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From: VALAT C. <Cha...@an...> - 2016-07-27 12:59:55
|
Dear users, After alignment, in the scaffolds_contigs file, I found complement strands, however in the graph, I did not found these contigs blocks below the center line as expected, please could you explain me that? Many thanks Charlotte Valat |
From: Raymond W. <rwa...@gm...> - 2016-07-24 16:47:57
|
Hi Joe, First of all, my apologies for getting back to you so late! A deadline that just passed kept me occupied the entire week... Second, thanks a lot for replying to an old posting of mine -- that is very much appreciated! On Fri, Jul 15, 2016 at 7:17 AM, Joseph Fass <jos...@gm...> wrote: > Raymond, you've probably figured this out already, but since I was looking > for discussion of these files, I'll answer your email. The SNP file doesn't > address gaps, doesn't depend on the contig mover. The three fields for every > genome represent the contig name (the fasta header line of the sequence > containing the position of the SNP), the position in that particular contig > (i.e. 1-based position of the SNP in that particular fasta entry), and the > position in the whole genome (i.e. if you concatenated all contigs in order > together into one sequence, what would be the coordinate of the SNP). This > last obviously applies to a "draft" or multi-chromosomal genome that > contains multiple fasta entries in one file; if you're dealing with a single > chromosome, then the "position in contig" and "genome-wide position" will > match. Unfortunately, I didn't figure out what you mentioned here. The project that I was using Mauve for is "on hold" for reasons completely unrelated to Mauve. I still would like to get back to it some day. Thank you for this explanation! It is useful information to know whenever I return to that project and I hope it is useful for others reading the list. Thank you! Ray |
From: Joseph F. <jos...@gm...> - 2016-07-14 23:18:13
|
Raymond, you've probably figured this out already, but since I was looking for discussion of these files, I'll answer your email. The SNP file doesn't address gaps, doesn't depend on the contig mover. The three fields for every genome represent the contig name (the fasta header line of the sequence containing the position of the SNP), the position in that particular contig (i.e. 1-based position of the SNP in that particular fasta entry), and the position in the whole genome (i.e. if you concatenated all contigs in order together into one sequence, what would be the coordinate of the SNP). This last obviously applies to a "draft" or multi-chromosomal genome that contains multiple fasta entries in one file; if you're dealing with a single chromosome, then the "position in contig" and "genome-wide position" will match. ~Joe On Sat, Feb 28, 2015 at 4:16 AM, Raymond Wan <rw...@cu...> wrote: > > Dear Aaron (or anyone else who knows), > > I've noticed that the SNP file format has changed in version 2.4.0 > compared to > what's mentioned here: > > http://darlinglab.org/mauve/user-guide/files.html > > The first column is still "SNP pattern". But what use to be coordinates > for > each genome has now tripled. For each genome there is now: > > sequence_1_Contig sequence_1_PosInContg sequence_1_GenWidePos1 ... > > Would I be correct in saying that: > > 1) *_Contig is null if it contributes a gap to the SNP pattern. > Otherwise, it > gives the range of the contig. > > 2) *_PosInContg is 0 if it contributes a gap to the SNP pattern; > otherwise, it > is the position within that contig. > > 3) *_GenWidePos1 is 0 if it contributes a gap to the SNP pattern; > otherwise it > is the position within that genome. > > I'm thinking aloud a bit. :-) But it sounds like the old SNP file is just > column 3. Is that correct? > > However, I'm a bit puzzled what contig means in this context. Does it > refer to > usage of the Mauve Contig Mover? That is, if MCM isn't used, then columns > (2) > and columns (3) are identical in value? (This is what I'm noticing and I'm > trying to understand why...I think this is the reason, since I haven't used > MCM.) > > Thank you! > > Ray > > > > > ------------------------------------------------- > This e-mail is sent by CUHK WebMail http://webmail.cuhk.edu.hk > > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, > sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for > all > things parallel software development, from weekly thought leadership blogs > to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > -- Joseph Fass Bioinformatics Data Analyst UC Davis Genome Center - Bioinformatics Core http://bioinformatics.ucdavis.edu/ jn...@uc... phone ~ 530.752.2698 |
From: Joseph F. <jos...@gm...> - 2016-07-14 21:23:03
|
Hi all, Has anyone tried to convert the SNP and/or indel format that Mauve exports into a VCF-like format? I've aligned assembled genomes to a reference genome, and would like to predict the effect of various differences, and tools like snpEff required VCF input. I plan to try to write my own, but I wondered if anyone's dealt with this before. Thanks for any advice, leads, etc. ... ~Joe -- Joseph Fass Bioinformatics Data Analyst UC Davis Genome Center - Bioinformatics Core http://bioinformatics.ucdavis.edu/ jn...@uc... phone ~ 530.752.2698 |
