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From: annalisa g. <ann...@ho...> - 2016-05-24 14:15:36
|
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 500Error in XMFA file formatBefore line 463Expecting 340 characters based on deflineActually read 397 characters of sequenceException InvalidFileFormat thrown fromUnknown() 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 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: Lu H. <luh...@gm...> - 2016-04-12 11:57:00
|
Hi Dan, Bring this to class, I'll show you! The hard part is getting RAST annotation and re-aligned contigs to "talk". See you soon, Luisa On Mon, Apr 11, 2016 at 4:38 PM, Daniel Evans <dr...@an...> wrote: > I am a student at the University of Pittsburgh who is trying to export a > multiple-contig genome sequence from Mauve into a .gbk, .fasta, or other > file type that can be used for annotation. > > I reordered the contigs of our sequence to match a reference sequence but > haven't been able to export (or copy) this reordered sequence for further > study. Is there a function in Mauve that would accomplish this? > > Thanks, > > Dan Evans > University of Pittsburgh > Department of Microbiology and Molecular Genetics > > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > > -- Luisa Hiller Ph.D. Department of Biological Sciences Carnegie Mellon University 4400 Fifth Avenue Pittsburgh, PA 15213 and Allegheny Health Network Center of Excellence for Biofilm Research tel: 412-268-2081 |
From: Aaron D. <aar...@ut...> - 2016-04-11 23:08:06
|
Hi Dan, When the reorderer module runs, it creates a series of folders called alignmentN inside the chosen output location. These contain successive runs of the reordering algorithm, which continues either until the contig ordering converges or a defined limit on the number of iterations is reached. Inside each of those alignmentN subfolders is a contigs fasta file that contains the reordered contigs produced at that iteration. It sounds like that is the file you're seeking, so no need to do any further processing/export. Best, -Aaron On Mon, 2016-04-11 at 16:38 -0400, Daniel Evans wrote: > I am a student at the University of Pittsburgh who is trying to export > a multiple-contig genome sequence from Mauve into a .gbk, .fasta, or > other file type that can be used for annotation. > > > I reordered the contigs of our sequence to match a reference sequence > but haven't been able to export (or copy) this reordered sequence for > further study. Is there a function in Mauve that would accomplish > this? > > > Thanks, > > > Dan Evans > University of Pittsburgh > Department of Microbiology and Molecular Genetics > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > _______________________________________________ > 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: Daniel E. <dr...@an...> - 2016-04-11 21:09:04
|
I am a student at the University of Pittsburgh who is trying to export a multiple-contig genome sequence from Mauve into a .gbk, .fasta, or other file type that can be used for annotation. I reordered the contigs of our sequence to match a reference sequence but haven't been able to export (or copy) this reordered sequence for further study. Is there a function in Mauve that would accomplish this? Thanks, Dan Evans University of Pittsburgh Department of Microbiology and Molecular Genetics |
From: Tagliamonte,Massimiliano S <mst...@uf...> - 2016-03-02 18:52:00
|
Dear Aaron, Dear Mauvers, I am using ProgressiveMauve 20150226 in Windows 8.1 (GUI) and trying to align 28 viral genomes (~10,000 bp). I have single fasta files, which seem to be in the correct format to me. When trying to align them, I receive the following exception: Exception FileNotOpened thrown fromSequence loaded successfully. C:\Users\...\filename.fasta 10649 base pairs. Unknown() in ..\libGenome\gnFileSource.cpp 67 Called by Unknown() Exited with error code: -1073741811 Trying several times, the name of the offending file changes. If I remove 3 or 4 sequences (not even the ones mentioned in the exception), the program runs just fine. Have I hit some kind of threshold? Do I need to increase the memory dedicated to Mauve in some way (i.e. through Java)? Please advice. Thanks for your help, Max Massimiliano S. Tagliamonte Graduate Student University of Florida College of Veterinary Medicine Department of Infectious Diseases and Pathology |
From: Ahmad R. <ra...@sl...> - 2016-02-20 19:25:27
|
Hello, I read in the online manual, under *Computing a pairwise breakpoint distance matrix, *that "Prior to alignment, progressiveMauve attempts to compute a conservative estimate of the number of rearrangement breakpoints among any pair of genomes." Is it possible to obtain this number? Thanks, Ahmad |
From: Maria M. D. <mar...@sy...> - 2016-02-15 20:37:06
