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From: Akshaya R. <ar...@bu...> - 2014-10-03 19:29:23
|
Dear All, I am trying to view my .asm file that was generated by the Celera assembler and plan on using the toAmos_new for the same. To use this script, I need to configure amos using the --with-CA-dir function. I have looked at this thread (http://sourceforge.net/p/amos/mailman/message/29093782/) and realized that I have followed all steps but no luck (I do not think the author had success either). These are the steps that I followed: ./configure --with-qmake-qt4=/usr/local/lib/qt-4.8.4/bin/qmake NUCMER=/media/raid10/programs/MUMmer3.23/nucmer DELTAFILTER=/media/raid10/programs/MUMmer3.23/delta-filter SHOWCOORDS=/media/raid10/programs/MUMmer3.23/show-coords BLAT=/media/raid10/programs/blat --with-CA-dir=/media/raid10/archive_programs/wgs-8.1/Linux-amd64/ and I still get checking for CA... yes checking whether CA works... no When I look at the following lines from the config file: CA_DIR="$amos_ca_dir" CA_LDADD="$amos_ca_dir/lib/libCA.a" CA_CXXFLAGS="-I$amos_ca_dir/../src -I$amos_ca_dir/../src/AS_MSG -I$amos_ca_dir/../src/AS_UTL -DAMOS_HAVE_CA" # All variables are defined, report the result I realize that amos is loking for libCA.a (which exists and the correct path), src (which exists and correct path), AS-MSG and AS-UTL (which also exists and has the correct path). I did compile Celera from source-code so that amos could access the src/ directory Does anyone have any idea or suggestions that can help me fix this problem? Thank you in advance for your help. Best, Akshaya -- Akshaya Ramesh PhD candidate Kepler Lab Laboratory of Computational Immunology Boston University School of Medicine 72 E Concord Street, Room 504D Boston, MA 02118 |
From: Florent A. <flo...@gm...> - 2014-09-12 00:48:27
|
Hi Igor, >From the log, it looks like the following command fails: /diag/software/MUMmer//nucmer -maxmatch -c 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged I would suggest that you inspect that the inputs for nucmer look sane, and then try running the command manually to glean more information about what went wrong. Cheers, Florent On Fri, Sep 12, 2014 at 8:08 AM, Igor Tiago <igo...@gm...> wrote: > Hi amos users > I'm trying to use minimus2 to reassemble several contigs from a metagenome, > but unfortunately I'm having low success... > I'm sending the error logs > and I really need > help me on this one. > Thanking you in advance. > > use this commands in a shell *.sh file > > #!/bin/bash > > # Setup some environmental variables just in case our PATH is > # screwed up when we submit to SGE > PATH=$PATH:/diag/software/amos-3.1.0/bin/ > export PERL5LIB=$PERL5LIB:/diag/software/MUMmer/scripts/ > > # Make sure we are in the right directory > cd /diag/home/itiago/minimus2/ > > # Now we want to execute our velvet commands in sequence > export PERL5LIB=$PERL5LIB:/diag/software/MUMmer/scripts/ > minimus2 contigs_merged -D CONSERR=0.08 -D MINID=98 -D MAXTRIM=25 > > > got this log file with error: > > !!! 2014-06-21 13:20:13 Started by it...@hn... on Sat > Jun 21 13:20:13 2014 > > !!! 2014-06-21 13:20:13 Doing step 10: Building AMOS bank & Dumping reads > !!! 2014-06-21 13:20:13 Running: rm -fr contigs_merged.bnk > !!! 2014-06-21 13:20:13 Done! Elapsed time:0d 0h 0m 0s > > !!! 2014-06-21 13:20:13 Doing step 11 > !!! 2014-06-21 13:20:13 Running: > /diag/software/amos-3.1.0/bin/bank-transact -c -z -b contigs_merged.bnk -m > contigs_merged.afg > START DATE: Sat Jun 21 13:20:13 2014 > Bank is: contigs_merged.bnk > 0% 100% > AFG .................................................. > Messages read: 1490914 > Objects added: 1490914 > Objects deleted: 0 > Objects replaced: 0 > END DATE: Sat Jun 21 13:21:15 2014 > !!! 2014-06-21 13:21:15 Done! Elapsed time:0d 0h 1m 2s > > !!! 2014-06-21 13:21:15 Doing step 12 > !!! 2014-06-21 13:21:15 Running: /diag/software/amos-3.1.0/bin/dumpreads > contigs_merged.bnk -M 0 > contigs_merged.ref.seq > Objects seen: 745455 > Objects written: 745455 > !!! 2014-06-21 13:22:24 Done! Elapsed time:0d 0h 1m 9s > > !!! 2014-06-21 13:22:24 Doing step 13 > !!! 2014-06-21 13:22:24 Running: /diag/software/amos-3.1.0/bin/dumpreads > contigs_merged.bnk -m 0 > contigs_merged.qry.seq > Objects seen: 745455 > Objects written: 745455 > !!! 2014-06-21 13:23:32 Done! Elapsed time:0d 0h 1m 8s > > !!! 2014-06-21 13:23:32 Doing step 20: Getting overlaps > !!! 2014-06-21 13:23:32 Running: /diag/software/MUMmer//nucmer -maxmatch -c > 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged > 1: PREPARING DATA > 2,3: RUNNING mummer AND CREATING CLUSTERS > # reading input file "contigs_merged.ntref" of length 405876736 > # construct suffix tree for sequence of length 405876736 > # (maximum reference length is 536870908) > # (maximum query length is 4294967295) > # process 4058767 characters per dot > #...........................................................................................ERROR: > mummer and/or mgaps returned non-zero > !!! 2014-06-21 13:28:51 Command: /diag/software/MUMmer//nucmer -maxmatch -c > 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged exited > with status: 1 > !!! END - Elapsed time: 0d 0h 8m 38s > > !!! 2014-06-21 13:36:28 Started by it...@hn... on Sat > Jun 21 13:36:28 2014 > > !!! 2014-06-21 13:36:28 Doing step 10: Building AMOS bank & Dumping reads > !!! 2014-06-21 13:36:28 Running: rm -fr contigs_merged.bnk > !!! 2014-06-21 13:36:28 Done! Elapsed time:0d 0h 0m 0s > > !!! 2014-06-21 13:36:28 Doing step 11 > !!! 2014-06-21 13:36:28 Running: > /diag/software/amos-3.1.0/bin/bank-transact -c -z -b contigs_merged.bnk -m > contigs_merged.afg > START DATE: Sat Jun 21 13:36:28 2014 > Bank is: contigs_merged.bnk > 0% 100% > AFG .................................................. > Messages read: 1490914 > Objects added: 1490914 > Objects deleted: 0 > Objects replaced: 0 > END DATE: Sat Jun 21 13:37:30 2014 > !!! 2014-06-21 13:37:30 Done! Elapsed time:0d 0h 1m 2s > > !!! 2014-06-21 13:37:30 Doing step 12 > !!! 2014-06-21 13:37:30 Running: /diag/software/amos-3.1.0/bin/dumpreads > contigs_merged.bnk -M 0 > contigs_merged.ref.seq > Objects seen: 745455 > Objects written: 745455 > !!! 2014-06-21 13:38:38 Done! Elapsed time:0d 0h 1m 8s > > !!! 2014-06-21 13:38:38 Doing step 13 > !!! 2014-06-21 13:38:38 Running: /diag/software/amos-3.1.0/bin/dumpreads > contigs_merged.bnk -m 0 > contigs_merged.qry.seq > Objects seen: 745455 > Objects written: 745455 > !!! 2014-06-21 13:39:47 Done! Elapsed time:0d 0h 1m 9s > > !!! 2014-06-21 13:39:47 Doing step 20: Getting overlaps > !!! 