mauve-users Mailing List for Mauve (Page 2)
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From: Aaron D. <aar...@ut...> - 2017-02-09 02:49:18
|
Hi Emiko, yes, those programs are available but they are buried down in the directory structure a few levels, see here: http://darlinglab.org/mauve/snapshots/2015/2015-02-25/MacOS/ I will look into linking these directly from the download page, it would probably avoid a lot of confusion. -Aaron On Wed, 2017-02-08 at 13:47 -0700, Emiko Sano wrote: > Hi all, > > I've been looking into how to obtain the mauve LCB boundary file, and > I think I found a way to do it from a previous post on this message > board. > However, the links to obtain the accessory programs are not live. > See: > http://darlinglab.org/mauve/snapshots/ > > I need to be able to access the projectAndStrip and makeBadgerMatrix > programs for Mac OS X. They are supposed to be under all other > programs in snapshots. > > Does anyone have a way to get those two programs? > > Any help is appreciated. > > -Emiko > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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: Emiko S. <emi...@gm...> - 2017-02-08 20:47:30
|
Hi all, I've been looking into how to obtain the mauve LCB boundary file, and I think I found a way to do it from a previous post on this message board. However, the links to obtain the accessory programs are not live. See: http://darlinglab.org/mauve/snapshots/ I need to be able to access the projectAndStrip and makeBadgerMatrix programs for Mac OS X. They are supposed to be under all other programs in snapshots. Does anyone have a way to get those two programs? Any help is appreciated. -Emiko |
From: Aaron D. <aar...@ut...> - 2017-02-08 20:39:15
|
Hello Mathias, The information you are asking for exists in the XMFA file, and in fact if you just delete the sequences from the XMFA file the representation of that information becomes fairly succinct. Maybe a clever series of grep commands could get you there, or some regular expressions. I guess you are seeking this information in a tab delemited format? There are no programs bundled with Mauve that would produce the info in a such a format. The closest would probably be the .bbcols and .backbone files, but those also break up the blocks at the boundaries of gain & loss events that are longer than around 20nt, so probably wouldn't be quite what you want for your score idea. Not sure if its helpful for your goals, but Mauve has a few rearrangment distances implemented in the GUI, including double-cut join and single-cut join, and breakpoint counts themselves have been used as a statistic for genome rearrangement. These distances can only be defined on genome alignments that have equal gene content in all genomes, which isn't usually the case with progressiveMauve unless the subset LCBs have been stripped out, or just 2 genomes were aligned. Best, -Aaron On Wed, 2017-02-08 at 06:51 -0500, Mathias Lorieux (GMail box) wrote: > Hi all, > > I’d be grateful if I could get help on how to obtain summary > statistics on alignments that Mauve produces. > > What I am looking for is a summary of the rank position, size, start- > stop of each ’block’ that Mauve identifies, for each compared > sequence. > > From these statistics I aim to calculate a kind of re-shuffling score > between two sequences. > > Thanks very much, > Mathias > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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: Mathias L. (G. box) <m.l...@gm...> - 2017-02-08 11:51:26
|
Hi all, I’d be grateful if I could get help on how to obtain summary statistics on alignments that Mauve produces. What I am looking for is a summary of the rank position, size, start-stop of each ’block’ that Mauve identifies, for each compared sequence. From these statistics I aim to calculate a kind of re-shuffling score between two sequences. Thanks very much, Mathias |
From: Aaron D. <aar...@ut...> - 2017-02-01 10:50:40
|
I see. It looks like you've got some large assemblies that are likely to be multichromosomal and possibly in multiple contigs. Unfortunately xmfa2maf only supports finished unichromosomal assemblies. Depending on what you intend to do next you might be able to get a hackish solution by simply concatenating all of the contigs in those genomes before assembling with progressiveMauve. But if you need the contig information that won't work obviously and I can't offer an easy solution right now. -Aaron On Wed, 2017-02-01 at 10:41 +0100, ait zai Lynda wrote: > Hi Aaron, i executed the xmfa2tomaf in the original locations, it > doesn't work completely. > i don't know what i must edit in the .xmfa file. May be i must masque > first the repeated sequences of the genomes before progressiveMauve > ? > > Here what i did: > > $ ./xmfa2maf threeway.xmfa threeway.maf > Sequence loaded successfully. > Pol1_final_sorted.fasta 52638403 base pairs. > Sequence loaded successfully. > Polytomella_capuana_v1_id8.fasta 80325395 base pairs. > Sequence loaded successfully. > Polytomella_magna_v1_id8.fasta 68237959 base pairs. > Sequence loaded successfully. > Polytomella_parva_v1_id8.fasta 46970636 base pairs. > Sequence loaded successfully. > Polytomella_piriformis_v1_id8.fasta 47387763 base pairs. > interval 108 seq 3 left 45472019 right 45472019 > l_baseI 1 r_baseI 5917 l_contigI 5831 r_contigI 5830 name > Pparva_contig_5832_cov_64_99 db=Polytomella_parva_v1_id8 > Error, input alignment spans multiple contigs/chromosomes. Unable to > translate to MAF > > > > 2017-01-31 23:24 GMT+01:00 Aaron Darling <aar...@ut...