|
Dear Aaron, Thanks for answering. At the moment I'm trying in the HPC system of the university and I could run 20 genomes in one core with 20 cpu in less than two hours. So it seems that it was a problem of computer resources. But is good to know that I should keep my comparison under 50 genomes. Thanks again. Elena Elena Martinez Postdoctoral Research Fellow Centre for Infectious Diseases and Microbiology Level 3, ICPMR Building, Westmead Hospital PO Box 533 Wentworthville NSW 2145 Ph (+612) 9845 5541 mar...@sy... ________________________________ From: Aaron Darling [aar...@ut...] Sent: Tuesday, February 16, 2016 6:14 AM To: mau...@li... Subject: Re: [Mauve-users] problems when scaling number of samples error 134, libc++abi.dylib: terminating Hi Elena, How much RAM does the computer running progressiveMauve have? The software's memory requirements grow quickly with additional sequences, and with the degree of divergence among those sequences, and it seems likely that running out of memory could cause the problems you are observing. I would suggest trying this alignment on a machine with at least 32GB RAM. However, I can't rule out an implementation bug from the error messages you indicated. Finally, please note that as you go beyond 50 bacterial genomes you will quickly reach the practical limits of the current algorithm as the running time and memory required become excessive. Best, -Aaron On Mon, 2016-02-15 at 00:38 +0000, Maria Martinez Diaz wrote: Dear All Mauve users, I have been trying to run an alignment in mauve but it is continuously finishing with an error message when I scale the number of isolates. I have 34 genomes from M. abscessus (one annotated reference , two complete genenomes, contigs download from NCBI, and contigs generated by me from fastq). I have arranged the contigs using the tools in mauve and check that the gbk from the reference has the sequence at the end as suggested in blogs. I run a test with only two of each kind of files in the snapshot_2015-02-25 in a mac pro computer and it finish without error. However, when I scale to 34 or even 20 samples it has finish once with error 11 and another time with error 134 after running for more than 6 hours. Greedy BPE Scoring with scaled breakpoint penalty: 86146.9 1%..2%..3%..4%..5%..6%..7%..8%..9%.. 10%..11%..12%..13%..14%..15%..16%..17%..18%..19%.. 20%..21%..22%..23%..24%..25%..26%..done Arrived at 24 intervals Adding unaligned intervals addUnalignedIntervals yields 67 intervals Merging unaligned intervals Marbling gaps Propagating descendant breakpoints descendant 0(29) has 48 intervals descendant 1(36) has 1 intervals propagateDescendantBreakpoints yields 71 intervals Creating ancestral ordering Previous anchoring score: 6.71385e+08, new anchor score: 1.31356e+09 Backing up alignment tree... propagating ancestral breakpoints recursive anchor search 0,0 have 821 new matches outside LCBs 1,0 have 1100 new matches outside LCBs 2,0 have 1097 new matches outside LCBs 3,0 have 1483 new matches outside LCBs libc++abi.dylib: terminating Exited with error code: 134 Much appreciate your help. Thanks, Elena Martinez Postdoctoral Research Fellow Centre for Infectious Diseases and Microbiology Level 3, ICPMR Building, Westmead Hospital PO Box 533 Wentworthville NSW 2145 Ph (+612) 9845 5541 mar...@sy... ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140<redir.aspx?REF=JMXbhwhzOvY2bfKv06B-PQJKkPosOmJonq_CuWRSxZh34lg0RzbTCAFodHRwOi8vcHViYWRzLmcuZG91YmxlY2xpY2submV0L2dhbXBhZC9jbGs_aWQ9MjcyNDg3MTUxJml1PS80MTQw> _______________________________________________ Mauve-users mailing list Mau...@li...<redir.aspx?REF=cIn5ue8Wf4A5jPp_4W-Mv10tPwH2TQhptfsTzPSfvGl34lg0RzbTCAFtYWlsdG86TWF1dmUtdXNlcnNAbGlzdHMuc291cmNlZm9yZ2UubmV0> https://lists.sourceforge.net/lists/listinfo/mauve-users<redir.aspx?REF=aDUAeFfIYlKYBOehKWniPrWooAJ3dp2ecxeVDefs9Nd34lg0RzbTCAFodHRwczovL2xpc3RzLnNvdXJjZWZvcmdlLm5ldC9saXN0cy9saXN0aW5mby9tYXV2ZS11c2Vycw..> -- 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...> - 2016-02-15 19:15:01
|
Hi Elena, How much RAM does the computer running progressiveMauve have? The software's memory requirements grow quickly with additional sequences, and with the degree of divergence among those sequences, and it seems likely that running out of memory could cause the problems you are observing. I would suggest trying this alignment on a machine with at least 32GB RAM. However, I can't rule out an implementation bug from the error messages you indicated. Finally, please note that as you go beyond 50 bacterial genomes you will quickly reach the practical limits of the current algorithm as the running time and memory required become excessive. Best, -Aaron On Mon, 2016-02-15 at 00:38 +0000, Maria Martinez Diaz wrote: > Dear All Mauve users, > > > > > I