2014-06-21 13:39:47 Running: /diag/software/MUMmer//nucmer -maxmatch -c > 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged > 1: PREPARING DATA > 2,3: RUNNING mummer AND CREATING CLUSTERS > # reading input file "contigs_merged.ntref" of length 405876736 > # construct suffix tree for sequence of length 405876736 > # (maximum reference length is 536870908) > # (maximum query length is 4294967295) > # process 4058767 characters per dot > #...........................................................................................ERROR: > mummer and/or mgaps returned non-zero > !!! 2014-06-21 13:45:05 Command: /diag/software/MUMmer//nucmer -maxmatch -c > 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged exited > with status: 1 > !!! END - Elapsed time: 0d 0h 8m 37s > > > Any help is welcome! > > Best > > -- > Igor Tiago, M.Sc Ph.D > Laboratório de Microbiologia > Departamento de Ciências da Vida > Universidade de Coimbra > 3004-517 Coimbra, Portugal > Telefone: +351 239 824 024 > > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce > Perforce version control. Predictably reliable. > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk > _______________________________________________ > AMOS-help mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-help > |
From: Igor T. <igo...@gm...> - 2014-09-11 22:08:12
|
Hi amos users I'm trying to use minimus2 to reassemble several contigs from a metagenome, but unfortunately I'm having low success... I'm sending the error logs and I really need help me on this one. Thanking you in advance. *use this commands in a shell *.sh file* #!/bin/bash # Setup some environmental variables just in case our PATH is # screwed up when we submit to SGE PATH=$PATH:/diag/software/amos-3.1.0/bin/ export PERL5LIB=$PERL5LIB:/diag/software/MUMmer/scripts/ # Make sure we are in the right directory cd /diag/home/itiago/minimus2/ # Now we want to execute our velvet commands in sequence export PERL5LIB=$PERL5LIB:/diag/software/MUMmer/scripts/ minimus2 contigs_merged -D CONSERR=0.08 -D MINID=98 -D MAXTRIM=25 *got this log file with error:* !!! 2014-06-21 13:20:13 Started by it...@hn... on Sat Jun 21 13:20:13 2014 !!! 2014-06-21 13:20:13 Doing step 10: Building AMOS bank & Dumping reads !!! 2014-06-21 13:20:13 Running: rm -fr contigs_merged.bnk !!! 2014-06-21 13:20:13 Done! Elapsed time:0d 0h 0m 0s !!! 2014-06-21 13:20:13 Doing step 11 !!! 2014-06-21 13:20:13 Running: /diag/software/amos-3.1.0/bin/bank-transact -c -z -b contigs_merged.bnk -m contigs_merged.afg START DATE: Sat Jun 21 13:20:13 2014 Bank is: contigs_merged.bnk 0% 100% AFG .................................................. Messages read: 1490914 Objects added: 1490914 Objects deleted: 0 Objects replaced: 0 END DATE: Sat Jun 21 13:21:15 2014 !!! 2014-06-21 13:21:15 Done! Elapsed time:0d 0h 1m 2s !!! 2014-06-21 13:21:15 Doing step 12 !!! 2014-06-21 13:21:15 Running: /diag/software/amos-3.1.0/bin/dumpreads contigs_merged.bnk -M 0 > contigs_merged.ref.seq Objects seen: 745455 Objects written: 745455 !!! 2014-06-21 13:22:24 Done! Elapsed time:0d 0h 1m 9s !!! 2014-06-21 13:22:24 Doing step 13 !!! 2014-06-21 13:22:24 Running: /diag/software/amos-3.1.0/bin/dumpreads contigs_merged.bnk -m 0 > contigs_merged.qry.seq Objects seen: 745455 Objects written: 745455 !!! 2014-06-21 13:23:32 Done! Elapsed time:0d 0h 1m 8s !!! 2014-06-21 13:23:32 Doing step 20: Getting overlaps !!! 2014-06-21 13:23:32 Running: /diag/software/MUMmer//nucmer -maxmatch -c 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS # reading input file "contigs_merged.ntref" of length 405876736 # construct suffix tree for sequence of length 405876736 # (maximum reference length is 536870908) # (maximum query length is 4294967295) # process 4058767 characters per dot #...........................................................................................ERROR: mummer and/or mgaps returned non-zero !!! 2014-06-21 13:28:51 Command: /diag/software/MUMmer//nucmer -maxmatch -c 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged exited with status: 1 !!! END - Elapsed time: 0d 0h 8m 38s !!! 2014-06-21 13:36:28 Started by it...@hn... on Sat Jun 21 13:36:28 2014 !!! 2014-06-21 13:36:28 Doing step 10: Building AMOS bank & Dumping reads !!! 2014-06-21 13:36:28 Running: rm -fr contigs_merged.bnk !!! 2014-06-21 13:36:28 Done! Elapsed time:0d 0h 0m 0s !!! 2014-06-21 13:36:28 Doing step 11 !!! 2014-06-21 13:36:28 Running: /diag/software/amos-3.1.0/bin/bank-transact -c -z -b contigs_merged.bnk -m contigs_merged.afg START DATE: Sat Jun 21 13:36:28 2014 Bank is: contigs_merged.bnk 0% 100% AFG .................................................. Messages read: 1490914 Objects added: 1490914 Objects deleted: 0 Objects replaced: 0 END DATE: Sat Jun 21 13:37:30 2014 !!! 2014-06-21 13:37:30 Done! Elapsed time:0d 0h 1m 2s !!! 2014-06-21 13:37:30 Doing step 12 !!! 2014-06-21 13:37:30 Running: /diag/software/amos-3.1.0/bin/dumpreads contigs_merged.bnk -M 0 > contigs_merged.ref.seq Objects seen: 745455 Objects written: 745455 !!! 2014-06-21 13:38:38 Done! Elapsed time:0d 0h 1m 8s !!! 2014-06-21 13:38:38 Doing step 13 !!! 2014-06-21 13:38:38 Running: /diag/software/amos-3.1.0/bin/dumpreads contigs_merged.bnk -m 0 > contigs_merged.qry.seq Objects seen: 745455 Objects written: 745455 !!! 2014-06-21 13:39:47 Done! Elapsed time:0d 0h 1m 9s !!! 2014-06-21 13:39:47 Doing step 20: Getting overlaps !!! 2014-06-21 13:39:47 Running: /diag/software/MUMmer//nucmer -maxmatch -c 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS # reading input file "contigs_merged.ntref" of length 405876736 # construct suffix tree for sequence of length 405876736 # (maximum reference length is 536870908) # (maximum query length is 4294967295) # process 4058767 characters per dot #...........................................................................................ERROR: mummer and/or mgaps returned non-zero !!! 2014-06-21 13:45:05 Command: /diag/software/MUMmer//nucmer -maxmatch -c 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged exited with status: 1 !!! END - Elapsed time: 0d 0h 8m 37s Any help is welcome! Best -- Igor Tiago, M.Sc Ph.D Laboratório de Microbiologia Departamento de Ciências da Vida Universidade de Coimbra 3004-517 Coimbra, Portugal Telefone: +351 239 824 024 |
From: Igor T. <it...@ci...> - 2014-06-30 14:27:48
|