>: > > Hi Lynda, xmfa2maf needs to read the sequence files that went into > > threeway.xmfa, and the "FileNotOpened" exception is probably > > happening because they are no longer accessible at the original > > paths stored in the xmfa. There are a few options: > > 1) restore the sequence files and the xmfa to their original > > locations and run xmfa2maf from there > > 2) edit threeway.xmfa to point to the current file paths to the > > sequence files > > 3) re-run the genome alignment, then run xmfa2maf on the resulting > > xmfa > > > > > > > > On Tue, 2017-01-31 at 21:29 +0100, ait zai Lynda wrote: > > > Hi Aaron, Thank you for your answer. > > > > > > $bunzip2 xmfa2maf and $chmod 755 xmfa2maf works well. > > > But when i try to execute i get this results : > > > > > > $./xmfa2maf threeway.xmfa threeway.maf > > > > > > Exception FileNotOpened thrown from > > > Unknown() in gnFileSource.cpp 67 > > > Called by Unknown() > > > Segmentation fault (core dumped) > > > > > > Would you know how to do to execute the xmaf2maf proprly? > > > > > > > > > Thank you fore your help :) > > > > > > 2017-01-31 21:21 GMT+01:00 Aaron Darling > > > u>: > > > > Hi Lynda, can you please reply on list instead of privately? > > > > > > > > On Tue, 2017-01-31 at 17:12 +0100, ait zai Lynda wrote: > > > > > Hi Aaron, Thank you for your answer. > > > > > > > > > > $bunzip2 xmfa2maf and $chmod 755 xmfa2maf works well. > > > > > But when i try to execute i get this results : > > > > > > > > > > $./xmfa2maf threeway.xmfa threeway.maf > > > > > > > > > > Exception FileNotOpened thrown from > > > > > Unknown() in gnFileSource.cpp 67 > > > > > Called by Unknown() > > > > > Segmentation fault (core dumped) > > > > > > > > > > Would you know how to do to execute the xmaf2maf proprly? > > > > > > > > > > > > > > > Thank you fore your help :) > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 2017-01-30 2:35 GMT+01:00 Aaron Darling > > > > > u.au>: > > > > > > Hi Lynda, have you tried using the xmfa2maf program that is > > > > > > part of the Mauve codebase? A build for linux is available > > > > > > here: > > > > > > http://darlinglab.org/mauve/snapshots/2015/2015-02-13/linux > > > > > > -x64/xmfa2maf.bz2 > > > > > > > > > > > > to run one must first do: > > > > > > bunzip2 xmfa2maf > > > > > > chmod 755 xmfa2maf > > > > > > > > > > > > If you've already tried that without luck can you describe > > > > > > the problems you encountered? > > > > > > > > > > > > Cheers, > > > > > > -Aaron > > > > > > > > > > > > On Sun, 2017-01-29 at 16:37 +0100, ait zai Lynda wrote: > > > > > > > hi everyone, > > > > > > > > > > > > > > i'm new in the alignment, i want to convert my XMFA file > > > > > > > to MAF file. > > > > > > > Does anyone know how i can do it? > > > > > > > > > > > > > > > > > > > > > thank you in advance > > > > > > > ------------------------------------------------------- > > > > > > > ----------------------- > > > > > > > Check out the vibrant tech community on one of the > > > > > > > world's most > > > > > > > engaging tech sites, SlashDot.org! http://sdm.link/slashd > > > > > > > ot > > > > > > > _______________________________________________ > > > > > > > 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. > > > > > > > > > > > > --------------------------------------------------------- > > > > > > --------------------- > > > > > > Check out the vibrant tech community on one of the world's > > > > > > most > > > > > > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > > > > _______________________________________________ > > > > > > 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. > > > > > > > --------------------------------------------------------------- > > > --------------- > > > Check out the vibrant tech community on one of the world's most > > > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > _______________________________________________ > > > 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. > > > > ----------------------------------------------------------------- > > ------------- > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > _______________________________________________ > > Mauve-users mailing list > > Mau...@li... > > https://lists.sourceforge.net/lists/listinfo/mauve-users > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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: ait z. L. <ait...@gm...> - 2017-02-01 09:41:27
|
Hi Aaron, i executed the xmfa2tomaf in the original locations, it doesn't work completely. i don't know what i must edit in the .xmfa file. May be i must masque first the repeated sequences of the genomes before progressiveMauve ? Here what i did: $ ./xmfa2maf threeway.xmfa threeway.maf Sequence loaded successfully. Pol1_final_sorted.fasta 52638403 base pairs. Sequence loaded successfully. Polytomella_capuana_v1_id8.fasta 80325395 base pairs. Sequence loaded successfully. Polytomella_magna_v1_id8.fasta 68237959 base pairs. Sequence loaded successfully. Polytomella_parva_v1_id8.fasta 46970636 base pairs. Sequence loaded successfully. Polytomella_piriformis_v1_id8.fasta 47387763 base pairs. interval 108 seq 3 left 45472019 right 45472019 l_baseI 1 r_baseI 5917 l_contigI 5831 r_contigI 5830 name Pparva_contig_5832_cov_64_99 db=Polytomella_parva_v1_id8 Error, input alignment spans multiple contigs/chromosomes. Unable to translate to MAF 2017-01-31 23:24 GMT+01:00 Aaron Darling <aar...@ut...