have been trying to run an alignment in mauve but it is continuously > finishing with an error message when I scale the number of isolates. > > I have 34 genomes from M. abscessus (one annotated reference , two > complete genenomes, contigs download from NCBI, and contigs generated > by me from fastq). I have arranged the contigs using the tools in > mauve and check that the gbk from the reference has the sequence at > the end as suggested in blogs. I run a test with only two of each kind > of files in the snapshot_2015-02-25 in a mac pro computer and it > finish without error. However, when I scale to 34 or even 20 samples > it has finish once with error 11 and another time with error 134 after > running for more than 6 hours. > > > > > > > Greedy BPE > Scoring with scaled breakpoint penalty: 86146.9 > 1%..2%..3%..4%..5%..6%..7%..8%..9%.. > 10%..11%..12%..13%..14%..15%..16%..17%..18%..19%.. > 20%..21%..22%..23%..24%..25%..26%..done > Arrived at 24 intervals > Adding unaligned intervals > addUnalignedIntervals yields 67 intervals > Merging unaligned intervals > Marbling gaps > Propagating descendant breakpoints > descendant 0(29) has 48 intervals > descendant 1(36) has 1 intervals > propagateDescendantBreakpoints yields 71 intervals > Creating ancestral ordering > Previous anchoring score: 6.71385e+08, new anchor score: 1.31356e+09 > Backing up alignment tree... > propagating ancestral breakpoints > recursive anchor search > 0,0 have 821 new matches outside LCBs > 1,0 have 1100 new matches outside LCBs > 2,0 have 1097 new matches outside LCBs > 3,0 have 1483 new matches outside LCBs > libc++abi.dylib: terminating > Exited with error code: 134 > > > > Much appreciate your help. > > > > Thanks, > > > > > Elena Martinez > Postdoctoral Research Fellow > > Centre for Infectious Diseases and Microbiology > Level 3, ICPMR Building, Westmead Hospital > PO Box 533 Wentworthville NSW 2145 > > Ph (+612) 9845 5541 > > mar...@sy... > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > 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: Maria M. D. <mar...@sy...> - 2016-02-15 00:38:56
|
Dear All Mauve users, I have been trying to run an alignment in mauve but it is continuously finishing with an error message when I scale the number of isolates. I have 34 genomes from M. abscessus (one annotated reference , two complete genenomes, contigs download from NCBI, and contigs generated by me from fastq). I have arranged the contigs using the tools in mauve and check that the gbk from the reference has the sequence at the end as suggested in blogs. I run a test with only two of each kind of files in the snapshot_2015-02-25 in a mac pro computer and it finish without error. However, when I scale to 34 or even 20 samples it has finish once with error 11 and another time with error 134 after running for more than 6 hours. Greedy BPE Scoring with scaled breakpoint penalty: 86146.9 1%..2%..3%..4%..5%..6%..7%..8%..9%.. 10%..11%..12%..13%..14%..15%..16%..17%..18%..19%.. 20%..21%..22%..23%..24%..25%..26%..done Arrived at 24 intervals Adding unaligned intervals addUnalignedIntervals yields 67 intervals Merging unaligned intervals Marbling gaps Propagating descendant breakpoints descendant 0(29) has 48 intervals descendant 1(36) has 1 intervals propagateDescendantBreakpoints yields 71 intervals Creating ancestral ordering Previous anchoring score: 6.71385e+08, new anchor score: 1.31356e+09 Backing up alignment tree... propagating ancestral breakpoints recursive anchor search 0,0 have 821 new matches outside LCBs 1,0 have 1100 new matches outside LCBs 2,0 have 1097 new matches outside LCBs 3,0 have 1483 new matches outside LCBs libc++abi.dylib: terminating Exited with error code: 134 Much appreciate your help. Thanks, Elena Martinez Postdoctoral Research Fellow Centre for Infectious Diseases and Microbiology Level 3, ICPMR Building, Westmead Hospital PO Box 533 Wentworthville NSW 2145 Ph (+612) 9845 5541 mar...@sy... |
From: Aaron D. <aar...@ut...> - 2016-02-12 05:02:01
|
Hi Taher, Can you tell us a bit more about the sequences you're trying to align, and give the command-line you ran to create the alignment? From the log it looks like you've got a large number of very short (~400nt?) sequences. progressiveMauve wasn't really designed for this kind of input, and while it may work, you're likely to get better results with standard multiple sequence alignment programs. The output should be in whatever file was specified with the --output option on the command-line. Have you checked? Best, -Aaron On Wed, 2016-02-10 at 14:41 +0300, UZ ZAMAN, TAHER wrote: > We would like to seek your help and guidance in resolving this > problem. We were using Progressive –Mauve aligner to generate > multi-fasta alignment files and we got this problem. We were