Hi All I'm trying to use minimus2 to reassemble several contigs from a metagenome, but unfortunately I'm having low success... I'm sending the error logs so that some one could help me on this one. Thanking you in advance. *use this commands in a shell *.sh file* #!/bin/bash # Setup some environmental variables just in case our PATH is # screwed up when we submit to SGE PATH=$PATH:/diag/software/amos-3.1.0/bin/ export PERL5LIB=$PERL5LIB:/diag/software/MUMmer/scripts/ # Make sure we are in the right directory cd /diag/home/itiago/minimus2/ # Now we want to execute our velvet commands in sequence export PERL5LIB=$PERL5LIB:/diag/software/MUMmer/scripts/ minimus2 contigs_merged -D CONSERR=0.08 -D MINID=98 -D MAXTRIM=25 *got this log file with error:* !!! 2014-06-21 13:20:13 Started by it...@hn... on Sat Jun 21 13:20:13 2014 !!! 2014-06-21 13:20:13 Doing step 10: Building AMOS bank & Dumping reads !!! 2014-06-21 13:20:13 Running: rm -fr contigs_merged.bnk !!! 2014-06-21 13:20:13 Done! Elapsed time:0d 0h 0m 0s !!! 2014-06-21 13:20:13 Doing step 11 !!! 2014-06-21 13:20:13 Running: /diag/software/amos-3.1.0/bin/bank-transact -c -z -b contigs_merged.bnk -m contigs_merged.afg START DATE: Sat Jun 21 13:20:13 2014 Bank is: contigs_merged.bnk 0% 100% AFG .................................................. Messages read: 1490914 Objects added: 1490914 Objects deleted: 0 Objects replaced: 0 END DATE: Sat Jun 21 13:21:15 2014 !!! 2014-06-21 13:21:15 Done! Elapsed time:0d 0h 1m 2s !!! 2014-06-21 13:21:15 Doing step 12 !!! 2014-06-21 13:21:15 Running: /diag/software/amos-3.1.0/bin/dumpreads contigs_merged.bnk -M 0 > contigs_merged.ref.seq Objects seen: 745455 Objects written: 745455 !!! 2014-06-21 13:22:24 Done! Elapsed time:0d 0h 1m 9s !!! 2014-06-21 13:22:24 Doing step 13 !!! 2014-06-21 13:22:24 Running: /diag/software/amos-3.1.0/bin/dumpreads contigs_merged.bnk -m 0 > contigs_merged.qry.seq Objects seen: 745455 Objects written: 745455 !!! 2014-06-21 13:23:32 Done! Elapsed time:0d 0h 1m 8s !!! 2014-06-21 13:23:32 Doing step 20: Getting overlaps !!! 2014-06-21 13:23:32 Running: /diag/software/MUMmer//nucmer -maxmatch -c 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS # reading input file "contigs_merged.ntref" of length 405876736 # construct suffix tree for sequence of length 405876736 # (maximum reference length is 536870908) # (maximum query length is 4294967295) # process 4058767 characters per dot #...........................................................................................ERROR: mummer and/or mgaps returned non-zero !!! 2014-06-21 13:28:51 Command: /diag/software/MUMmer//nucmer -maxmatch -c 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged exited with status: 1 !!! END - Elapsed time: 0d 0h 8m 38s !!! 2014-06-21 13:36:28 Started by it...@hn... on Sat Jun 21 13:36:28 2014 !!! 2014-06-21 13:36:28 Doing step 10: Building AMOS bank & Dumping reads !!! 2014-06-21 13:36:28 Running: rm -fr contigs_merged.bnk !!! 2014-06-21 13:36:28 Done! Elapsed time:0d 0h 0m 0s !!! 2014-06-21 13:36:28 Doing step 11 !!! 2014-06-21 13:36:28 Running: /diag/software/amos-3.1.0/bin/bank-transact -c -z -b contigs_merged.bnk -m contigs_merged.afg START DATE: Sat Jun 21 13:36:28 2014 Bank is: contigs_merged.bnk 0% 100% AFG .................................................. Messages read: 1490914 Objects added: 1490914 Objects deleted: 0 Objects replaced: 0 END DATE: Sat Jun 21 13:37:30 2014 !!! 2014-06-21 13:37:30 Done! Elapsed time:0d 0h 1m 2s !!! 2014-06-21 13:37:30 Doing step 12 !!! 2014-06-21 13:37:30 Running: /diag/software/amos-3.1.0/bin/dumpreads contigs_merged.bnk -M 0 > contigs_merged.ref.seq Objects seen: 745455 Objects written: 745455 !!! 2014-06-21 13:38:38 Done! Elapsed time:0d 0h 1m 8s !!! 2014-06-21 13:38:38 Doing step 13 !!! 2014-06-21 13:38:38 Running: /diag/software/amos-3.1.0/bin/dumpreads contigs_merged.bnk -m 0 > contigs_merged.qry.seq Objects seen: 745455 Objects written: 745455 !!! 2014-06-21 13:39:47 Done! Elapsed time:0d 0h 1m 9s !!! 2014-06-21 13:39:47 Doing step 20: Getting overlaps !!! 2014-06-21 13:39:47 Running: /diag/software/MUMmer//nucmer -maxmatch -c 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS # reading input file "contigs_merged.ntref" of length 405876736 # construct suffix tree for sequence of length 405876736 # (maximum reference length is 536870908) # (maximum query length is 4294967295) # process 4058767 characters per dot #...........................................................................................ERROR: mummer and/or mgaps returned non-zero !!! 2014-06-21 13:45:05 Command: /diag/software/MUMmer//nucmer -maxmatch -c 40 contigs_merged.ref.seq contigs_merged.qry.seq -p contigs_merged exited with status: 1 !!! END - Elapsed time: 0d 0h 8m 37s Any help is welcome! Best -- Igor Tiago, M.Sc Ph.D Laboratório de Microbiologia Departamento de Ciências da Vida Universidade de Coimbra 3004-517 Coimbra, Portugal Telefone: +351 239 824 024 |
From: Igor T. <it...@ci...> - 2014-06-30 14:25:49
|
Hi All I'm trying to use minimus2 to reassemble several contigs from a metagenome, but unfortunately I'm having low success... I'm sending the error logs so that some one could help me on this one. Thanking you in advance. use this commands in a shell *.sh file #!/bin/bash # Setup some environmental variables just in case our PATH is # screwed up when we submit to SGE PATH=$PATH:/diag/software/amos-3.1.0/bin/ export PERL5LIB=$PERL5LIB:/diag/software/MUMmer/scripts/ # Make sure we are in the right directory cd /diag/home/itiago/minimus2/ # Now we want to execute our velvet commands in sequence export PERL5LIB=$PERL5LIB:/diag/software/MUMmer/scripts/ minimus2 contigs_merged -D CONSERR=0.08 -D MINID=98 -D MAXTRIM=25 got this log file with error: -- Igor Tiago, M.Sc Ph.D Laboratório de Microbiologia Departamento de Ciências da Vida Universidade de Coimbra 3004-517 Coimbra, Portugal Telefone: +351 239 824 024 |
From: Gemma L. <gb...@sa...> - 2014-06-26 08:53:19
|
Hi I am using minimus2 to help me to circularise genomes we've generated using PacBio sequences (as per the guidelines on https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Circularizing-and-trimming). For the most part, this has been going smoothly, but I now have a number of genomes where minimus2 has aborted part way through, and I can't figure out why! In each case, the command that fails is make-consensus, with the initial error in the log given as 'make-consensus -B -e 0.06 -b NCTC1_circle.bnk -w 15 failed: likely through abort() or coredump' Our informatics team here did a little digging for me, and unlocked the bank and tried running the make-consensus command again, which then produced this error: Read bank is NCTC1_circle.bnk Alignment error rate is 0.06 Minimum overlap bases is 5 Output will be written to the bank ** AMOS Exception ** WHAT: Invalid Header, Map file is corrupted for NCTC1_circle.bnk/CTG.0.map LINE: 511 FILE: IDMap_AMOS.cc Can you give me any advice on what I should look at next, or why this might be happening? Many thanks Gemma -- Gemma Langridge, PhD Pathogen Genomics Wellcome Trust Sanger Institute Hinxton, Cambridge CB10 1SA -- 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. |
