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From: Brian H. <bh...@br...> - 2015-09-08 16:19:27
|
Thanks for the insights! This tool hasn't been well maintained, but I'll aim to look into it at some point. thx, ~brian On Fri, Sep 4, 2015 at 8:48 AM, alc <al...@sa...> wrote: > Hello, > I found a problem with running Transposon PSI on very fragmented genome > assemblies, with ~100,000 scaffolds - it is very slow, taking >1 week to > run. I got around this by glueing together short scaffolds into 'fake > scaffolds' (separating each pair of scaffolds by 1000 'N's), and it ran > very quickly, in 40 minutes! I thought you could be interested in making > this an option in the program? > > Regards, > > Avril > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a company > registered in England with number 2742969, whose registered office is 215 > Euston Road, London, NW1 2BE. > -- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas> |
From: Brian H. <bh...@br...> - 2014-04-26 12:18:50
|
For the archive: The NCBI blast from year 2005 works, as per tests run by Wei. best, ~brian On Wed, Apr 23, 2014 at 4:02 PM, Wei-Jen Chang <ich...@gm...>wrote: > Hello, > > We are trying to run TransposonPSI.... only to realize that blastall and > blastgp are no longer included in Blast+ package. Is there a particular > version that we should install to make it work? > > Thanks, > > > WJ > > > ------------------------------------------------------------------------------ > Start Your Social Network Today - Download eXo Platform > Build your Enterprise Intranet with eXo Platform Software > Java Based Open Source Intranet - Social, Extensible, Cloud Ready > Get Started Now And Turn Your Intranet Into A Collaboration Platform > http://p.sf.net/sfu/ExoPlatform > _______________________________________________ > Transposonpsi-users mailing list > Tra...@li... > https://lists.sourceforge.net/lists/listinfo/transposonpsi-users > > -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
From: Wei-Jen C. <ich...@gm...> - 2014-04-23 20:02:55
|
Hello, We are trying to run TransposonPSI.... only to realize that blastall and blastgp are no longer included in Blast+ package. Is there a particular version that we should install to make it work? Thanks, WJ |
From: Brian H. <bh...@br...> - 2013-12-26 13:51:02
|
This looks like a blast problem. You might try installing a different version of blastall and see if that works. good luck! On Wed, Dec 25, 2013 at 2:12 AM, <zh...@zj...> wrote: > Dear sir : > Thank you for providing the software TransposonPSI online.The software > TransposonPSI is really a very functional software.Today,I download it > online and run the software according to the manual to intend to generate > the result files for my subsequent studies. Then i run the commands > "transposonPSI.pl baicao_filter_pep.fasta prot" according to the README > ,but some errors appeared . I checked the process but i failed to find out > the problem. I will be very appreciated if you can help me solve this > problem .I'm sorry to trouble you .The attachment is the screenshot of > the process. > > Best regards > Haiqiang Zhang > Zhejiang University , Hangzhou, China > > > ------------------------------------------------------------------------------ > Rapidly troubleshoot problems before they affect your business. Most IT > organizations don't have a clear picture of how application performance > affects their revenue. With AppDynamics, you get 100% visibility into your > Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics > Pro! > http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk > _______________________________________________ > Transposonpsi-users mailing list > Tra...@li... > https://lists.sourceforge.net/lists/listinfo/transposonpsi-users > > -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
From: Brian H. <bh...@br...> - 2012-10-05 13:07:44
|