From: Hongxian He <hon...@gm...> - 2016-07-07 13:54:06
|
Hi Aaron, Thanks for your reply. Coincidentally I found out why I was getting the error. The gbk files checked out just fine. The problem was that I did not have the write permission to the directory where one of the GenBank files was located (it turned out that the program would create the .sslist file in the same directory where the gbk file is located - instead of /tmp or the output directory which I was thinking of). The program works now! Thank you for all help! Best, Hongxian On Fri, Jul 1, 2016 at 1:31 AM, Aaron Darling <aar...@ut...> wrote: > Hello Hongxian, > > Where/how did you obtain those GBK files? Downloads from the NCBI web site > in GBK format can fail to include the actual genome sequence. Can you check > whether your gbk files have the actual nucleotide sequence at the end? The > file sizes should each be around 9Mb for those two genomes. > > To test it out, I obtained copies of those two genomes from the GenBank > ftp archive: > > ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/Bacillus_licheniformis_ATCC_14580_uid12388/CP000002.gbk > > ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/Bacillus_licheniformis_9945A_uid49115/CP005965.gbk > > and it appears to work as expected with Mauve (the snapshot for linux), so > perhaps you can try again with the files from those ftp links? > > Best, > -Aaron > > > On Thu, 2016-06-30 at 11:28 -0400, Hongxian He wrote: > > > > Hi, > > I am new to Mauve. I've downloaded both stable 2.4.0 release and latest > snapshot, but I am running into problems while trying to align two genomes > in GenBank formats. Both genomes were downloaded from NCBI (full gbk files > with nucleotide sequences). I've tried both versions, and tried both > regular aligner and progressiveMauve aligner, and I got errors in both > cases. I have increased the default memory setting with > "JAVA_ARGS="-Xms8000M -Xmx32000M" (I have 32GB RAM on my workstation). > There is 16GB free space in /tmp. > > However, when I aligned them using their raw FASTA files, it worked. > > Has anyone seen this kind of error before? > > Thanks very much, > Hongxian > > [Error Message] > > trying path /opt/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve > Running alignment. > Executing > /opt/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve > > --output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A > > --output-guide-tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.guide_tree > > --backbone-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.backbone > > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk > > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk > Storing raw sequence at /tmp/rawseq15048.000 > Sequence loaded successfully. > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk > 4222645 base pairs. > Storing raw sequence at /tmp/rawseq15048.001 > Sequence loaded successfully. > Error creating sorted mer list > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk > 4376305 base pairs. > > terminate called after throwing an instance of 'genome::gnException > 'Using weight 15 mers for initial seeds > Creating sorted mer list > Exited with error code: 134 > > trying path /opt/mauve_snapshot_2015-02-13/linux-x64/mauveAligner > Running alignment. > Executing > /opt/mauve_snapshot_2015-02-13/linux-x64/mauveAligner > > --output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A > --island-size=50 > > --island-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.islands > --backbone-size=50 > --max-backbone-gap=50 > > --backbone-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.backbone > > --id-matrix=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.id_matrix > > --output-alignment=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.alignment > > --output-guide-tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.guide_tree > > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk > > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk.sslist > > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk > > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk.sslist > Error creating sorted mer listSequence loaded successfully. > > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk > 4222645 base pairs. > Sequence loaded successfully. > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk > 4376305 base pairs. > Using weight 15 mers for initial seeds > Creating sorted mer list > Unhandled gnException: Exception FileNotOpened thrown from > Unknown() in FileSML.cpp 125 > Unable to open file for writing. > > Exited with error code: 246 > > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today.http://sdm.link/attshape > > _______________________________________________ > Mauve-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/mauve-users > > -- > Aaron E. Darling, Ph.D. > Associate Professor, ithree institute > University of Technology Sydney > Australia > http://darlinglab.org > twitter: @koadman > > > > ------------------------------ > UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any > accompanying attachments may contain confidential information. If you are > not the intended recipient, do not read, use, disseminate, distribute or > copy this message or attachments. If you have received this message in > error, please notify the sender immediately and delete this message. Any > views expressed in this message are those of the individual sender, except > where the sender expressly, and with authority, states them to be the views > of the University of Technology Sydney. Before opening any attachments, > please check them for viruses and defects. Think. Green. Do. Please > consider the environment before printing this email. > > |