>: > Hi Lynda, xmfa2maf needs to read the sequence files that went into > threeway.xmfa, and the "FileNotOpened" exception is probably happening > because they are no longer accessible at the original paths stored in the > xmfa. There are a few options: > 1) restore the sequence files and the xmfa to their original locations and > run xmfa2maf from there > 2) edit threeway.xmfa to point to the current file paths to the sequence > files > 3) re-run the genome alignment, then run xmfa2maf on the resulting xmfa > > > > On Tue, 2017-01-31 at 21:29 +0100, ait zai Lynda wrote: > > Hi Aaron, Thank you for your answer. > > $bunzip2 xmfa2maf and $chmod 755 xmfa2maf works well. > But when i try to execute i get this results : > > $./xmfa2maf threeway.xmfa threeway.maf > > Exception FileNotOpened thrown from > Unknown() in gnFileSource.cpp 67 > Called by Unknown() > Segmentation fault (core dumped) > > Would you know how to do to execute the xmaf2maf proprly? > > > Thank you fore your help :) > > 2017-01-31 21:21 GMT+01:00 Aaron Darling <aar...@ut...>: > > Hi Lynda, can you please reply on list instead of privately? > > On Tue, 2017-01-31 at 17:12 +0100, ait zai Lynda wrote: > > Hi Aaron, Thank you for your answer. > > $bunzip2 xmfa2maf and $chmod 755 xmfa2maf works well. > But when i try to execute i get this results : > > $./xmfa2maf threeway.xmfa threeway.maf > > Exception FileNotOpened thrown from > Unknown() in gnFileSource.cpp 67 > Called by Unknown() > Segmentation fault (core dumped) > > Would you know how to do to execute the xmaf2maf proprly? > > > Thank you fore your help :) > > > > > > > 2017-01-30 2:35 GMT+01:00 Aaron Darling <aar...@ut...>: > > Hi Lynda, have you tried using the xmfa2maf program that is part of the > Mauve codebase? A build for linux is available here: > http://darlinglab.org/mauve/snapshots/2015/2015-02-13/linux- > x64/xmfa2maf.bz2 > > to run one must first do: > bunzip2 xmfa2maf > chmod 755 xmfa2maf > > If you've already tried that without luck can you describe the problems > you encountered? > > Cheers, > -Aaron > > On Sun, 2017-01-29 at 16:37 +0100, ait zai Lynda wrote: > > hi everyone, > > i'm new in the alignment, i want to convert my XMFA file to MAF file. > Does anyone know how i can do it? > > > thank you in advance > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > _______________________________________________ > 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. > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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. > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > _______________________________________________ > 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. > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > > |
From: Aaron D. <aar...@ut...> - 2017-01-31 22:24:43
|
Hi Lynda, xmfa2maf needs to read the sequence files that went into threeway.xmfa, and the "FileNotOpened" exception is probably happening because they are no longer accessible at the original paths stored in the xmfa. There are a few options: 1) restore the sequence files and the xmfa to their original locations and run xmfa2maf from there 2) edit threeway.xmfa to point to the current file paths to the sequence files 3) re-run the genome alignment, then run xmfa2maf on the resulting xmfa On Tue, 2017-01-31 at 21:29 +0100, ait zai Lynda wrote: > Hi Aaron, Thank you for your answer. > > $bunzip2 xmfa2maf and $chmod 755 xmfa2maf works well. > But when i try to execute i get this results : > > $./xmfa2maf threeway.xmfa threeway.maf > > Exception FileNotOpened thrown from > Unknown() in gnFileSource.cpp 67 > Called by Unknown() > Segmentation fault (core dumped) > > Would you know how to do to execute the xmaf2maf proprly? > > > Thank you fore your help :) > > 2017-01-31 21:21 GMT+01:00 Aaron Darling <aar...@ut...>: > > Hi Lynda, can you please reply on list instead of privately? > > > > On Tue, 2017-01-31 at 17:12 +0100, ait zai Lynda wrote: > > > Hi Aaron, Thank you for your answer. > > > > > > $bunzip2 xmfa2maf and $chmod 755 xmfa2maf works well. > > > But when i try to execute i get this results : > > > > > > $./xmfa2maf threeway.xmfa threeway.maf > > > > > > Exception FileNotOpened thrown from > > > Unknown() in gnFileSource.cpp 67 > > > Called by Unknown() > > > Segmentation fault (core dumped) > > > > > > Would you know how to do to execute the xmaf2maf proprly? > > > > > > > > > Thank you fore your help :) > > > > > > > > > > > > > > > > > > > > > 2017-01-30 2:35 GMT+01:00 Aaron Darling <aar...@ut... > > > >: > > > > Hi Lynda, have you tried using the xmfa2maf program that is > > > > part of the Mauve codebase? A build for linux is available > > > > here: > > > > http://darlinglab.org/mauve/snapshots/2015/2015-02-13/linux-x64 > > > > /xmfa2maf.bz2 > > > > > > > > to run one must first do: > > > > bunzip2 xmfa2maf > > > > chmod 755 xmfa2maf > > > > > > > > If you've already tried that without luck can you describe the > > > > problems you encountered? > > > > > > > > Cheers, > > > > -Aaron > > > > > > > > On Sun, 2017-01-29 at 16:37 +0100, ait zai Lynda wrote: > > > > > hi everyone, > > > > > > > > > > i'm new in the alignment, i want to convert my XMFA file to > > > > > MAF file. > > > > > Does anyone know how i can do it? > > > > > > > > > > > > > > > thank you in advance > > > > > ----------------------------------------------------------- > > > > > ------------------- > > > > > Check out the vibrant tech community on one of the world's > > > > > most > > > > > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > > > _______________________________________________ > > > > > 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. > > > > > > > > ------------------------------------------------------------- > > > > ----------------- > > > > Check out the vibrant tech community on one of the world's most > > > > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > > _______________________________________________ > > > > 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. > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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: ait z. L. <ait...@gm...> - 2017-01-31 20:29:26