From: John J. <jo...@ms...> - 2014-05-22 19:48:03
|
Thanks. Yes I have, and it seems to get up to about 33GB of memory usage before it quits on the user's data. The user had reserved 64GB of RAM for his job, so that seems to not be the problem. I did run a test solo on a non-cluster node with 256GB of RAM and it did get farther, but failed once it got to the nucmer step. I also would have expected the resource mgr. to auto-kill the job before the system memory was exhausted (i.e., should get killed if/when 64GB is breached). John On 5/22/14, 3:42 PM, Adam Phillippy wrote: > Hi John, > Have you tracked the memory of these jobs? Sounds like it may be > exhausting system memory--that's generally the only way I see my > cluster nodes bricked. If not, that's Mike Schatz's code, he may have > more insight. > > Best, > -Adam > > > > On Sun, May 18, 2014 at 10:24 PM, John Johnston <jo...@ms... > <mailto:jo...@ms...>> wrote: > > Hello, > > I have a user that is attempting to use the "amosvalidate" utility > on a > HPC cluster, and it appears to be crashing nodes. > > The process appears to proceed normally until reaching the > "analyzeSNPs" > step with the command (obtained from the log file): > > analyzeSNPs -i -b/ /assembly.bnk -S -cumqv 40 -minsnps 2 -r -H > > assembly.snps > > Searching 223685 contigs > > At this point, log output ceases, the job terminates abnormally, > and the > scheduling system on that node registers in a "down" state. We've > seen this > on multiple nodes. > > Other users have used other parts of the AMOS package over the last 3 > years on the system without these problems (though *not* > specifically amosvalidate). > AMOS is installed on a RHEL 6 system with the torque/PBS resource > manager and moab scheduler. > > The version in use is 3.1.0 released in 2011. > > Has anyone seen anything like this or might someone have any > insight on this issue? > > Thanks. > > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. > Get unparalleled scalability from the best Selenium testing > platform available > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > _______________________________________________ > AMOS-help mailing list > AMO...@li... > <mailto:AMO...@li...> > https://lists.sourceforge.net/lists/listinfo/amos-help > > |
From: Adam P. <aph...@gm...> - 2014-05-22 19:42:33
|
Hi John, Have you tracked the memory of these jobs? Sounds like it may be exhausting system memory--that's generally the only way I see my cluster nodes bricked. If not, that's Mike Schatz's code, he may have more insight. Best, -Adam On Sun, May 18, 2014 at 10:24 PM, John Johnston <jo...@ms...> wrote: > Hello, > > I have a user that is attempting to use the "amosvalidate" utility on a > HPC cluster, and it appears to be crashing nodes. > > The process appears to proceed normally until reaching the "analyzeSNPs" > step with the command (obtained from the log file): > > analyzeSNPs -i -b/ /assembly.bnk -S -cumqv 40 -minsnps 2 -r -H > > assembly.snps > > Searching 223685 contigs > > At this point, log output ceases, the job terminates abnormally, and the > scheduling system on that node registers in a "down" state. We've seen > this > on multiple nodes. > > Other users have used other parts of the AMOS package over the last 3 > years on the system without these problems (though *not* specifically > amosvalidate). > AMOS is installed on a RHEL 6 system with the torque/PBS resource > manager and moab scheduler. > > The version in use is 3.1.0 released in 2011. > > Has anyone seen anything like this or might someone have any insight on > this issue? > > Thanks. > > > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. > Get unparalleled scalability from the best Selenium testing platform > available > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > _______________________________________________ > AMOS-help mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-help > |
From: <The...@cs...> - 2014-05-22 05:45:25
|
Hi, I am trying to install amos on 64 bit Debian v. 3.10.11. ./configure gives me the errors: WARNING! Qt4 toolkit was not found but is required to run AMOS GUIs install Qt4 or locate Qt4 with configure to build GUIs see config.log for more information on what went wrong WARNING! Statistics::Descriptive Perl module was not found but is required to run some AMOS scripts WARNING! XML::Parser Perl module was not found but is required to run some AMOS scripts But if I try to use: ./configure -with-Qt-/usr/include or any other locations I get 'invlaid package name' error. Do you have any advice on installing the dependencies? There do seem to be a lot. Thanks very much, Theo Dr Theo R. Allnutt Project Scientist: Bioinformatics | Food Microbiology and Safety Group Animal, Food and Health Sciences CSIRO Phone: +61 397 313 204 | Fax: +61 3 9731 3201 the...@cs...<mailto:Nar...@cs...> | www.csiro.au<http://www.csiro.au/> Address: CAFHS, 671 Sneydes Road, Werribee, VIC 3030; and AAHL, PO Bag 24 Geelong VIC 3220. |
From: John J. <jo...@ms...> - 2014-05-19 02:24:52
|
Hello, I have a user that is attempting to use the "amosvalidate" utility on a HPC cluster, and it appears to be crashing nodes. The process appears to proceed normally until reaching the "analyzeSNPs" step with the command (obtained from the log file): analyzeSNPs -i -b/ /assembly.bnk -S -cumqv 40 -minsnps 2 -r -H > assembly.snps Searching 223685 contigs At this point, log output ceases, the job terminates abnormally, and the scheduling system on that node registers in a "down" state. We've seen this on multiple nodes. Other users have used other parts of the AMOS package over the last 3 years on the system without these problems (though *not* specifically amosvalidate). AMOS is installed on a RHEL 6 system with the torque/PBS resource manager and moab scheduler. The version in use is 3.1.0 released in 2011. Has anyone seen anything like this or might someone have any insight on this issue? Thanks. |
From: Lionel G. <guy...@gm...> - 2014-03-17 17:24:01
|