From: Cedric C. <ced...@sf...> - 2016-07-05 17:07:43
|
Hello The Mauve file formats guide (http://darlinglab.org/mauve/user-guide/files.html) states that one can obtain a permutation matrix file, together with an LCB boundary file. I am using the version 2.4 of Mauve, through the GUI, to align a few bacterial genomes, but when I export, through the GUI, the permutation I do not obtain the LCB boundary file. Is-it a feature that is not available any more in Mauve 2.4, or that can be obtained through the command line ? To be complete, I tried to obtain LCB boundaries from the backbone file, but the permutation exported through the GUI has 72 blocks, and the permutation I obtain from the backbone has 58 colinear blocks, and the rearrangement history I obtain from both are very different so I assume I missed something in interpreting the backbone file properly. So I'd be happy to know how to obtain the LCB boundary coordinates. Thanks Cedric Chauve, PhD Professor, Department of Mathematics Simon Fraser University http://paleogenomics.irmacs.sfu.ca/ http://www.cecm.sfu.ca/~cchauve |
From: Ali C. B. <ali...@gm...> - 2016-07-04 10:39:18
|
Dear Dr. Darling I hope you are fine and everything is OK with you. I have a problem in working with Progressive Mauve. I have 42 bacterial genome sequences and I want to have a phylogenetic tree with them. I installed and used progressiveMauve for alignment. But I do not have bootstrap or such numbers in the obtained tree. And I cannot obtain aligned FASTA file. How can I resolve these challenges? Could you please help me. Regards -- Ali Chenari Bouket Ph.D. in Plant Pathology |
From: Peter H. <pet...@ok...> - 2016-07-01 15:24:49
|
Hi Hongxian, I was able to do those alignments on a windows desktop with 16GB RAM, so my recommendation is to re-download the genebank files from NCBI, and try again using the DEFAULT parameters (including NOT renaming the output files). the error "Unhandled gnException: Exception FileNotOpened thrown from Unknown() in FileSML.cpp 125 Suggests the software was looking for a file it couldn't find.... maybe because you renamed some output files. My Java settings were: "C:\Program Files\Java\jre1.8.0_91\bin\javaw.exe" -jar -XX:NewSize=4000m -XX:MaxNewSize=4000m -XX:+UseParallelGC -XX:NewRatio=8 -Xmx8000m -Xss512M -Xms8000m Mauve.jar Hope that helps. Peter On 06/30/2016 10:28 AM, Hongxian He wrote: > > > Hi, > > I am new to Mauve. I've downloaded both stable 2.4.0 release and > latest snapshot, but I am running into problems while trying to align > two genomes in GenBank formats. Both genomes were downloaded from NCBI > (full gbk files with nucleotide sequences). I've tried both versions, > and tried both regular aligner and progressiveMauve aligner, and I got > errors in both cases. I have increased the default memory setting with > "JAVA_ARGS="-Xms8000M -Xmx32000M" (I have 32GB RAM on my workstation). > There is 16GB free space in /tmp. > > However, when I aligned them using their raw FASTA files, it worked. > > Has anyone seen this kind of error before? > > Thanks very much, > Hongxian > > [Error Message] > > trying path /opt/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve > Running alignment. > Executing > /opt/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve > --output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A > --output-guide-tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.guide_tree > --backbone-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.backbone > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk > Storing raw sequence at /tmp/rawseq15048.000 > Sequence loaded successfully. > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk > 4222645 base pairs. > Storing raw sequence at /tmp/rawseq15048.001 > Sequence loaded successfully. > Error creating sorted mer list > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk > 4376305 base pairs. > > terminate called after throwing an instance of 'genome::gnException > 'Using weight 15 mers for initial seeds > Creating sorted mer list > Exited with error code: 134 > > trying path /opt/mauve_snapshot_2015-02-13/linux-x64/mauveAligner > Running alignment. > Executing > /opt/mauve_snapshot_2015-02-13/linux-x64/mauveAligner > --output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A > --island-size=50 > --island-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.islands > --backbone-size=50 > --max-backbone-gap=50 > --backbone-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.backbone > --id-matrix=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.id_matrix > --output-alignment=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.alignment > --output-guide-tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.guide_tree > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk.sslist > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk.sslist > Error creating sorted mer listSequence loaded successfully. > > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk > 4222645 base pairs. > Sequence loaded successfully. > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk > 4376305 base pairs. > Using weight 15 mers for initial seeds > Creating sorted mer list > Unhandled gnException: Exception FileNotOpened thrown from > Unknown() in FileSML.cpp 125 > Unable to open file for writing. > > Exited with error code: 246 > > > > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > > > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users |