|
Hi Aaron, Thank you for your answer. $bunzip2 xmfa2maf and $chmod 755 xmfa2maf works well. But when i try to execute i get this results : $./xmfa2maf threeway.xmfa threeway.maf Exception FileNotOpened thrown from Unknown() in gnFileSource.cpp 67 Called by Unknown() Segmentation fault (core dumped) Would you know how to do to execute the xmaf2maf proprly? Thank you fore your help :) 2017-01-31 21:21 GMT+01:00 Aaron Darling <aar...@ut...>: > Hi Lynda, can you please reply on list instead of privately? > > On Tue, 2017-01-31 at 17:12 +0100, ait zai Lynda wrote: > > Hi Aaron, Thank you for your answer. > > $bunzip2 xmfa2maf and $chmod 755 xmfa2maf works well. > But when i try to execute i get this results : > > $./xmfa2maf threeway.xmfa threeway.maf > > Exception FileNotOpened thrown from > Unknown() in gnFileSource.cpp 67 > Called by Unknown() > Segmentation fault (core dumped) > > Would you know how to do to execute the xmaf2maf proprly? > > > Thank you fore your help :) > > > > > > > 2017-01-30 2:35 GMT+01:00 Aaron Darling <aar...@ut...>: > > Hi Lynda, have you tried using the xmfa2maf program that is part of the > Mauve codebase? A build for linux is available here: > http://darlinglab.org/mauve/snapshots/2015/2015-02-13/linux- > x64/xmfa2maf.bz2 > > to run one must first do: > bunzip2 xmfa2maf > chmod 755 xmfa2maf > > If you've already tried that without luck can you describe the problems > you encountered? > > Cheers, > -Aaron > > On Sun, 2017-01-29 at 16:37 +0100, ait zai Lynda wrote: > > hi everyone, > > i'm new in the alignment, i want to convert my XMFA file to MAF file. > Does anyone know how i can do it? > > > thank you in advance > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > _______________________________________________ > 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. > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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...> - 2017-01-30 01:35:42
|
Hi Lynda, have you tried using the xmfa2maf program that is part of the Mauve codebase? A build for linux is available here: http://darlinglab.org/mauve/snapshots/2015/2015-02-13/linux-x64/xmfa2ma f.bz2 to run one must first do: bunzip2 xmfa2maf chmod 755 xmfa2maf If you've already tried that without luck can you describe the problems you encountered? Cheers, -Aaron On Sun, 2017-01-29 at 16:37 +0100, ait zai Lynda wrote: > hi everyone, > > i'm new in the alignment, i want to convert my XMFA file to MAF > file. > Does anyone know how i can do it? > > > thank you in advance > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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: ait z. L. <ait...@gm...> - 2017-01-29 15:37:32
|
hi everyone, i'm new in the alignment, i want to convert my XMFA file to MAF file. Does anyone know how i can do it? thank you in advance |
From: Eun J. Na <en...@co...> - 2017-01-25 13:17:35
|
Dear All, Any suggestion to successfully load the annotations from the .gbk file? --- For more background, I am aligning eleven bacterial genomes using progressiveMauve, and much to my delight, succeeded in doing so! Except that the annotations from the .gbk file won't load. I read through the email archive and accordingly have tried clearing alignment cache, but that doesn't seem to help. The error message I received is as follows: 1월 25, 2017 9:55:25 오후 java.util.prefs.WindowsPreferences <init> WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5. Error reading file. org.biojava.bio.BioException: Could not read sequence at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:108) at org.gel.mauve.format.BaseFormat$2.nextSequence(Unknown Source) at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source) at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source) at org.gel.mauve.GenomeBuilder.buildGenome(Unknown Source) at org.gel.mauve.XmfaViewerModel.init(Unknown Source) at org.gel.mauve.XmfaViewerModel.<init>(Unknown Source) at org.gel.mauve.ModelBuilder.buildModel(Unknown Source) at org.gel.mauve.gui.FrameLoader.loadFile(Unknown Source) at org.gel.mauve.gui.FrameLoader.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Caused by: java.lang.StringIndexOutOfBoundsException: String index out of range: 12 at java.lang.String.substring(Unknown Source) at org.biojava.bio.seq.io.GenbankContext.processHeaderLine(GenbankContext.java:310) at org.biojava.bio.seq.io.GenbankContext.processLine(GenbankContext.java:129) at org.biojava.bio.seq.io.GenbankFormat.readSequence(GenbankFormat.java:146) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:105) ... 10 more --- Any feedback would be much appreciated, as being able to see the annotation results directly in Mauve would make things much easier for me. Thank you! Best, Eun Jung |
From: Eugeni B. <eug...@gm...> - 2017-01-09 15:17:40
|