Hi Ives, The software requires that you have the old NCBI blastall software installed, including the formatdb utility. I think you can get it here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST best, -brian On Wed, Oct 3, 2012 at 5:58 AM, Ives Vanstechelman <iv...@ps...> wrote: > Hello, > > I am using transposon PSI for looking if there are transposons in a fasta > seq with this command: > > transposonPSI.pl sctg_285.fa nuc > > It is not working, I have this error > > Error, formatdb -i > transposonPSI.7461.vampire.psblocal.tmp/sctg_285/sctg_285.seq -p F (ret -1) > at /software/shared/apps/x86_64/TransposonPSI/08222010//transposonPSI.pl > line 115, <$filehandle> line 1. > > Do you have any comments on this? > > Thanks in advance, > > Ives > > -- > > ================================================================== > Ives Vanstechelman > > Tel:+32 (0)9 331 38 63 fax:+32 (0)9 3313809 > VIB Department of Plant Systems Biology, Ghent University > Technologiepark 927, 9052 Gent, BELGIUM > iv...@ps... http://www.psb.vib-ugent.be > ================================================================== > > > > ------------------------------------------------------------------------------ > Don't let slow site performance ruin your business. Deploy New Relic APM > Deploy New Relic app performance management and know exactly > what is happening inside your Ruby, Python, PHP, Java, and .NET app > Try New Relic at no cost today and get our sweet Data Nerd shirt too! > http://p.sf.net/sfu/newrelic-dev2dev > _______________________________________________ > Transposonpsi-users mailing list > Tra...@li... > https://lists.sourceforge.net/lists/listinfo/transposonpsi-users > -- -- Brian J. Haas Manager, Genome Annotation and Analysis, Research and Development The Broad Institute http://broad.mit.edu/~bhaas |
From: Ives V. <iv...@ps...> - 2012-10-03 10:15:53
|
Hello, I am using transposon PSI for looking if there are transposons in a fasta seq with this command: transposonPSI.pl sctg_285.fa nuc It is not working, I have this error Error, formatdb -i transposonPSI.7461.vampire.psblocal.tmp/sctg_285/sctg_285.seq -p F (ret -1) at /software/shared/apps/x86_64/TransposonPSI/08222010//transposonPSI.pl line 115, <$filehandle> line 1. Do you have any comments on this? Thanks in advance, Ives -- ================================================================== Ives Vanstechelman Tel:+32 (0)9 331 38 63 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM iv...@ps... http://www.psb.vib-ugent.be ================================================================== |
From: Brian H. <bh...@br...> - 2012-03-18 11:36:08
|
Hi Robert, If you could share one of the failed targets, I could try running it myself and try to debug it. best, -brian 2012/3/18 robert <ro...@ma...> > ** > Dear Brian, > > There is a big genome sequences, so i split it to 32 datasets and write a > shell to batch run TransposonPSI . 28 datasets are successful, but another > four is failure, There are no files with type > of *TPSI.allHits.chains,*TPSI.allHits.chains.gff3,*TPSI.allHits.chains.bestPerLocus,*TPSI.allHits.chains.bestPerLocus.gff3, > But there is a *TPSI.topHits. > > So Why? Would you like to tell me how to solve it? > > Thanks you very much! > > Best Regards! > > Yours Daojun Yuan > > ------------------------------ > Dr. Daojun Yuan > National Key Laboratory of Crop Genetic Improvement, > College of Plant Science and Technology > Huazhong Agricultural University > Wuhan, Hubei 430070, PR China > Tel: + 86-27-87283955 > Fax: + 86-27-87280196 > Email:ro...@ma... > Rob...@gm... > -- -- Brian J. Haas Manager, Genome Annotation and Analysis Research and Development The Broad Institute http://broad.mit.edu/~bhaas |
From: robert <ro...@ma...> - 2012-03-18 09:41:22
|
Dear Brian, There is a big genome sequences, so i split it to 32 datasets and write a shell to batch run TransposonPSI . 28 datasets are successful, but another four is failure, There are no files with type of *TPSI.allHits.chains,*TPSI.allHits.chains.gff3,*TPSI.allHits.chains.bestPerLocus,*TPSI.allHits.chains.bestPerLocus.gff3, But there is a *TPSI.topHits. So Why? Would you like to tell me how to solve it? Thanks you very much! Best Regards! Yours Daojun Yuan Dr. Daojun Yuan National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology Huazhong Agricultural University Wuhan, Hubei 430070, PR China Tel: + 86-27-87283955 Fax: + 86-27-87280196 Email:ro...@ma... Rob...@gm... |
From: Brian J H. <bh...@br...> - 2011-08-01 13:06:33
|
After you download the software from sourceforge, you'll find a README file which describes how to use it. best, -brian 2011/8/1 Zhang yanni <ynz...@si...> > Hi, I am a graduate student in Shanghai, I want to ask how to use the > TransposonPSI, because I can not find any link address > > > Thank you > > > Sincerely, Zhang yanni > > > > Zhang yanni,ynz...@si...<%3C!--AID_FROMADDRESS_BEGIN--%3Ey...@si...%3C!--AID_FROMADDRESS_END--%3E> > 2011-08-01 > > > ------------------------------------------------------------------------------ > Got Input? Slashdot Needs You. > Take our quick survey online. Come on, we don't ask for help often. > Plus, you'll get a chance to win $100 to spend on ThinkGeek. > http://p.sf.net/sfu/slashdot-survey > > _______________________________________________ > Transposonpsi-users mailing list > Tra...@li... > https://lists.sourceforge.net/lists/listinfo/transposonpsi-users > > -- -- Brian J. Haas Manager, Genome Annotation Research and Development The Broad Institute http://broad.mit.edu/~bhaas |