From: Mohan A. <moh...@gm...> - 2016-07-01 09:28:43
|
I am Mohan Amarasiri from Hokkaido University. I am using the MAUVE software for constructing a draft genome of a bacterium isolated in our lab. I went through the 2009 paper and succeeded in obtaining the fasta file as the output. However, in the output file I can only see the contig order has been changed. But they haven't been joined to make the complete draft genome. In this case what is the next step to be taken? If you can help me with this, it would be of great help. Please apologize me for taking your valuable time. -- *Mohan Amarasiri* *Water Quality Control Engineering Laboratory* *Graduate School of EngineeringHokkaido UniversitySapporo 060-8628, Japan* *http://www.eng.hokudai.ac.jp/labo/water/English/E_memberMohanAmarasiri.html <http://www.eng.hokudai.ac.jp/labo/water/English/E_memberMohanAmarasiri.html>* |
From: Aaron D. <aar...@ut...> - 2016-07-01 05:32:08
|
Hello Hongxian, Where/how did you obtain those GBK files? Downloads from the NCBI web site in GBK format can fail to include the actual genome sequence. Can you check whether your gbk files have the actual nucleotide sequence at the end? The file sizes should each be around 9Mb for those two genomes. To test it out, I obtained copies of those two genomes from the GenBank ftp archive: ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/Bacillus_li cheniformis_ATCC_14580_uid12388/CP000002.gbk ftp://ftp.ncbi.nih.gov/genomes/archive/old_genbank/Bacteria/Bacillus_li cheniformis_9945A_uid49115/CP005965.gbk and it appears to work as expected with Mauve (the snapshot for linux), so perhaps you can try again with the files from those ftp links? Best, -Aaron On Thu, 2016-06-30 at 11:28 -0400, Hongxian He wrote: > > > Hi, > > I am new to Mauve. I've downloaded both stable 2.4.0 release and > latest snapshot, but I am running into problems while trying to align > two genomes in GenBank formats. Both genomes were downloaded from > NCBI (full gbk files with nucleotide sequences). I've tried both > versions, and tried both regular aligner and progressiveMauve > aligner, and I got errors in both cases. I have increased the default > memory setting with "JAVA_ARGS="-Xms8000M -Xmx32000M" (I have 32GB > RAM on my workstation). There is 16GB free space in /tmp. > > However, when I aligned them using their raw FASTA files, it worked. > > Has anyone seen this kind of error before? > > Thanks very much, > Hongxian > > [Error Message] > > trying path /opt/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve > Running alignment. > Executing > /opt/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve > -- > output=/home/hongxian/projects/bacillus_platform/genome_comparison/DS > M13_vs_9945A > --output-guide- > tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM1 > 3_vs_9945A.guide_tree > --backbone- > output=/home/hongxian/projects/bacillus_platform/genome_comparison/DS > M13_vs_9945A.backbone > > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322. > gbk > > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362. > gbk > Storing raw sequence at /tmp/rawseq15048.000 > Sequence loaded successfully. > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322. > gbk 4222645 base pairs. > Storing raw sequence at /tmp/rawseq15048.001 > Sequence loaded successfully. > Error creating sorted mer list > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362. > gbk 4376305 base pairs. > > terminate called after throwing an instance of 'genome::gnException > 'Using weight 15 mers for initial seeds > Creating sorted mer list > Exited with error code: 134 > > trying path /opt/mauve_snapshot_2015-02-13/linux-x64/mauveAligner > Running alignment. > Executing > /opt/mauve_snapshot_2015-02-13/linux-x64/mauveAligner > -- > output=/home/hongxian/projects/bacillus_platform/genome_comparison/DS > M13_vs_9945A > --island-size=50 > --island- > output=/home/hongxian/projects/bacillus_platform/genome_comparison/DS > M13_vs_9945A.islands > --backbone-size=50 > --max-backbone-gap=50 > --backbone- > output=/home/hongxian/projects/bacillus_platform/genome_comparison/DS > M13_vs_9945A.backbone > --id- > matrix=/home/hongxian/projects/bacillus_platform/genome_comparison/DS > M13_vs_9945A.id_matrix > --output- > alignment=/home/hongxian/projects/bacillus_platform/genome_comparison > /DSM13_vs_9945A.alignment > --output-guide- > tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM1 > 3_vs_9945A.guide_tree > > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322. > gbk > > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322. > gbk.sslist > > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362. > gbk > > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362. > gbk.sslist > Error creating sorted mer listSequence loaded successfully. > > /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322. > gbk 4222645 base pairs. > Sequence loaded successfully. > /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362. > gbk 4376305 base pairs. > Using weight 15 mers for initial seeds > Creating sorted mer list > Unhandled gnException: Exception FileNotOpened thrown from > Unknown() in FileSML.cpp 125 > Unable to open file for writing. > > Exited with error code: 246 > > > > ------------------------------------------------------------------- > ----------- > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in > San > Francisco, CA to explore cutting-edge tech and listen to tech > luminaries > present their vision of the future. This family event has something > for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |
From: Hongxian He <hon...@gm...> - 2016-06-30 15:28:59
|
Hi, I am new to Mauve. I've downloaded both stable 2.4.0 release and latest snapshot, but I am running into problems while trying to align two genomes in GenBank formats. Both genomes were downloaded from NCBI (full gbk files with nucleotide sequences). I've tried both versions, and tried both regular aligner and progressiveMauve aligner, and I got errors in both cases. I have increased the default memory setting with "JAVA_ARGS="-Xms8000M -Xmx32000M" (I have 32GB RAM on my workstation). There is 16GB free space in /tmp. However, when I aligned them using their raw FASTA files, it worked. Has anyone seen this kind of error before? Thanks very much, Hongxian [Error Message] trying path /opt/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve Running alignment. Executing /opt/mauve_snapshot_2015-02-13/linux-x64/progressiveMauve --output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A --output-guide-tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.guide_tree --backbone-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.backbone /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk Storing raw sequence at /tmp/rawseq15048.000 Sequence loaded successfully. /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk 4222645 base pairs. Storing raw sequence at /tmp/rawseq15048.001 Sequence loaded successfully. Error creating sorted mer list /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk 4376305 base pairs. terminate called after throwing an instance of 'genome::gnException 'Using weight 15 mers for initial seeds Creating sorted mer list Exited with error code: 134 trying path /opt/mauve_snapshot_2015-02-13/linux-x64/mauveAligner Running alignment. Executing /opt/mauve_snapshot_2015-02-13/linux-x64/mauveAligner --output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A --island-size=50 --island-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.islands --backbone-size=50 --max-backbone-gap=50 --backbone-output=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.backbone --id-matrix=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.id_matrix --output-alignment=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.alignment --output-guide-tree=/home/hongxian/projects/bacillus_platform/genome_comparison/DSM13_vs_9945A.guide_tree /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk.sslist /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk.sslist Error creating sorted mer listSequence loaded successfully. /home/hongxian/projects/bacillus_platform/annotation/DSM13/NC_006322.gbk 4222645 base pairs. Sequence loaded successfully. /home/hongxian/projects/bacillus_platform/annotation/9945A/NC_021362.gbk 4376305 base pairs. Using weight 15 mers for initial seeds Creating sorted mer list Unhandled gnException: Exception FileNotOpened thrown from Unknown() in FileSML.cpp 125 Unable to open file for writing. Exited with error code: 246 |
From: Paulina D. P. B. <pd...@co...> - 2016-06-13 21:04:29
|
Option 1 that I used: 1. Convert xmfa to fasta using the script convertAlignment.pl (found online https://github.com/lskatz/lskScripts/blob/master/convertAlignment.pl) perl ./convertAlignment.pl -i inputfilename.xmfa -o outputfilename_step1_int.fasta -f fasta -g xmfa -c 2. Convert the output from step 1 into a sequential fasta file with this command: perl -MBio::SeqIO -e 'my $seqin = Bio::SeqIO->new(-fh => \*STDIN, -format => 'fasta'); while (my $seq = $seqin->next_seq) { print ">",$seq->id,"\n",$seq->seq,"\n"; }' < ouputfilename_step1_int.fasta > outputfilename_step2_seq.fasta 3. Remove all the weird little characters that get added to the sequence names by the script (hashtags etc) Option 2, which, if I recall correctly, doesn't require any additional steps: Use this script: https://github.com/kjolley/seq_scripts/blob/master/xmfa2fasta.pl perl xmfa2fasta.pl --file inputfile.xmfa > outputfile.fasta From: TATIANA MURILLO CORRALES <TAT...@uc...<mailto:TAT...@uc...>> Date: Sunday, June 12, 2016 at 10:37 PM To: "Mau...@li...<mailto:Mau...@li...>" <Mau...@li...<mailto:Mau...@li...>> Subject: [Mauve-users] Whole genome alignment for Gubbins Hello dr. Darling and Mauve users, I am interested to generate whole genome alignments with Mauve in order to analyse them with Gubbins. I wanted to ask for advice on how would be the best way to transform the xmfa files produced with Mauve to multifasta as in input for Gubbins. Thank you, Tatiana Murillo -- Tatiana Murillo Corrales Research Centre for Tropical Diseases University of Costa Rica San José, Costa Rica Phone number +50625118616 |