Hello Aaron, Thanks a lot for your quick response. I’ve checked and there was a problem apparently with sequence IDs; after sequence renaming MCM works fine. All the best Eugeni > On 9 Jan 2017, at 12:26, Aaron Darling <aar...@ut...> wrote: > > Hi Eugeni, > Before the malloc error, the aligner issued a warning message about the file CAG00011_hs9.9_v3.fna, which contains characters or formatting that the software was not expecting in a FastA file. I suggest carefully checking that file first. > > -Aaron > > On Mon, 2017-01-09 at 10:44 +0100, Eugeni Belda wrote: >> Hello, >> I’m trying to reorder a set of E.coli contigs from a draft metagenomic assembly (5000 contigs approximately) against the reference E. coli K12-MG1335 sequence using the MCM option of Mauve, but the following error message appears on Mauve console: >> >> Copying... >> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/GCF_000005845.2_ASM584v2_genomic.fna >> to >> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna >> Copying... >> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/CAG00011_hs9.9_v3.fna >> to >> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/CAG00011_hs9.9_v3.fna >> Running alignment. >> Executing >> /Applications/Mauve.app/Contents/MacOS/progressiveMauve >> --output=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/alignment1 >> --skip-refinement >> --weight=200 >> --output-guide-tree=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/alignment1.guide_tree >> --backbone-output=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/alignment1.backbone >> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna >> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/CAG00011_hs9.9_v3.fna >> Storing raw sequence at /var/folders/68/q1l_zkrx2ll01m7rq3y3cl900000gn/T/rawseq44633.000 >> Sequence loaded successfully. >> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna 4641652 base pairs. >> Storing raw sequence at /var/folders/68/q1l_zkrx2ll01m7rq3y3cl900000gn/T/rawseq44633.001 >> Sequence loaded successfully.ERROR! gap character encountered at genome sequence position 201558 >> >> /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/CAG00011_hs9.9_v3.fna 4278085 base pairs.Input sequences must be unaligned and ungapped! >> >> Using weight 15 mers for initial seeds >> Creating sorted mer list >> Create time was: 2 seconds. >> Creating sorted mer list >> progressiveMauve(44633,0x7fffa7cd83c0) malloc: *** error for object 0x7f9810531b50: pointer being freed was not allocated >> *** set a breakpoint in malloc_error_break to debug >> Exited with error code: 134 >> >> I’ve looked on the mauve-users mailing list for similar problem but I haven’t found anything related. Any support will be very appreciated. >> Yours sincerely >> Eugeni Belda >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot <http://sdm.link/slashdot> >> _______________________________________________ >> Mauve-users mailing list >> Mau...@li... <mailto:Mau...@li...> >> https://lists.sourceforge.net/lists/listinfo/mauve-users <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. > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot_______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users |
From: Aaron D. <aar...@ut...> - 2017-01-09 11:26:39
|
Hi Eugeni, Before the malloc error, the aligner issued a warning message about the file CAG00011_hs9.9_v3.fna, which contains characters or formatting that the software was not expecting in a FastA file. I suggest carefully checking that file first. -Aaron On Mon, 2017-01-09 at 10:44 +0100, Eugeni Belda wrote: > Hello, > I’m trying to reorder a set of E.coli contigs from a draft > metagenomic assembly (5000 contigs approximately) against the > reference E. coli K12-MG1335 sequence using the MCM option of Mauve, > but the following error message appears on Mauve console: > > Copying... > /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherich > ia/GCF_000005845.2_ASM584v2_genomic.fna > to > /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherich > ia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna > Copying... > /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherich > ia/CAG00011_hs9.9_v3.fna > to > /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherich > ia/testdir5/alignment1/CAG00011_hs9.9_v3.fna > Running alignment. > Executing > /Applications/Mauve.app/Contents/MacOS/progressiveMauve > -- > output=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escheric > hia/testdir5/alignment1/alignment1 > --skip-refinement > --weight=200 > --output-guide- > tree=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichi > a/testdir5/alignment1/alignment1.guide_tree > --backbone- > output=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escheric > hia/testdir5/alignment1/alignment1.backbone > > /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/tes > tdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna > > /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/tes > tdir5/alignment1/CAG00011_hs9.9_v3.fna > Storing raw sequence at > /var/folders/68/q1l_zkrx2ll01m7rq3y3cl900000gn/T/rawseq44633.000 > Sequence loaded successfully. > /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/tes > tdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna 4641652 base > pairs. > Storing raw sequence at > /var/folders/68/q1l_zkrx2ll01m7rq3y3cl900000gn/T/rawseq44633.001 > Sequence loaded successfully.ERROR! gap character encountered at > genome sequence position 201558 > > /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/tes > tdir5/alignment1/CAG00011_hs9.9_v3.fna 4278085 base pairs.Input > sequences must be unaligned and ungapped! > > Using weight 15 mers for initial seeds > Creating sorted mer list > Create time was: 2 seconds. > Creating sorted mer list > progressiveMauve(44633,0x7fffa7cd83c0) malloc: *** error for object > 0x7f9810531b50: pointer being freed was not allocated > *** set a breakpoint in malloc_error_break to debug > Exited with error code: 134 > > I’ve looked on the mauve-users mailing list for similar problem but I > haven’t found anything related. Any support will be very appreciated. > Yours sincerely > Eugeni Belda > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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: Eugeni B. <eug...@gm...> - 2017-01-09 09:44:36