unable to > get the output files. I’m herewith enclosing the snapshot of the > screen. Please advise. > > > > Best regards > > > > Taher > > > > Riyadh, Saudi Arabia. > > > > > > > > > > ______________________________________________________________________ > This Email and any files transmitted may contain confidential and/or > privileged information and is intended solely for the addressee(s) > named. If you have received this information in error, or are being > posted by accident, please notify the sender by return Email, do not > redistribute this email message, delete it immediately and keep no > copies of it. All opinions and/or views expressed in this email are > solely those of the author and do not necessarily represent those of > NGHA. Any purchase order, purchase advice or legal commitment is only > valid once backed by the signed hardcopy by the authorized person from > NGHA. > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > 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: UZ Z. T. <uzzamanta@NGHA.MED.SA> - 2016-02-10 11:41:47
|
We would like to seek your help and guidance in resolving this problem. We were using Progressive -Mauve aligner to generate multi-fasta alignment files and we got this problem. We were unable to get the output files. I'm herewith enclosing the snapshot of the screen. Please advise. Best regards Taher Riyadh, Saudi Arabia. ________________________________ This Email and any files transmitted may contain confidential and/or privileged information and is intended solely for the addressee(s) named. If you have received this information in error, or are being posted by accident, please notify the sender by return Email, do not redistribute this email message, delete it immediately and keep no copies of it. All opinions and/or views expressed in this email are solely those of the author and do not necessarily represent those of NGHA. Any purchase order, purchase advice or legal commitment is only valid once backed by the signed hardcopy by the authorized person from NGHA. |
From: Susan B. F. <fo...@ug...> - 2016-02-09 18:41:37
|
Hi Prabh, I was never able to work around the error and visualize the core extraction. I can import the fasta into geneious and look at the alignment that way but when I do that my annotations are lost. Sorry I can’t be of assistance. -S From: Prabh Basra [mailto:bas...@gm...] Sent: Tuesday, February 09, 2016 11:08 AM To: Susan Beth Fogelson Cc: mau...@li... Subject: Re: [Mauve-users] stripsubsetLCBs error Hi Susan I was wondering if you were able to visualize the care alignment in the GUI. It continues to give me the following error: Exception in thread "Thread-4" java.lang.ArrayIndexOutOfBoundsException: genome E.fergusonii_ATCC.fasta position 1 at org.gel.mauve.XMFAAlignment.getLCB(Unknown Source) at org.gel.mauve.XMFAAlignment.getRange(Unknown Source) at org.gel.mauve.SimilarityIndex.calculateIndex(Unknown Source) at org.gel.mauve.SimilarityIndex.<init>(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(Thread.java:745) Thanks Prabh On Jan 25, 2016, at 4:45 PM, Susan Beth Fogelson <fo...@ug...<mailto:fo...@ug...>> wrote: Hi Aaron, My first issue is that I ran the alignment on my PC using the windows version, which in turn used my local/external hard drive for the path’s. I didn’t realize that when I ran the alignment so to fix it I tried to write a substitution statement to replace the paths so that it would be pointing to the correct directory when I moved the file into my linux server to extract the core alignment. I finally just broke down and re-ran the alignment using the linux version so that the paths would be consistent throughout the whole process. The original alignments were run using each genome in its own file. Once I ran the alignments on the linux server I was easily able to extract the LCBs and build a core alignment. Once you extract the LCB’s and concatenate them into one file, are you able to visualize the resultant core file in the Mauve windows GUI? When I try to do this the program says it is reading the sequences but nothing ever appears on the screen. -Susan From: Aaron Darling [mailto:aar...@ut...] Sent: Sunday, January 24, 2016 7:58 PM To: mau...@li...<mailto:mau...@li...