From: TATIANA M. C. <TAT...@uc...> - 2016-06-13 02:52:24
|
> Hello dr. Darling and Mauve users, > > I am interested to generate whole genome alignments with Mauve in order to analyse them with Gubbins. I wanted to ask for advice on how would be the best way to transform the xmfa files produced with Mauve to multifasta as in input for Gubbins. > > Thank you, > > Tatiana Murillo -- Tatiana Murillo Corrales Research Centre for Tropical Diseases University of Costa Rica San José, Costa Rica Phone number +50625118616 |
From: Aaron D. <aar...@ut...> - 2016-06-11 21:13:52
|
Hi Hattie, There is currently no way to instruct the aligner to only align a portion of each genome. Extracting the region desired for alignment is the preferred approach, via script or other means. Best, -Aaron On Fri, 2016-06-10 at 01:24 +0300, Hattie Chung wrote: > Hi Mauve users, > > I would like to visualize the neighboring genes of a particular gene > across ~30 genomes. > Since whole-genome alignment is computationally intensive, I'd like > to specify and anchor the alignment for one particular gene, and not > align the rest of the genome. Is this possible with Mauve? > > (I thought about writing a script to grab the flanking ~10k bp of the > gene's homolog in each genome, but Mauve's visualization is quite > nice and I'd rather not write scripts for making nice graphics.) > > Thank you, > Hattie > ------------------------------------------------------------------- > ----------- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and > protocols are > consuming the most bandwidth. Provides multi-vendor support for > NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using > capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659 > 582;e > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |
From: Aaron D. <aar...@ut...> - 2016-06-09 23:58:26
|
Hi Aleksander, that still doesn't sound right. Can you send me the data (via dropbox or google drive, not as an email!) for closer inspection? Best, -Aaron On Thu, 2016-06-09 at 16:14 +0200, Aleksander Mahnič wrote: > Hi, > > Thank you very much for the prompt reply. > > I replaced the Mauve.jar. The SNP extract has now been running for a > few hours, but the output is still empty. > I do expect quite a large file so I'll just let it run. > > But still, is there any way to check if anything is happening in the > background? > There is a few second burst in CPU usage by javaw.exe after I run SNP > export and then the CPU drops to 0.0 and memory holds still. > > If I can provide any other information, please let me know. > > Best regards, > > Aleksander > > -- > The National Laboratory of Health, Environment and Food (NLZOH) > Prvomajska ulica 1, 2000 Maribor, Slovenia > tel: +386 (0)2 4500 175 > ------------------------------------------------------------------- > ----------- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and > protocols are > consuming the most bandwidth. Provides multi-vendor support for > NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using > capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659 > 582;e > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |
From: Hattie C. <hc...@fa...> - 2016-06-09 22:25:17
|
Hi Mauve users, I would like to visualize the neighboring genes of a particular gene across ~30 genomes. Since whole-genome alignment is computationally intensive, I'd like to specify and anchor the alignment for one particular gene, and not align the rest of the genome. Is this possible with Mauve? (I thought about writing a script to grab the flanking ~10k bp of the gene's homolog in each genome, but Mauve's visualization is quite nice and I'd rather not write scripts for making nice graphics.) Thank you, Hattie |
From: Aleksander M. <ale...@nl...> - 2016-06-09 14:14:08
|
Hi, Thank you very much for the prompt reply. I replaced the Mauve.jar. The SNP extract has now been running for a few hours, but the output is still empty. I do expect quite a large file so I'll just let it run. But still, is there any way to check if anything is happening in the background? There is a few second burst in CPU usage by javaw.exe after I run SNP export and then the CPU drops to 0.0 and memory holds still. If I can provide any other information, please let me know. Best regards, Aleksander -- The National Laboratory of Health, Environment and Food (NLZOH) Prvomajska ulica 1, 2000 Maribor, Slovenia tel: +386 (0)2 4500 175 |
From: Aaron D. <aar...@ut...> - 2016-06-08 22:26:30
|