|
Hello, I’m trying to reorder a set of E.coli contigs from a draft metagenomic assembly (5000 contigs approximately) against the reference E. coli K12-MG1335 sequence using the MCM option of Mauve, but the following error message appears on Mauve console: Copying... /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/GCF_000005845.2_ASM584v2_genomic.fna to /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna Copying... /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/CAG00011_hs9.9_v3.fna to /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/CAG00011_hs9.9_v3.fna Running alignment. Executing /Applications/Mauve.app/Contents/MacOS/progressiveMauve --output=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/alignment1 --skip-refinement --weight=200 --output-guide-tree=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/alignment1.guide_tree --backbone-output=/Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/alignment1.backbone /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/CAG00011_hs9.9_v3.fna Storing raw sequence at /var/folders/68/q1l_zkrx2ll01m7rq3y3cl900000gn/T/rawseq44633.000 Sequence loaded successfully. /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/GCF_000005845.2_ASM584v2_genomic.fna 4641652 base pairs. Storing raw sequence at /var/folders/68/q1l_zkrx2ll01m7rq3y3cl900000gn/T/rawseq44633.001 Sequence loaded successfully.ERROR! gap character encountered at genome sequence position 201558 /Users/Eugeni/Documents/ICAN/Antoine/faecalibacterium/escherichia/testdir5/alignment1/CAG00011_hs9.9_v3.fna 4278085 base pairs.Input sequences must be unaligned and ungapped! Using weight 15 mers for initial seeds Creating sorted mer list Create time was: 2 seconds. Creating sorted mer list progressiveMauve(44633,0x7fffa7cd83c0) malloc: *** error for object 0x7f9810531b50: pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug Exited with error code: 134 I’ve looked on the mauve-users mailing list for similar problem but I haven’t found anything related. Any support will be very appreciated. Yours sincerely Eugeni Belda |
From: Hans v. L. <han...@ou...> - 2016-12-30 10:20:11
|
Hi all, I'm a new user to Mauve but ran into a problem . Aligning fasta files of large bacterial genomes goes fine! (progressiveMauve). However, aligning Genbank files of the same genomes gives an error (see below) As this error was reported before on this forum: https://sourceforge.net/p/mauve/mailman/message/35206741/ I also tried those two genomes Aaron suggested but failed. -Don't think it's a permission problem (admin and fasta stored same place). -Renaming files either as I renamed the Fasta files as well. -I used default alignment parameters Any help is appreciated. Happy New Year, Hans I am running Mauve is 2.4.0, latest JRE version (8u112) on a 64-bit Windows 8 computer. ------------------------------------------------------ Running alignment. Executing win64\progressiveMauve --output=C:\Users\Hans\Desktop\Aaron\SuggestionAaron --output-guide-tree=C:\Users\Hans\Desktop\Aaron\SuggestionAaron.guide_tree --backbone-output=C:\Users\Hans\Desktop\Aaron\SuggestionAaron.backbone C:\Users\Hans\Desktop\Aaron\CP000002.gbk.txt C:\Users\Hans\Desktop\Aaron\CP005965.gbk.txt Storing raw sequence at C:\Users\Hans\AppData\Local\Temp\raw883E.tmp Sequence loaded successfully. This application has requested the Runtime to terminate it in an unusual way. C:\Users\Hans\Desktop\Aaron\CP000002.gbk.txt 4535451 base pairs. Please contact the application's support team for more information. Storing raw sequence at C:\Users\Hans\AppData\Local\Temp\raw8BAA.tmp Exited with error code: 3 ------------------------------------------------------------------- |
From: Aleksander M. <ale...@nl...> - 2016-12-13 16:18:12
|
Hi, It worked perfectly from the command line. If the following information will be in any help: I'm running the latest snapshot of Mauve. When working with viewer no error messages appeared in terminal, the log window in viewer did not open. Mauve created a bunch of java jobs and ran them on all available cores and then just stopped after a few minutes with the output remaining empty. Thank you for your help. Best, Aleksander ----- Izvirno sporočilo ----- Od: "aaron darling" <aar...@ut...> Za: "mauve-users" <mau...@li...> Poslano: Torek, 13. December 2016 16:05:28 Zadeva: Re: [Mauve-users] SNP extraction Hi Aleksander, No the guide tree is not used in the SNP extraction. Did your progressiveMauve run generate the .backbone and .bbcols files? Are you generating the SNP file from the command line or within the viewer? Are there any messages in either the terminal or the console log window? Best, -Aaron On Tue, 2016-12-13 at 15:07 +0100, Aleksander Mahnič wrote: > Hi all, > > I have some problems with SNP extraction from alignment of 48 genomes > (the output file remains empty). > I noticed, that we did not set the progressiveMauve to save the guide > tree. Could this play a role in SNP extract failing? > > If so.. Is there a fast option to make a guide tree from the > alignment or is it easier to just run alignment again? > > Thank you. > > Best, > Aleksander > > -- > National Laboratory of Health, Environment and Food (NLZOH) > Prvomajska ulica 1, 2000 Maribor, Slovenia > tel: +386 (0)2 4500 175 > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Mauve-users mailing list Mau...@li... https://lists.sourceforge.net/lists/listinfo/mauve-users |