Good old consed might be worth looking into as well. The work that David Gordon has done on the bam importer is quite interesting! Lionel > On 17 mars 2014, at 17:04, Adam Phillippy <aph...@gm...> wrote: > > Hi David, > Hawkeye is not well suited for short read assemblies. I typically use Tablet (http://ics.hutton.ac.uk/tablet/download-tablet/) or IGV (http://www.broadinstitute.org/igv/home). I expect you'll have a better experience with those ... and there are many others if you look around a bit. > > Best, > -Adam > > > >> On Mon, Mar 17, 2014 at 11:50 AM, David Durán <dav...@gm...> wrote: >> Hi good afternoon. >> >> my name is David, I am a PhD student fighting with genomes :) >> >> I'm interested in using hawkeye to visualize some assemblies that I have done with Spades and would like to know how and what files should be converted to generate libraries of Amos that I require, if you could guide me, is the really appreciate it. >> >> Regards >> David >> >> >> -- >> David Durán Wendt >> >> >> >> Se un viajero..... no un turista >> >> ------------------------------------------------------------------------------ >> Learn Graph Databases - Download FREE O'Reilly Book >> "Graph Databases" is the definitive new guide to graph databases and their >> applications. Written by three acclaimed leaders in the field, >> this first edition is now available. Download your free book today! >> http://p.sf.net/sfu/13534_NeoTech >> _______________________________________________ >> AMOS-help mailing list >> AMO...@li... >> https://lists.sourceforge.net/lists/listinfo/amos-help > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/13534_NeoTech > _______________________________________________ > AMOS-help mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-help |
From: Adam P. <aph...@gm...> - 2014-03-17 16:04:32
|
Hi David, Hawkeye is not well suited for short read assemblies. I typically use Tablet (http://ics.hutton.ac.uk/tablet/download-tablet/) or IGV ( http://www.broadinstitute.org/igv/home). I expect you'll have a better experience with those ... and there are many others if you look around a bit. Best, -Adam On Mon, Mar 17, 2014 at 11:50 AM, David Durán <dav...@gm...>wrote: > Hi good afternoon. > > my name is David, I am a PhD student fighting with genomes :) > > I'm interested in using hawkeye to visualize some assemblies that I have > done with Spades and would like to know how and what files should be > converted to generate libraries of Amos that I require, if you could guide > me, is the really appreciate it. > > Regards > David > > > -- > David Durán Wendt > > > > Se un viajero..... no un turista > > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/13534_NeoTech > _______________________________________________ > AMOS-help mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-help > > |
From: David D. <dav...@gm...> - 2014-03-17 15:50:50
|
Hi good afternoon. my name is David, I am a PhD student fighting with genomes :) I'm interested in using hawkeye to visualize some assemblies that I have done with Spades and would like to know how and what files should be converted to generate libraries of Amos that I require, if you could guide me, is the really appreciate it. Regards David -- David Durán Wendt Se un viajero..... no un turista |
From: sami y. <sam...@gm...> - 2013-12-17 10:35:57
|
Hi every one. I have a problem with my CFA statistic through Amos. After identifying the model and running the analysis, Amos didn`t provide the Chi-square and instead of the " FINISH" message at the left side of the diagram, I found this message: '' READING DATA". However, To my great surprise, Amos provided the rest of the output & tables thoroughly!! What should I do to display it? |
From: patrick s. <pa...@si...> - 2013-11-25 07:48:20
|
Hi, I'm running MetaVelvet for my metagenomics dataset. I just curious that is it normal taken a long time to complete "MarkRepeats" under "Advanced topics 2: Use Bambus2 scaffolding module (>= 1.1.01)"? My server still running "MarkRepeats" for two days. My metagenomics dataset is Illumina pair-end, 100 nt, 36,997,186 reads. I'm using amos_3.0.0 and MetaVelvet-1.2.02 version. Thanks for any advice. Looking forward to hear from you. best regards Patrick Research Student at UM |
From: Adam P. <aph...@gm...> - 2013-11-22 14:38:15
|
Hi Juan, Hawkeye is not well suited for visualizing the outputs of De Bruijn assemblers like SOAPdenovo. Instead, I would recommend you map your original reads to your assembly using a tool like BWA and then visualize the resulting BAM file in a short read viewer like IGV or Tablet. Best, -Adam On Fri, Nov 22, 2013 at 8:49 AM, Lobaton Garces, Juan David (CIAT) < j.d...@cg...> wrote: > Hello > > > Have a good day > > > > My name is Juan. I am just starting in bioinformatics and I have a task to > assemble *denovo* several paired end reads from different types of bean. > > > > I used SOAPdenovo for this and now I want to visualize the results. That’s > why Hawkeye is important to me. > > > > I already got the AMOS winzip but am not and expertise person in > computational so am having trouble to install it and I don’t want to make > it wrong. > > > > Please can you help to install the software… I am using a windows 64 bites > platform. > > > > Thanks for your time and collaboration > > > > Best regards > > > > > > Juan David Lobaton Garces > > M.Sc. Molecular genetics > > University of Leicester > > CIAT bioinformatics > > Bean research group > > > > > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up > now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > _______________________________________________ > AMOS-help mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-help > > |
From: Lobaton G. J. D. (CIAT) <j.d...@cg...> - 2013-11-22 13:49:33
|
Hello Have a good day My name is Juan. I am just starting in bioinformatics and I have a task to assemble denovo several paired end reads from different types of bean. I used SOAPdenovo for this and now I want to visualize the results. That's why Hawkeye is important to me. I already got the AMOS winzip but am not and expertise person in computational so am having trouble to install it and I don't want to make it wrong. Please can you help to install the software... I am using a windows 64 bites platform. Thanks for your time and collaboration Best regards Juan David Lobaton Garces M.Sc. Molecular genetics University of Leicester CIAT bioinformatics Bean research group |
From: DUARTE, J. <jor...@bi...> - 2013-11-13 15:18:55
|