> Subject: Re: [Mauve-users] stripsubsetLCBs error Hi Susan, what operating system are you using, and what operating system was the alignment done with? Have you tried moving the sequence files, alignment file, and .bbcols to be located in the same directory? If done carefully, it should be possible to do a total search & replace on pathnames to strip them out of the XMFA (e.g. to replace the directory name with nothing), which might help if there are some troublesome characters in the path names. It might also help us help you if you were to copy & paste the paths involved into the next email. The suggestion to improve the error message about which file failed to open is a good one, I agree it's unfortunately generic and vague. Chances are high that it's failing on the first sequence file in your alignment. One last question, did you run the original alignment from a single multifasta, or with each genome sequence in its own file? Best, -Aaron On Fri, 2016-01-22 at 18:53 +0000, Susan Beth Fogelson wrote: Hello, I am attempting to extract the LCBs from my genome alignment and I am getting the common error message: Exception FileNotOpened thrown from Unknown() in gnFileSource.cpp 67 Called by Unknown() Read 28814 backbone entries seq_count is: 0 From previous post this means that one of the paths in my xmfa file is not correct so the files cannot be opened. I have been through the file 5 times now and cannot find an abnormality in the paths to my files. Is there a way to get more information about which file the program can’t open just to give me a more focused search for the error in my file? Thank you for your time -Susan ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ Mauve-users mailing list Mau...@li...<mailto: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<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. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________ Mauve-users mailing list Mau...@li...<mailto:Mau...@li...> https://lists.sourceforge.net/lists/listinfo/mauve-users |
From: Prabh B. <bas...@gm...> - 2016-02-09 16:08:37
|
Hi Susan I was wondering if you were able to visualize the care alignment in the GUI. It continues to give me the following error: Exception in thread "Thread-4" java.lang.ArrayIndexOutOfBoundsException: genome E.fergusonii_ATCC.fasta position 1 at org.gel.mauve.XMFAAlignment.getLCB(Unknown Source) at org.gel.mauve.XMFAAlignment.getRange(Unknown Source) at org.gel.mauve.SimilarityIndex.calculateIndex(Unknown Source) at org.gel.mauve.SimilarityIndex.<init>(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(Thread.java:745) Thanks Prabh > On Jan 25, 2016, at 4:45 PM, Susan Beth Fogelson <fo...@ug...> wrote: > > Hi Aaron, > > > My first issue is that I ran the alignment on my PC using the windows version, which in turn used my local/external hard drive for the path’s. I didn’t realize that when I ran the alignment so to fix it I tried to write a substitution statement to replace the paths so that it would be pointing to the correct directory when I moved the file into my linux server to extract the core alignment. I finally just broke down and re-ran the alignment using the linux version so that the paths would be consistent throughout the whole process. The original alignments were run using each genome in its own file. > > > Once I ran the alignments on the linux server I was easily able to extract the LCBs and build a core alignment. Once you extract the LCB’s and concatenate them into one file, are you able to visualize the resultant core file in the Mauve windows GUI? When I try to do this the program says it is reading the sequences but nothing ever appears on the screen. > > > -Susan > > From: Aaron Darling [mailto:aar...@ut...] > Sent: Sunday, January 24, 2016 7:58 PM > To: mau...@li... > Subject: Re: [Mauve-users] stripsubsetLCBs error > > Hi Susan, what operating system are you using, and what operating system was the alignment done with? > Have you tried moving the sequence files, alignment file, and .bbcols to be located in the same directory? > If done carefully, it should be possible to do a total search & replace on pathnames to strip them out of the XMFA (e.g. to replace the directory name with nothing), which might help if there are some troublesome characters in the path names. It might also help us help you if you were to copy & paste the paths involved into the next email. > > The suggestion to improve the error message about which file failed to open is a good one, I agree it's unfortunately generic and vague. Chances are high that it's failing on the first sequence file in your alignment. > > One last question, did you run the original alignment from a single multifasta, or with each genome sequence in its own file? > > Best, > -Aaron > > On Fri, 2016-01-22 at 18:53 +0000, Susan Beth Fogelson wrote: > Hello, > > > > I am attempting to extract the LCBs from my genome alignment and I am getting the common error message: > > Exception FileNotOpened thrown from > > Unknown() in gnFileSource.cpp 67 > > Called by Unknown() > > Read 28814 backbone entries > > seq_count is: 0 > > > > From previous post this means that one of the paths in my xmfa file is not correct so the files cannot be opened. I have been through the file 5 times now and cannot find an abnormality in the paths to my files. Is there a way to get more information about which file the program can’t open just to give me a more focused search for the error in my file? Thank you for your time > > > > -Susan > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 <http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140> > _______________________________________________ > 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 <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. > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users |