From: Aaron D. <aar...@ut...> - 2016-12-13 15:06:10
|
Hi Aleksander, No the guide tree is not used in the SNP extraction. Did your progressiveMauve run generate the .backbone and .bbcols files? Are you generating the SNP file from the command line or within the viewer? Are there any messages in either the terminal or the console log window? Best, -Aaron On Tue, 2016-12-13 at 15:07 +0100, Aleksander Mahnič wrote: > Hi all, > > I have some problems with SNP extraction from alignment of 48 genomes > (the output file remains empty). > I noticed, that we did not set the progressiveMauve to save the guide > tree. Could this play a role in SNP extract failing? > > If so.. Is there a fast option to make a guide tree from the > alignment or is it easier to just run alignment again? > > Thank you. > > Best, > Aleksander > > -- > National Laboratory of Health, Environment and Food (NLZOH) > Prvomajska ulica 1, 2000 Maribor, Slovenia > tel: +386 (0)2 4500 175 > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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: Aleksander M. <ale...@nl...> - 2016-12-13 14:36:01
|
Hi all, I have some problems with SNP extraction from alignment of 48 genomes (the output file remains empty). I noticed, that we did not set the progressiveMauve to save the guide tree. Could this play a role in SNP extract failing? If so.. Is there a fast option to make a guide tree from the alignment or is it easier to just run alignment again? Thank you. Best, Aleksander -- 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...> - 2016-11-07 20:27:07
|
Hi Christine, There are two levels of the algorithm to consider when it comes to ambiguities. The first is the alignment anchoring, which is using spaced seeds to find strings of gap-free matches among the input sequences. For this, the sequences become encoded in a two-bit representation, e.g. 00 for A, 01 for C, etc. Any IUPAC ambiguity that contains an A will be collapsed to 00, any remaining ambiguity with a C will become 01, and so on for G and T. This means that for example M and S will not match in the two bit representation even though they could both encode a C. However, the anchoring tolerates mismatches in positions dictated by the seed pattern, see the Darling et al 2006 WABI publication for more details about those seed patterns. Second, once a set of anchors have been selected, progressiveMauve is using the MUSCLE algorithm to compute the gapped alignment between anchors and to subsequently refine the alignment around anchors. In this stage the sequences, with any IUPAC codes, are passed onto MUSCLE. For details about how MUSCLE handles these characters I think your best bet is to inquire with Bob Edgar, who should be able to give the authoritative answer. Best, -Aaron On Fri, 2016-11-04 at 15:03 +0000, Christine Jandrasits wrote: > Dear mauve-users, > > I am trying to align sequences with a lot of ambiguous DNA bases (M, > R, W, S, Y, ...) with progressiveMauve and I was wondering how the > tool is handling these. > > E.g. is the pair (A, M) considered a match or mismatch? How about (M, > R)? > (M = A or C; R = A or G). Are ambigiuous bases even considered when > matching or are they replaced by "N" as with some other (alignment-) > tools? > > I tried to find my answer through the used substitution matrix but > all references to the HOXD matrix only contain A, T, C, G... > > Thanks in advance, > Christine > ------------------------------------------------------------------- > ----------- > Developer Access Program for Intel Xeon Phi Processors > Access to Intel Xeon Phi processor-based developer platforms. > With one year of Intel Parallel Studio XE. > Training and support from Colfax. > Order your platform today. http://sdm.link/xeonphi > _______________________________________________ > 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: Christine J. <chr...@gm...> - 2016-11-04 15:04:01
|
Dear mauve-users, I am trying to align sequences with a lot of ambiguous DNA bases (M, R, W, S, Y, ...) with progressiveMauve and I was wondering how the tool is handling these. E.g. is the pair (A, M) considered a match or mismatch? How about (M, R)? (M = A or C; R = A or G). Are ambigiuous bases even considered when matching or are they replaced by "N" as with some other (alignment-) tools? I tried to find my answer through the used substitution matrix but all references to the HOXD matrix only contain A, T, C, G... Thanks in advance, Christine |
From: Aaron D. <aar...@ut...> - 2016-10-17 19:42:42
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Hi Karla, The "1. no extension" file you mention is the XMFA file. Now, onto your question about LCB boundaries, the quantities you are asking for actually ill-defined. The issue is that when unequal gene content is present in a genome alignment, and there are three or more genomes involved, it is no longer possible to precisely delimit the boundaries of LCBs. The blocks reported by progressiveMauve can have (but do not always have) arbitrary endpoints that do not necessarily indicate exactly where the rearrangement breakpoint is located. Nevertheless, if you want to simply convert the coordinates in the XMFA, which use a coordinate system defined by concatenating all contigs in a genome in the order they appear in the input file, to contig-local coordinates that should be possible, and would require you to do a bit of custom scripting. Best, -Aaron On Fri, 2016-10-07 at 12:13 -0300, Karla Pollyanna wrote: > Dear all, > > I'm struggling in a Mauve analysis and wonder if