From: Zhang yanni<ynz...@si...> - 2011-08-01 07:54:37
|
Hi, I am a graduate student in Shanghai, I want to ask how to use the TransposonPSI, because I can not find any link address Thank you Sincerely, Zhang yanni Zhang yanni,ynz...@si... 2011-08-01 |
From: Brian J H. <bh...@br...> - 2011-04-06 11:40:31
|
Hi Karsten, You could cite it as: Brian J. Haas, TransposonPSI, 2007-2011 <http://transposonpsi.sourceforge.net> Best regards, -brian On Wed, Apr 6, 2011 at 2:32 AM, <Kar...@cs...> wrote: > > Hey Brian, > Dear Users, > How should I cite TransposonPSI? > Thanks, > Karsten > > > Dr. Karsten Oelkers > OCE Postdoctoral Fellow > CSIRO Plant Industry > PO Box 350 > Glen Osmond SA 5064 > Australia > > Phone : +61 (0)8 8303 8799 > Mobile: +61 (0)4 2305 3101 > Email : kar...@cs... > > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ > Transposonpsi-users mailing list > Tra...@li... > https://lists.sourceforge.net/lists/listinfo/transposonpsi-users > -- -- Brian J. Haas Manager, Bioinformatics Outreach, Genome Annotation and Analysis The Broad Institute http://broad.mit.edu/~bhaas |
From: <Kar...@cs...> - 2011-04-06 06:45:16
|
Hey Brian, Dear Users, How should I cite TransposonPSI? Thanks, Karsten Dr. Karsten Oelkers OCE Postdoctoral Fellow CSIRO Plant Industry PO Box 350 Glen Osmond SA 5064 Australia Phone : +61 (0)8 8303 8799 Mobile: +61 (0)4 2305 3101 Email : kar...@cs... |
From: Brian H. <bh...@br...> - 2010-10-11 14:30:08
|
Fantastic! Best, -brian On Mon, Oct 11, 2010 at 10:27 AM, Anna Esteve Codina <Ann...@ua...> wrote: > > thanks it works now! > > Anna Esteve Codina > Departament de Ciència Animal i dels Aliments > Facultat de Veterinària > Universitat Autònoma de Barcelona > telf:93 5814260 > > ----- Missatge original ----- > De: Brian Haas <bh...@br...> > Data: Dilluns, Octubre 11, 2010 2:56 pm > Assumpte: transposonpsi and getting psiblast to work. > >> Hi Anna, >> >> If you don't have one already, you may need to set up a ~/.ncbirc file >> that indicates the path to the blast-installed data directory, where >> the blosum matrix exists. >> >> Some info on the .ncbirc file is here: >> http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html >> >> My file looks like so: >> >> [NCBI] >> DATA=/seq/annotation/bio_tools/NCBI_BLAST/blast-2.2.17/data >> >> >> Best, >> >> -brian >> >> >> >> >> ----------------- >> Hello, I am having this problem when trying to run transposonPSI.pl >> with my proteins fasta file: >> >> perl transposonPSI.pl >> /Volumes/disk3/AnnaE/programs/cufflinks- >> 0.9.0.OSX_x86_64/24GONA_novo/common_u_NO_artifacts-genes-longest- >> f100-prot-exactlyone-aug-prot.fasta >> prot >> >> processing CUFF.1333761.1. >> blast against >> /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq >> CMD: blastpgp -i >> /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq >> -d transposonPSI.71995.i122mc137.vu- >> wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq-R >> /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk-j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn >> [blastpgp 2.2.24] WARNING: -t larger than 1 not supported when >> restarting from a checkpoint; setting -t to 1 >> >> [blastpgp 2.2.24] WARNING: Unable to open BLOSUM62 >> [blastpgp 2.2.24] WARNING: BlastScoreBlkMatFill returned non-zero >> status[blastpgp 2.2.24] WARNING: SetUpBlastSearch failed. >> sh: line 1: 72000 Bus error blastpgp -i >> /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq >> -d transposonPSI.71995.i122mc137.vu- >> wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq-R >> /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk-j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn >> Error blastpgp -i >> /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq >> -d transposonPSI.71995.i122mc137.vu- >> wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq-R >> /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk-j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn >> 35328 at transposonPSI.pl line 142, <$filehandle> line 1. >> >> Any idea about how to solve this? >> Thanks a lot! >> >> Anna Esteve Codina >> Departament de Ciència Animal i dels Aliments >> Facultat de Veterinària >> Universitat Autònoma de Barcelona >> telf:93 5814260 >> >> >> >> >> -- >> -- >> Brian J. Haas >> Manager, Bioinformatics Outreach, Genome Annotation and Analysis >> The Broad Institute >> http://broad.mit.edu/~bhaas >> > > -- -- Brian J. Haas Manager, Bioinformatics Outreach, Genome Annotation and Analysis The Broad Institute http://broad.mit.edu/~bhaas |