Hi, I would like to install AMOS package in order to use the pacBioToCA pipeline. I’ve tried to install v3.1.0 and 3.0.1, and both fail during compilation with error : if icpc -DHAVE_CONFIG_H -I. -I. -I../.. -I../../src/AMOS -O3 -xsse4.2 -fp-model fast -ip -g -MT delcher.o -MD -MP -MF ".deps/delcher.Tpo" -c -o delcher.o delcher.cc; \ then mv -f ".deps/delcher.Tpo" ".deps/delcher.Po"; else rm -f ".deps/delcher.Tpo"; exit 1; fi /usr/include/c++/4.5/iomanip(64): error: expected an expression { return { __mask }; } ^ /usr/include/c++/4.5/iomanip(94): error: expected an expression { return { __mask }; } ^ /usr/include/c++/4.5/iomanip(125): error: expected an expression { return { __base }; } ^ /usr/include/c++/4.5/iomanip(193): error: expected an expression { return { __n }; } ^ /usr/include/c++/4.5/iomanip(223): error: expected an expression { return { __n }; } ^ compilation aborted for delcher.cc (code 2) make[3]: *** [delcher.o] Error 1 make[3]: Leaving directory `/usr/local/bioinfo/tools/amos-3.0.1/src/Common' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/usr/local/bioinfo/tools/amos-3.0.1/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/usr/local/bioinfo/tools/amos-3.0.1' make: *** [all] Error 2 Can you help ? Thank you Jorge _________________________________ Jorge Duarte Bioinformatics Engineer Upstream Genomics BIOGEMMA Route d'Ennezat SITE DE LA GARENNE CS 90126 63720 CHAPPES Tel: +33 (0)4-73-67-88-55 _________________________________ BIOGEMMA S.A.S. au capital social de 48.335.652,00 € 1, Rue Edouard Colonne - 75001 PARIS RCS PARIS 412 514 366 This message and any attachments are confidential and intended solely for the use of the addressee(s) named above. The information contained in this email may also be legally privileged. If you have received this email in error, please notify us immediately by reply email or by fax and then delete it. Any use, distribution or reproduction of this message is strictly prohibited. The integrity or authenticity of this message cannot be guaranteed. We therefore shall not be liable for the message if altered, changed or falsified. Thank you. Cet email et ses pièces jointes sont strictement confidentiels et destinés uniquement à l'usage du (des) destinataire(s) sus-indiqué(s). Les informations contenues dans cet email sont légalement protégées. Si vous avez reçu cet email par erreur, merci de nous le retourner immédiatement par courrier électronique ou télécopie avant de le supprimer. Toute utilisation ou reproduction de cet email est strictement interdite. La véracité et l'authenticité de cet email et de son contenu ne peuvent être garanties et nous ne pouvons être tenus responsables de leur altération, modification ou falsification. Merci. |
From: <R.K...@ls...> - 2013-11-11 18:49:31
|
Hello there, Please could anyone advise on how to run multiple mediators in Amos? I have two IVs, 3 mediators and two DVs. The Amos outputs do not show all indirect paths that I need. Thank you, Rashi Please access the attached hyperlink for an important electronic communications disclaimer: http://lse.ac.uk/emailDisclaimer |
From: Anthony B. <ant...@aw...> - 2013-11-03 23:51:10
|
Hi, I have a collection of ~12,000 BAC-sized scaffolds that were produced by sequencing 96 separate pools of ~100 BACs on the Hiseq (2 x100bp) created from a heterozygous plant genome (500 Mb). Each of these pools were assembled and scaffolded separately (using SSPACE and whole-genome mate-pair data). The resulting data appears to be dominated by scaffold representing complete BACs from each pool. I have performed some initial BLAST analysis on these 12,000 scaffolds and am able to reliably find overlaps between BACs and to define long-range haplotypes, however this requires overlaps to be made across stretches of "N's" in specific scaffolds or to have gaps inserted due to some contig overlaps being detected by SSPACE. I have just tried to apply minimus2 on the collection of BACs to determine if this program can perform these overlaps in an automated fashion, however only a very small proportion (~900) contigs were able to be overlapped. I am presuming that this is primarily due to the problem of potenitally long stretches of N's and insertions between homologous scaffolds as as I have seen examples where short stretches of N's are reliably dealt with. Does anyone know if there are any parameters that could be altered within mininus2 to help deal with these type of differences between scaffolds or, alternatively, if one of the other amos tools may be better suited to this type of assembly problem (I am currently running minimo but this is taking an extremely long time to run). Cheers, Anthony Anthony Borneman Principal Research Scientist - Molecular Biology | The Australian Wine Research Institute Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 | Map PO Box 197, Glen Osmond SA 5064, Australia T: +61 8 83136613 (direct) | F: +61 8 83136601 | www: www.awri.com.au | AWRI Events This communication, including attachments, is intended only for the addressee(s) and contains information which might be confidential and/or the copyright of The Australian Wine Research Institute (AWRI) or a third party. If you are not the intended recipient of this communication please immediately delete and destroy all copies and contact the sender. If you are the intended recipient of this communication you should not copy, disclose or distribute any of the information contained herein without the consent of the AWRI and the sender. Any views expressed in this communication are those of the individual sender except where the sender specifically states them to be the views of the AWRI. No representation is made that this communication, including attachments, is free of viruses. Virus scanning is recommended and is the responsibility of the recipient. |
From: Jawon S. <ja...@ta...> - 2013-10-15 20:24:13
|
Hi, I am currently working to distribute Amos 3.1 to large systems. Before I go ahead with installation, I need to test that local installation is working correctly. I am currently lacking some of the test data, so I was wondering if you can provide it. These are afg files and 1con files. Thanks, Jawon |
From: Michael S. <ms...@um...> - 2013-09-18 01:22:49
|