someone could help > me. > > I'm studying 13 genomes from diff bacteria and I performed a > progressiveMauve alignment from the graphical interface using > the last version of Mauve snapshot for Linux (2015-02-13). > > I have as output the follow files: 1. no extension (I use to open the > graphical interface); 2. .backbone; 3. .bbcols ; 4. .guide_tree. > > I would like to have the coordinates from LCBs, since I have multiple > genomes and they have up to 900 scaffolds. As example, I would like > to an output such as: > > scaffold start end genome > strand > > NZ_KB902575.1 1695199 1695311 - > > I checked in the list and saw an answer from Aaron about xmfa2maf > but, since I don't have a .xmfa file I tried it but I got a kinda NT > file that does not have every LCB. > > Does anyone know how can I get what I'm looking for? > > Thank you in advance. > > Best, > > > > Sent with Mailtrack > > Karla Pollyanna Vieira de Oliveira > Biologist / MSc. Bioinformatics, Laboratório de Tecnologias > Integradas (InteLab) +55 48 9133-9078 | +55 31 987-677-667 | karla.b > iot...@gm... | ka...@in... | Skype: > karla_pollyanna > > Get a signature like this: Click here! > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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: Brian C. <bec...@fl...> - 2016-10-17 18:34:47
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I recently updated my windows box to windows10. Since that time I have been unable to have a mauve complete successfully. The last run that I did..after selecting to run mauve as administrator..looked perfectly normal until it reached the end of the session..and mauve kicked back this error: done. root alignment has 369 superintervals root alignment length: 2905108 Organisms have 52.4% GCBig fat generic zero 1 Exited with error code: -2147483645 Any ideas? -- Brian Erich Caplin, Ph.D. Chief Science Officer Fluoresentric, Inc <http://www.fluoresentric.com/>. Hand-held NAAT Device <http://fluoresentric.com/xcr-in-action/> www.fluoresentric.com bec...@fl... *O:* 800.808.0490 *F:* 800.808.0490 *C:* 801.580.0490 “bringing something to awareness always dissolves what one has previously accepted" -Hans-Georg Gadamer *CONFIDENTIALITY STATEMENT:* The information contained in this email and any attachment is privileged, confidential, proprietary, and trade secret. It is intended only for the use of the individual named above. If you are not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message is prohibited. If you have received this message in error, please advise the sender by reply e-mail, and delete this message and any attachments. |
From: Aaron D. <aar...@ut...> - 2016-10-17 18:32:05
|
Hi Thierry, good question about the gap file & column headers. The first columns are as described by the file headers. The subsequent columns come in triplets, one triplet for each aligned genome, containing the following information: 1. The genomic position of the gap 2. The name of the chromosome where the gap is located 3. The contig-local position of the gap I agree this is confusing and this information should be added to the file headers in a future Mauve release. As for your second question, there is currently no way to produce a reordered GenBank format file with the contig mover. If you've got automatically generated annotations, then if possible I would suggest running the annotation after reordering contigs. Best, -Aaron On Wed, 2016-10-12 at 17:09 +0200, Thierry K.S. Janssens wrote: > Dear Dr. Darling/Aaron, > > I have a small question regarding the interpretation of the > coordinates > in the exported gap file. > The headers in this tab delimited file is less than the nuber of > colums. > This makes the interpretation cumbersome. > > Could you also give a hint how to maintain the annotations in from > the > Genbank, beyond the first iteration of the contig reordering? > > Thank you in advance for a short explanation on this. > > kind regards, > > Thierry Janssens > > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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...> - 2016-10-17 17:32:08
|
Hi LiXiang, The time complexity of the progressiveMauve algorithm scales at least cubically in the number of genomes being aligned, with length being an additional approximately n log n factor. In practice that means that the upper limit for progressiveMauve is usually datasets of around 30- 50 bacterial genomes. It should finish if you continue to wait, but you may be waiting a very long time. Depending on your analysis goals one option may be to reduce the set of input genomes. Do you need pan- genome alignment or just core genome alignment? If a core genome alignment is sufficient for your subsequent analysis tasks, you might have a look at the Harvest tools (parsnp, gingr) by Treangen et al. Best, -Aaron On Sun, 2016-10-16 at 17:04 +0800, LiXiangchen wrote: > Hi all, > > I used to run progressiveMauve with 49 bacterial genomes, each genome > is about 13MB. The job has been running for three weeks and is still > running now. Since I just use all default parameters, I have no idea > to improve it. > > Can you give me any suggestions? I am very grateful. > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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: LiXiangchen <lix...@ou...> - 2016-10-16 09:04:22
|
Hi all, I used to run progressiveMauve with 49 bacterial genomes, each genome is about 13MB. The job has been running for three weeks and is still running now. Since I just use all default parameters, I have no idea to improve it. Can you give me any suggestions? I am very grateful. |