From: Susan B. F. <fo...@ug...> - 2016-02-09 15:30:25
|
Hi Gopi, If you go to the link I gave you, the attachment is at the top of the first posting from Lu Cheng. It is a very small font and blue. -S From: Gopi Nath [mailto:its...@gm...] Sent: Tuesday, February 09, 2016 4:50 AM To: Susan Beth Fogelson Cc: mau...@li... Subject: Re: [Mauve-users] How to extract the alignment sequence Hi Susan, Thank you for the information. I have been trying to look at the xmfa2fasta.pl<http://xmfa2fasta.pl> script mentioned in the third step, but unfortunately it is not available. Do you have any idea if it has been to some other location ? On Wed, Feb 3, 2016 at 9:12 PM, Susan Beth Fogelson <fo...@ug...<mailto:fo...@ug...>> wrote: Hi Gopi, If I understand you correctly, you are trying to extract the LCBs from your alignments. I used the stripsubsetsLCB command to do this with the genomes I am working with. The only issue I had was that if you ran your alignment in the Windows GUI and not using Linux then the path names won’t recognize the input files. Below is the link to the linux commands that I used. Hope this is helpful. http://sourceforge.net/p/mauve/mailman/mauve-users/thread/51F...@he.../ -Susan From: Gopi Nath [mailto:its...@gm...<mailto:its...@gm...>] Sent: Wednesday, February 03, 2016 1:58 PM To: mau...@li...<mailto:mau...@li...> Subject: [Mauve-users] How to extract the alignment sequence Hi, I have aligned 5 bacterial genomes using the progressiveMauve. I would like to extract the part of the alignment having sequence in all the genome (eg: second and fourth line positions) using the alignment(.xmfa) file and backbone(.backbone) file. seq0_leftend seq0_rightend seq1_leftend seq1_rightend seq2_leftend seq2_rightend seq3_leftend seq3_rightend seq4_leftend seq4_rightend 0 0 23127 23463 20107 20443 32207 32543 29528 29864 -28145 -28315 23464 23633 20444 20613 32544 32713 29865 30034 0 0 23634 23814 20614 20794 32714 32894 30035 30215 -27824 -28003 23815 23997 20795 20977 32895 33077 30216 30398 Is there any utility to achieve this task ? How to extract only the lines having sequence from all the genomes(eg: 2nd, 4th) ? Thanks. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ Mauve-users mailing list Mau...@li...<mailto:Mau...@li...> https://lists.sourceforge.net/lists/listinfo/mauve-users |
From: Gopi N. <its...@gm...> - 2016-02-09 09:50:22
|
Hi Susan, Thank you for the information. I have been trying to look at the xmfa2fasta.pl script mentioned in the third step, but unfortunately it is not available. Do you have any idea if it has been to some other location ? On Wed, Feb 3, 2016 at 9:12 PM, Susan Beth Fogelson <fo...@ug...> wrote: > Hi Gopi, > > > > If I understand you correctly, you are trying to extract the LCBs from > your alignments. I used the stripsubsetsLCB command to do this with the > genomes I am working with. The only issue I had was that if you ran your > alignment in the Windows GUI and not using Linux then the path names won’t > recognize the input files. Below is the link to the linux commands that I > used. Hope this is helpful. > > > > > http://sourceforge.net/p/mauve/mailman/mauve-users/thread/51F...@he.../ > > > > > > -Susan > > > > *From:* Gopi Nath [mailto:its...@gm...] > *Sent:* Wednesday, February 03, 2016 1:58 PM > *To:* mau...@li... > *Subject:* [Mauve-users] How to extract the alignment sequence > > > > Hi, > > > > I have aligned 5 bacterial genomes using the progressiveMauve. I would > like to extract the part of the alignment having sequence in all the genome > (eg: second and fourth line positions) using the alignment(.xmfa) file and > backbone(.backbone) file. > > > > > > seq0_leftend seq0_rightend seq1_leftend seq1_rightend seq2_leftend > seq2_rightend seq3_leftend seq3_rightend seq4_leftend seq4_rightend > > 0 0 23127 23463 20107 20443 32207 32543 29528 29864 > > *-28145 -28315 23464 23633 20444 20613 32544 32713 29865 30034* > > 0 0 23634 23814 20614 20794 32714 32894 30035 30215 > > *-27824 -28003 23815 23997 20795 20977 32895 33077 30216 30398* > > > > > > Is there any utility to achieve this task ? How to extract only the lines > having sequence from all the genomes(eg: 2nd, 4th) ? > > > > Thanks. > > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > Mauve-users mailing list > Mau...@li... > https://lists.sourceforge.net/lists/listinfo/mauve-users > > |