Thats exactly it, there is already support for RF reads, but it interprets them as the old transposon-bombing sequencing: http://www.epibio.com/docs/default-source/forum-archive/forum-11-3---transposon-based-strategies-for-efficient-dna-sequencing-and-functional-genomics.pdf?sfvrsn=4 It would be a pretty substantial undertaking to rewrite this code, thats why I encourage you to try reversing those reads in the afg file. Alternatively, If you are interested in computing quality metrics, you could also try the FRcurve-BAM: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0052210 This maps the reads to the assembly so it would be easier to control. Good luck, Mike On Tue, Sep 17, 2013 at 8:10 PM, Anthony Borneman < ant...@aw...> wrote: > Hi Michael, > > Thanks for the quick response and for building such a great set of genomic > tools. > > I was hoping that it might be possible to implement something akin to the > existing "adj" flag for either the LIB record or for individual FRG records > to indicate that the pair of reads are "outies". Given the growing > application of these libraries I think it might be a useful feature to try > and implement in the future. I would be willing to help implement this, but > I'm afraid my basic programming skills would not be up to the job. > > In response to your advice, could you give me a pointer as to which field > to change in the afg file to get the reads reverse complemented for hawkeye > to make sure I'm on the right track with this? > > Cheers, > > Anthony > > > > > > On 18/09/2013, at 12:47 AM, Michael Schatz wrote: > > I just did a quick check and the RF reads are interpreted as transponsons > and are unhappy unless they are adjacent to each other. It is not a five > minute job to replace the analysis in the hawkeye code, so I would suggest > you flip the reads in the afg file > > Good luck, > > Mike > > > > On Tue, Sep 17, 2013 at 2:21 AM, Anthony Borneman < > ant...@aw...<mailto:ant...@aw...>> wrote: > > Hi, > I've been doing some extensive work on loading assemblies using the afg > output of the Ray assembler into Hawkeye for visualisation. I've been able > to successfully add both scaffold information (from SSPACE) and > short-insert pair information to the bare-bones afg file that Ray produces, > but I am having trouble representing the RF-orientated reads produced using > the illumina mate-pair protocol. > > As it stands, I can have these show up in Hawkeye with the correct > expected insert size etc. but they are depicted as "unhappy" as they have > the incorrect orientation, presumably as Hawkeye is expecting FR-based > reads. It there any way to alter the LIB, FRG or RED records to reflect the > RF orientation? I am trying to avoid having to reverse complement each read > to convert them to FR format as this will mean having to re-run the entire > assembly again as, the other tools that I am using (Ray, SSPACE) natively > deal with the RF orientation. > > Cheers, > > Anthony > > > > > [X] > > > Anthony Borneman > Principal Research Scientist - Molecular Biology | The Australian Wine > Research Institute > Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 > | <http://www.awri.com.au/contact/map.asp> Map< > http://www.awri.com.au/contact/maps-to-the-awri/> > > PO Box 197, Glen Osmond SA 5064, > Australia > •+61 8 83136613 (direct) |Ê+61 8 83136601 | | [X] @The_AWRI< > https://twitter.com/#!/The_AWRI> | The.AWRI< > http://www.facebook.com/#!/The.AWRI> > • www.awri.com.au<http://www.awri.com.au/> | AWRI Events< > http://www.awri.com.au/industry_support/courses-seminars-workshops/events/ > > > > > > > This communication, including attachments, is intended only for the > addressee(s) and contains information which might be confidential and/or > the copyright of The Australian Wine Research Institute (AWRI) or a third > party. If you are not the intended recipient of this communication please > immediately delete and destroy all copies and contact the sender. If you > are the intended recipient of this communication you should not copy, > disclose or distribute any of the information contained herein without the > consent of the AWRI and the sender. Any views expressed in this > communication are those of the individual sender except where the sender > specifically states them to be the views of the AWRI. No representation is > made that this communication, including attachments, is free of viruses. > Virus scanning is recommended and is the responsibility of the recipient. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------------------ > LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! > 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, > SharePoint > 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack > includes > Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. > http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk > > > > [cid:image5429ea.JPG@83ca19e4.4aab71e5] > > > Anthony Borneman > Principal Research Scientist - Molecular Biology | The Australian Wine > Research Institute > Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 > | <http://www.awri.com.au/contact/map.asp> Map< > http://www.awri.com.au/contact/maps-to-the-awri/> > PO Box 197, Glen Osmond SA 5064, Australia > •+61 8 83136613 (direct) |Ê+61 8 83136601 | | > [cid:imagea703c8.JPG@32b966e5.48a53835] @The_AWRI< > https://twitter.com/#!/The_AWRI> | The.AWRI< > http://www.facebook.com/#!/The.AWRI> > • www.awri.com.au<http://www.awri.com.au/> | AWRI Events< > http://www.awri.com.au/industry_support/courses-seminars-workshops/events/ > > > > > > This communication, including attachments, is intended only for the > addressee(s) and contains information which might be confidential and/or > the copyright of The Australian Wine Research Institute (AWRI) or a third > party. If you are not the intended recipient of this communication please > immediately delete and destroy all copies and contact the sender. If you > are the intended recipient of this communication you should not copy, > disclose or distribute any of the information contained herein without the > consent of the AWRI and the sender. Any views expressed in this > communication are those of the individual sender except where the sender > specifically states them to be the views of the AWRI. No representation is > made that this communication, including attachments, is free of viruses. > Virus scanning is recommended and is the responsibility of the recipient. > > > _______________________________________________ > AMOS-help mailing list > AMO...@li...<mailto:AMO...@li...> > https://lists.sourceforge.net/lists/listinfo/amos-help > > > > |
From: Michael S. <ms...@um...> - 2013-09-17 15:18:26
|
