me. > > You will have to edit this in a a few different files, like > tpp_models.pl...and a couple others I can't remember off the top of my > head. But just keep doing 'make' after you fix one, and the next one > it has > a problem with will appear. > > If any one has a nicer fix for this I would be happy to hear it as it > would > save me some time! > > FYI, this is only a problem, at least for me, in the latest version of > the > TPP (4.6.3). I was able to compile previous versions without issue. > > Chris > > > > > > > > Joseph Slagel <[email protected]> Nov 11 10:17AM -0800 > > Hi Qiaojun, > > What version of perl are you using (perl -V)? > > -Joe > > > > -- > Joe Slagel > Institute for Systems Biology > [email protected] > (206) 732-1362 > > > > > [email protected] Nov 11 09:57PM -0800 > > Hi, Josh, > > Thanks for the reply, I am using v5.18.1. However, I found the > PERL_LIB_CORE=/usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi/CORE/ > > I don't quite understand why it is under 5.10.0 folder, could this be > the > problem? How shall I correct this? > > Qiaojun > > > > > > [email protected] Nov 11 10:51PM -0800 > > Hi, Joe, > > I am using perl v.15.8. > > $ which perl > /usr/bin/perl > > however, the > PERL_LIB_CORE=/usr/lib64/perl5/5.10.0/x86_64-linux-thread-multi/CORE/ > > Not sure why it is installed under 5.10.0, which is the only folder in > perl5. Could this affect the compilation? How shall I correct it? > > Thanks a lot! > Qiaojun > > > > > > > [email protected] Nov 12 09:53PM -0800 > > Hi, Chris, > > Thanks for your reply. Sorry it took a while to reply since connect to > this group is slow and often fails from our country. > > The version of show_npsbin.pl is different in TPP4.4 or earlier, so I > simply replace it with and older version and make it compiled. > > However, if you run xinteract, did you get the syntax errors in the > tpp_model.pl? So I think something in my system is configured > differently > for TPP. > > Qiaojun > > > > > sequest and > tpp<http://groups.google.com/group/spctools-discuss/t/5bca6a16f37db26a> > > newuser <[email protected]> Nov 13 02:35AM -0800 > > dear all, > > I am a new user of TPP software. So far, I was using a Proteome > Discoverer > v 1.2 with sequest search engine. Now, I want to run the TPP using > sequest. > Unfortunatelly, I am not a bioinformatician, so I found it difficult > to set > the sequest based on the posted discussion so far. I would be glad for > the > explanation. Thank you in advance! > > > > -- > 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. > -- 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.