From: Susan B. F. <fo...@ug...> - 2016-02-03 19:46:04
|
Hi Gopi, If I understand you correctly, you are trying to extract the LCBs from your alignments. I used the stripsubsetsLCB command to do this with the genomes I am working with. The only issue I had was that if you ran your alignment in the Windows GUI and not using Linux then the path names won’t recognize the input files. Below is the link to the linux commands that I used. Hope this is helpful. http://sourceforge.net/p/mauve/mailman/mauve-users/thread/51F...@he.../ -Susan From: Gopi Nath [mailto:its...@gm...] Sent: Wednesday, February 03, 2016 1:58 PM To: mau...@li... Subject: [Mauve-users] How to extract the alignment sequence Hi, I have aligned 5 bacterial genomes using the progressiveMauve. I would like to extract the part of the alignment having sequence in all the genome (eg: second and fourth line positions) using the alignment(.xmfa) file and backbone(.backbone) file. seq0_leftend seq0_rightend seq1_leftend seq1_rightend seq2_leftend seq2_rightend seq3_leftend seq3_rightend seq4_leftend seq4_rightend 0 0 23127 23463 20107 20443 32207 32543 29528 29864 -28145 -28315 23464 23633 20444 20613 32544 32713 29865 30034 0 0 23634 23814 20614 20794 32714 32894 30035 30215 -27824 -28003 23815 23997 20795 20977 32895 33077 30216 30398 Is there any utility to achieve this task ? How to extract only the lines having sequence from all the genomes(eg: 2nd, 4th) ? Thanks. |
From: Gopi N. <its...@gm...> - 2016-02-03 18:58:00
|
Hi, I have aligned 5 bacterial genomes using the progressiveMauve. I would like to extract the part of the alignment having sequence in all the genome (eg: second and fourth line positions) using the alignment(.xmfa) file and backbone(.backbone) file. seq0_leftend seq0_rightend seq1_leftend seq1_rightend seq2_leftend seq2_rightend seq3_leftend seq3_rightend seq4_leftend seq4_rightend 0 0 23127 23463 20107 20443 32207 32543 29528 29864 *-28145 -28315 23464 23633 20444 20613 32544 32713 29865 30034* 0 0 23634 23814 20614 20794 32714 32894 30035 30215 *-27824 -28003 23815 23997 20795 20977 32895 33077 30216 30398* Is there any utility to achieve this task ? How to extract only the lines having sequence from all the genomes(eg: 2nd, 4th) ? Thanks. |
From: Mark M. <m-m...@no...> - 2016-02-03 16:26:09
|
Hi Michael, You might check the old archives for this mailing list. The guide tree has been a hot topic. Here is an excerpted reply from Aaron two months ago: Re: [Mauve-users] Guide tree question From: Aaron Darling <darling@cs...> - 2015-12-08 19:32:34 Attachments: Message as HTML The vagueness in that file is at least partially intentional -- the tree doesn't have a well-established interpretation outside of being a reflection of the order in which genomes were aligned. I think it would be dangerous to interpret it as a phylogeny, especially as one intended to represent vertical inheritance, as the topology is shaped heavily by gene content and there are well documented cases where independent lineages have converged in gene content (e.g. Shigella) and I've seen the guide tree and phylogeny conflict strongly in such datasets. Best, -Aaron See above discussion at: http://sourceforge.net/p/mauve/mailman/message/34680079/ Full list archives at: http://sourceforge.net/p/mauve/mailman/mauve-users/ Search for “guide tree” Take care, Mark ------------------------------ Mark J. Mandel, Ph.D. Assistant Professor Department of Microbiology-Immunology Northwestern University Feinberg School of Medicine 320 E. Superior St., Searle 3-403 Chicago, IL 60611 m-m...@no... http://labs.feinberg.northwestern.edu/mandel/ (312) 503-4138 Office (312) 503-2915 Lab (312) 503-9594 Fax On February 3, 2016 at 9:25:09 AM, mic...@ag... (mic...@ag...<mailto:mic...@ag...>) wrote: After running progressiveMauve I get the usual guide tree which I want to draw as a Figure. No problem, so far so good… But in the case of mauve, how to interpret the branch lengths (or the corresponding numbers)? Normally this is the base changes in percent, as far as I understand. Does it have the same meaning for Mauve? Sry, but could not find this info otherwise. If someone can point to a place where this is documented, would be great! Michael ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140_______________________________________________ Mauve-users mailing list Mau...@li... https://lists.sourceforge.net/lists/listinfo/mauve-users |
From: <mic...@ag...> - 2016-02-03 15:23:20
|
After running progressiveMauve I get the usual guide tree which I want to draw as a Figure. No problem, so far so good... But in the case of mauve, how to interpret the branch lengths (or the corresponding numbers)? Normally this is the base changes in percent, as far as I understand. Does it have the same meaning for Mauve? Sry, but could not find this info otherwise. If someone can point to a place where this is documented, would be great! Michael |