I just did a quick check and the RF reads are interpreted as transponsons and are unhappy unless they are adjacent to each other. It is not a five minute job to replace the analysis in the hawkeye code, so I would suggest you flip the reads in the afg file Good luck, Mike On Tue, Sep 17, 2013 at 2:21 AM, Anthony Borneman < ant...@aw...> wrote: > Hi, > I've been doing some extensive work on loading assemblies using the afg > output of the Ray assembler into Hawkeye for visualisation. I've been able > to successfully add both scaffold information (from SSPACE) and > short-insert pair information to the bare-bones afg file that Ray produces, > but I am having trouble representing the RF-orientated reads produced using > the illumina mate-pair protocol. > > As it stands, I can have these show up in Hawkeye with the correct > expected insert size etc. but they are depicted as "unhappy" as they have > the incorrect orientation, presumably as Hawkeye is expecting FR-based > reads. It there any way to alter the LIB, FRG or RED records to reflect the > RF orientation? I am trying to avoid having to reverse complement each read > to convert them to FR format as this will mean having to re-run the entire > assembly again as, the other tools that I am using (Ray, SSPACE) natively > deal with the RF orientation. > > Cheers, > > Anthony > > > > > > *Anthony Borneman > *Principal Research Scientist - Molecular Biology | The Australian Wine > Research Institute > Waite Precinct, Hartley Grove cnr Paratoo Road, Urrbrae (Adelaide) SA 5064 > | <http://www.awri.com.au/contact/map.asp>Map<http://www.awri.com.au/contact/maps-to-the-awri/> > > PO Box 197, Glen Osmond SA 5064, > Australia > ****(**+61 8 83136613 (direct) |**Ê+61 8 83136601 | ** | @The_AWRI<https://twitter.com/#!/The_AWRI> > | The.AWRI <http://www.facebook.com/#!/The.AWRI> > **8 **www.awri.com.au | AWRI Events<http://www.awri.com.au/industry_support/courses-seminars-workshops/events/> > > > This communication, including attachments, is intended only for the > addressee(s) and contains information which might be confidential and/or > the copyright of The Australian Wine Research Institute (AWRI) or a third > party. If you are not the intended recipient of this communication please > immediately delete and destroy all copies and contact the sender. If you > are the intended recipient of this communication you should not copy, > disclose or distribute any of the information contained herein without the > consent of the AWRI and the sender. Any views expressed in this > communication are those of the individual sender except where the sender > specifically states them to be the views of the AWRI. No representation is > made that this communication, including attachments, is free of viruses. > Virus scanning is recommended and is the responsibility of the recipient. > > ** > > > > ------------------------------------------------------------------------------ > LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! > 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, > SharePoint > 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack > includes > Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. > http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk > _______________________________________________ > AMOS-help mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-help > > |
From: Michael S. <ms...@um...> - 2013-09-11 15:11:38
|
Just committed it to the git repo. Thank you for your contribution! MIke On Tue, Sep 10, 2013 at 7:04 AM, James Abbott <j.a...@im...>wrote: > Hello, > > I see Shaun Jackmans' (abyss-)sam2afg script is available within the > Amos source repository. I find this very useful for coercing output from > assemblers which which don't track read location into amos by remapping > reads against the assembly and converting to afg - not ideal but better > than nothing when you don't have the 'real' read locations to work with. > > This fails, however when reads are aligned with 'bwa mem', which can > output multi-part alignments. sam2afg checks for reuse of the same read > id (presumably to prevent the generation of non-unique eid values), > consequently encountering multiple alignments for a read causes it to die. > > The following one-line patch allows sam2afg to skip these secondary > alignments present in 'bwa mem' output, provided bwa mem has been run > with the '-M' argument which sets the SAM 'secondary alignment' flag on > the alignments in question. > > Hopefully this will also be of use to others... > > Best Regards, > James > > *** /usr/biosoft/packages/abyss/current/bin/abyss-samtoafg > 2012-12-06 11:55:17.468551266 +0000 > --- ../bin/abyss-samtoafg 2013-09-10 11:45:31.267125932 +0100 > *************** > *** 105,110 **** > --- 105,111 ---- > die unless defined $qqual; > > $tstart--; # convert to zero-based coordinate > + next if $flag & 0x100; # secondary alignment > $qid .= "/1" if $flag & 0x40; #FREAD1 > $qid .= "/2" if $flag & 0x80; #FREAD2 > > > -- > Dr. James Abbott > Lead Bioinformatician > Bioinformatics Support Service > Imperial College, London > > > ------------------------------------------------------------------------------ > How ServiceNow helps IT people transform IT departments: > 1. Consolidate legacy IT systems to a single system of record for IT > 2. Standardize and globalize service processes across IT > 3. Implement zero-touch automation to replace manual, redundant tasks > http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk > _______________________________________________ > AMOS-help mailing list > AMO...@li... > https://lists.sourceforge.net/lists/listinfo/amos-help > |
From: James A. <j.a...@im...> - 2013-09-10 11:05:11
|
Hello, I see Shaun Jackmans' (abyss-)sam2afg script is available within the Amos source repository. I find this very useful for coercing output from assemblers which which don't track read location into amos by remapping reads against the assembly and converting to afg - not ideal but better than nothing when you don't have the 'real' read locations to work with. This fails, however when reads are aligned with 'bwa mem', which can output multi-part alignments. sam2afg checks for reuse of the same read id (presumably to prevent the generation of non-unique eid values), consequently encountering multiple alignments for a read causes it to die. The following one-line patch allows sam2afg to skip these secondary alignments present in 'bwa mem' output, provided bwa mem has been run with the '-M' argument which sets the SAM 'secondary alignment' flag on the alignments in question. Hopefully this will also be of use to others... Best Regards, James *** /usr/biosoft/packages/abyss/current/bin/abyss-samtoafg 2012-12-06 11:55:17.468551266 +0000 --- ../bin/abyss-samtoafg 2013-09-10 11:45:31.267125932 +0100 *************** *** 105,110 **** --- 105,111 ---- die unless defined $qqual; $tstart--; # convert to zero-based coordinate + next if $flag & 0x100; # secondary alignment $qid .= "/1" if $flag & 0x40; #FREAD1 $qid .= "/2" if $flag & 0x80; #FREAD2 -- Dr. James Abbott Lead Bioinformatician Bioinformatics Support Service Imperial College, London |