From: Brian H. <bh...@br...> - 2010-10-11 12:57:10
|
Hi Anna, If you don't have one already, you may need to set up a ~/.ncbirc file that indicates the path to the blast-installed data directory, where the blosum matrix exists. Some info on the .ncbirc file is here: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html My file looks like so: [NCBI] DATA=/seq/annotation/bio_tools/NCBI_BLAST/blast-2.2.17/data Best, -brian ----------------- Hello, I am having this problem when trying to run transposonPSI.pl with my proteins fasta file: perl transposonPSI.pl /Volumes/disk3/AnnaE/programs/cufflinks-0.9.0.OSX_x86_64/24GONA_novo/common_u_NO_artifacts-genes-longest-f100-prot-exactlyone-aug-prot.fasta prot processing CUFF.1333761.1. blast against /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq CMD: blastpgp -i /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq -d transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq -R /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk -j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn [blastpgp 2.2.24] WARNING: -t larger than 1 not supported when restarting from a checkpoint; setting -t to 1 [blastpgp 2.2.24] WARNING: Unable to open BLOSUM62 [blastpgp 2.2.24] WARNING: BlastScoreBlkMatFill returned non-zero status [blastpgp 2.2.24] WARNING: SetUpBlastSearch failed. sh: line 1: 72000 Bus error blastpgp -i /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq -d transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq -R /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk -j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn Error blastpgp -i /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq -d transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq -R /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk -j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn 35328 at transposonPSI.pl line 142, <$filehandle> line 1. Any idea about how to solve this? Thanks a lot! Anna Esteve Codina Departament de Ciència Animal i dels Aliments Facultat de Veterinària Universitat Autònoma de Barcelona telf:93 5814260 -- -- Brian J. Haas Manager, Bioinformatics Outreach, Genome Annotation and Analysis The Broad Institute http://broad.mit.edu/~bhaas |
From: Anna E. C. <Ann...@ua...> - 2010-10-11 10:59:59
|
Hello, I am having this problem when trying to run transposonPSI.pl with my proteins fasta file: perl transposonPSI.pl /Volumes/disk3/AnnaE/programs/cufflinks-0.9.0.OSX_x86_64/24GONA_novo/common_u_NO_artifacts-genes-longest-f100-prot-exactlyone-aug-prot.fasta prot processing CUFF.1333761.1. blast against /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq CMD: blastpgp -i /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq -d transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq -R /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk -j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn [blastpgp 2.2.24] WARNING: -t larger than 1 not supported when restarting from a checkpoint; setting -t to 1 [blastpgp 2.2.24] WARNING: Unable to open BLOSUM62 [blastpgp 2.2.24] WARNING: BlastScoreBlkMatFill returned non-zero status [blastpgp 2.2.24] WARNING: SetUpBlastSearch failed. sh: line 1: 72000 Bus error blastpgp -i /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq -d transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq -R /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk -j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn Error blastpgp -i /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.refSeq -d transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.seq -R /Volumes/disk3/AnnaE/programs/TransposonPSI_08222010/transposon_PSI_LIB/cacta.chk -j 1 -e 1e-5 > transposonPSI.71995.i122mc137.vu-wien.ac.at.tmp/CUFF_1333761_1/CUFF_1333761_1.cacta.refSeq.psitblastn 35328 at transposonPSI.pl line 142, <$filehandle> line 1. Any idea about how to solve this? Thanks a lot! Anna Esteve Codina Departament de Ciència Animal i dels Aliments Facultat de Veterinària Universitat Autònoma de Barcelona telf:93 5814260 |