Hi Aleksander, There appears to be a bug in the SNP exporter, wherein it fails to write the last part of the output. I have just committed a fix to the source code repository: https://sourceforge.net/p/mauve/code/4736/ I also posted a copy of the updated jar file into a repository for an unrelated project: https://github.com/cerebis/meta-sweeper/blob/multisample/external/mauve _snapshot_2015-02-13/Mauve.jar?raw=true If you can replace the Mauve.jar on your computer with that one it should hopefully resolve the problem, but do let us know if the issue persists. Best, -Aaron On Wed, 2016-06-08 at 10:11 +0200, Aleksander Mahnič wrote: > Greetings Mauve community, > > I have a small problem with extracting SNPs from our Mauve alignment. > > We have a set of 50 genomes (same species but quite diverse). When > extracting SNPs > from s subset alignment (15 genomes) it works perfectly, but when I > include all genomes, > the output file remains empty. > > Doesn't seem to be lack of CPU or memory and I let it run for almost > 12 hours. > > Do you have any experience with such problem? > Are there other ways to extract SNPs from Mauve alignment? > > Thank you for any help you can provide. > > Best regards, > > Aleksander > > -- > The National Laboratory of Health, Environment and Food (NLZOH) > Prvomajska ulica 1, 2000 Maribor, Slovenia > tel: +386 (0)2 4500 175 > ------------------------------------------------------------------- > ----------- > What NetFlow Analyzer can do for you? Monitors network bandwidth and > traffic > patterns at an interface-level. Reveals which users, apps, and > protocols are > consuming the most bandwidth. Provides multi-vendor support for > NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using > capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659 > 582;e > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |
From: Peter H. <pet...@ok...> - 2016-06-08 17:01:00
|
Hi Annalisa It isn't unusual for this to run for a week. As long as you aren't getting any errors, it's probably working. Peter On 06/08/2016 6:29 AM, annalisa giampetruzzi wrote: >> Dear Prof. Aaron Darling and Mauve users, >> I'm writing to you to ask some questions about the use of >> progressiveMauve. >> >> The topic of my work is to do a whole genome phylogeny and analyze (by >> ClonalOrigin) the recombination fluxes on a set of 27 whole genome >> sequences of bacteria, but most of them consist of contigs, since they >> are still in draft form. So I have installed Mauve in my linux64 server >> and I'm trying to launch progressiveMauve on 27 multifasta file. >> >> So the my first question is: Does progressiveMauve works fine on genome >> consisting of contigs? or Should I create a concatenamer of contigs in >> order to obtain only 27 fasta sequences? >> >> Then most of my genome sequences contain sequence/contigs annotated as >> plasmid. About this do you think it is better to run the >> progressiveMauve on chromosomes and on plasmids separately? Which is >> your experience? >> >> Actually I have already obtained a core_alignment.xmfa (LCB greater than >> 100) from my first attempt of running, and now I'm waiting for the >> result of Clonalframe (ClonalFrame -x 10000 -y 10000 -z 10 >> core_alignment.xmfa core_clonalframe.out.1 > cf_stdout.1 &...) >> I have launched the jobs 7 days ago but it is still running, so Is it >> normal that this job take so many time? How I could speed up this job? >> >> Thanks if you have the possibility to answer to these my several >> questions. >> Best regards >> >> Dott.ssa Annalisa Giampetruzzi > > *Dott.ssa Annalisa Giampetruzzi* > > Università degli Studi di Bari Aldo Moro > > Dipartimento di Scienze del Suolo, della Pianta e degli > Alimenti > > Di.S.S.P.A. > > Via Amendola 165/A 70126 BARI > > tel. 0805442538 > > fax. 0805443608 > > ann...@un... > > ann...@ho... > > skype giampe79 > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > > > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- - Peter R. Hoyt, Ph. D. Graduate Program Director, Bioinformatics Certification Oklahoma State University Department of Biochemistry and Molecular Biology |
From: annalisa g. <ann...@ho...> - 2016-06-08 11:29:43
|
Dear Prof. Aaron Darling and Mauve users, I'm writing to you to ask some questions about the use of progressiveMauve. The topic of my work is to do a whole genome phylogeny and analyze (by ClonalOrigin) the recombination fluxes on a set of 27 whole genome sequences of bacteria, but most of them consist of contigs, since they are still in draft form. So I have installed Mauve in my linux64 server and I'm trying to launch progressiveMauve on 27 multifasta file. So the my first question is: Does progressiveMauve works fine on genome consisting of contigs? or Should I create a concatenamer of contigs in order to obtain only 27 fasta sequences? Then most of my genome sequences contain sequence/contigs annotated as plasmid. About this do you think it is better to run the progressiveMauve on chromosomes and on plasmids separately? Which is your experience? Actually I have already obtained a core_alignment.xmfa (LCB greater than 100) from my first attempt of running, and now I'm waiting for the result of Clonalframe (ClonalFrame -x 10000 -y 10000 -z 10 core_alignment.xmfa core_clonalframe.out.1 > cf_stdout.1 &...) I have launched the jobs 7 days ago but it is still running, so Is it normal that this job take so many time? How I could speed up this job? Thanks if you have the possibility to answer to these my several questions. Best regards Dott.ssa Annalisa Giampetruzzi Dott.ssa Annalisa Giampetruzzi Università degli Studi di Bari Aldo Moro Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti Di.S.S.P.A. Via Amendola 165/A 70126 BARI tel. 0805442538 fax. 0805443608 ann...@un... ann...@ho... skype giampe79 |
From: Aleksander M. <ale...@nl...> - 2016-06-08 08:38:18
|
Greetings Mauve community, I have a small problem with extracting SNPs from our Mauve alignment. We have a set of 50 genomes (same species but quite diverse). When extracting SNPs from s subset alignment (15 genomes) it works perfectly, but when I include all genomes, the output file remains empty. Doesn't seem to be lack of CPU or memory and I let it run for almost 12 hours. Do you have any experience with such problem? Are there other ways to extract SNPs from Mauve alignment? Thank you for any help you can provide. Best regards, Aleksander -- The National Laboratory of Health, Environment and Food (NLZOH) Prvomajska ulica 1, 2000 Maribor, Slovenia tel: +386 (0)2 4500 175 |
From: Aaron D. <aar...@ut...> - 2016-05-25 23:49:40
|
Hi Keith, as you noticed the reordering of annotated genbank files is not currently supported in Mauve. If you want to use Mauve, the recommended approach is to order the contigs before annotating. Best, -Aaron On Wed, 2016-05-25 at 10:39 +0000, Keith Yamada wrote: > Hello, > > Is there anyway Mauve can order my contigs in genbank format and keep > them in .gbk format instead of converting it to a .fasta file? I > would like to view my draft genome annotations when I compare it to > other genomes. > > Cheers, > Keith > > ------------------------------------------------------------------- > ----------- > Mobile security can be enabling, not merely restricting. Employees > who > bring their own devices (BYOD) to work are irked by the imposition of > MDM > restrictions. Mobile Device Manager Plus allows you to control only > the > apps on BYO-devices by containerizing them, leaving personal data > untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. |
From: Guy P. I. <guy...@wi...> - 2016-05-25 13:06:45
|
Keith, Mauve itself align sequences as fasta, so when re-ordering contigs the annotations are lost. When possible, I always recommend ordering the contigs before annotation, but I realize that is not always possible. For contigs that are not reverse complemented during the process you can reorder the original .gbk file manually to reflect the final order, but you need to use some other solution for any “flipped” contigs. These days I use DNASTAR’s SeqNinja, but there are likely other tools out there — perhaps someone else can chime in. Cheers, Guy Dr. Guy Plunkett III Senior Scientist, Genome Center of Wisconsin Senior Scientist, DNASTAR, Inc. http://www.genome.wisc.edu/information/gplunkett.html On May 25, 2016, at 5:39 AM, Keith Yamada <kei...@ut...> wrote: > Hello, > > Is there anyway Mauve can order my contigs in genbank format and keep them in .gbk format instead of converting it to a .fasta file? I would like to view my draft genome annotations when I compare it to other genomes. > > Cheers, > Keith > > ------------------------------------------------------------------------------ > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j_______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users |
From: Keith Y. <kei...@ut...> - 2016-05-25 10:39:28
|
Hello, Is there anyway Mauve can order my contigs in genbank format and keep them in .gbk format instead of converting it to a .fasta file? I would like to view my draft genome annotations when I compare it to other genomes. Cheers, Keith? |
From: Susan B. F. <fo...@ug...> - 2016-05-24 15:48:55
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Hi Annalisa, To run the stripsubsetLCB's script I had to run progressive mauve in Linux and not the window GUI. The error I was getting related to a path that was created by the GUI in my xmfa file that Linux could not identify. Hope this helps. -Susan Sent from my iPhone On May 24, 2016, at 10:44 AM, annalisa giampetruzzi <ann...@ho...<mailto:ann...@ho...>> wrote: Dear Mauve users, I have launched a progressiveMauve align using Mauve on Windows now I want to launch the stripSubsetLCBs script (on Linux) on the .xmfa output but it returns this error: $ stripSubsetLCBs multiplealigngenome.xmfa multiplealigngenome.bbcols provaoutput_strip.xmfa 500 Error in XMFA file format Before line 463 Expecting 340 characters based on defline Actually read 397 characters of sequence Exception InvalidFileFormat thrown from Unknown() in /tmp/mauve_snapshot/build_scripts/build/include/libMems-1.6/libMems/IntervalList.h 531 Could you help me to understunding which is the problem? Annalisa Dott.ssa Annalisa Giampetruzzi Universit? degli Studi di Bari Aldo Moro Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti Di.S.S.P.A. Via Amendola 165/A 70126 BARI tel. 0805442538 fax. 0805443608 ann...@un...<mailto:ann...@un...> ann...@ho...<mailto:ann...@ho...> skype giampe79 ------------------------------------------------------------------------------ Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j _______________________________________________ Mauve-users mailing list Mau...@li...<mailto:Mau...@li...> https://lists.sourceforge.net/lists/listinfo/mauve-users |