From: Gopi N. <its...@gm...> - 2016-02-02 21:43:08
|
Hi, I have aligned 5 bacterial genomes using the progressiveMauve. I would like to extract the part of the alignment having sequence in all the genome (eg: second and fourth line positions) using the alignment(.xmfa) file and backbone(.backbone) file. seq0_leftend seq0_rightend seq1_leftend seq1_rightend seq2_leftend seq2_rightend seq3_leftend seq3_rightend seq4_leftend seq4_rightend 0 0 23127 23463 20107 20443 32207 32543 29528 29864 *-28145 -28315 23464 23633 20444 20613 32544 32713 29865 30034* 0 0 23634 23814 20614 20794 32714 32894 30035 30215 *-27824 -28003 23815 23997 20795 20977 32895 33077 30216 30398* Is there any utility to achieve this task ? How to extract only the lines having sequence from all the genomes(eg: 2nd, 4th) ? Thanks. |
From: Weigand, M. R. (CDC/OID/N. (CTR) <yr...@cd...> - 2016-02-01 17:21:05
|
Hi mauve users, I routinely use progressiveMauve via the command-line Linux x64 binary (snapshot 2015-02-13) to align closed bacterial genomes from many strains of the same species. These genomes differ very little in sequence (SNPS) and content (genes), but often have very heterogeneous structures due to rearrangements. I am attempting to characterize structural/rearrangement differences conserved among sub-sets of genomes, which are otherwise not collinear, by parsing the .backbone file. However, I frequently observe that backbone alignments of 'many' genomes (n>=50) are not consistent with alignments of 'few' genomes (n=5). That is to say, when inspecting LCBs or aligned sequence backbone blocks, the larger alignments often fail to match homologous stretches shared by a few genomes, while these same loci are matched in a smaller alignment. Further, my input is annotated genbank files and the genes in these un-matched blocks appear to be orthologs by manual inspection. In essence, the larger alignment 'over-calls' the number of LCBs shared by the set of genomes. These unmatched sequences are usually observable in the backbone file (and the xmfa) as additional strain-specific blocks (or LCBs), often of the same approximate length, like in this simplified example: seq0_leftend seq0_rightend seq1_leftend seq1_rightend 2123820 2129873 0 0 0 0 2123981 2129885 My approach to combat this has been to test many values for the parameters '-seed-weight' and '-hmm-identity', and select as the optimal combination that which produces the .backbone file with the fewest number of lines, ie. sequence blocks. The logic being that fewer unique blocks should mean fewer un-matched alignments between loci of 'true' homology shared between the genomes. This parameter optimization strategy has been successful, but only to a point, and analysis of the output still trips over apparent artifacts when I attempt to manually validate reported break-points with an independent alignment of 4-5 representative genomes. So I'm curious if other users have experienced similar issues of alignment reproducibility when scaling? If so, what approaches or parameters have been successful in making alignments of 'many' consistent with alignments of 'few'? Given that multiple alignments are 'built' from many pairwise alignments, I expect differences between n=2 and n=many alignments. Perhaps inputting a guide tree to control the order in which genomes should be added to the multiple alignment would help, particularly by first aligning genomes with the fewest rearrangement differences? I appreciate your suggestions and advice. Thanks. Mike ==================== Michael R. Weigand, PhD Bioinformatician | IHRC NCIRD/DBD/MVPDB Centers for Disease Control and Prevention MWe...@cd...<mailto:MWe...@cd...> 404.639.2473 |
From: Susan B. F. <fo...@ug...> - 2016-01-25 21:59:47
|
Hi Aaron, My first issue is that I ran the alignment on my PC using the windows version, which in turn used my local/external hard drive for the path’s. I didn’t realize that when I ran the alignment so to fix it I tried to write a substitution statement to replace the paths so that it would be pointing to the correct directory when I moved the file into my linux server to extract the core alignment. I finally just broke down and re-ran the alignment using the linux version so that the paths would be consistent throughout the whole process. The original alignments were run using each genome in its own file. Once I ran the alignments on the linux server I was easily able to extract the LCBs and build a core alignment. Once you extract the LCB’s and concatenate them into one file, are you able to visualize the resultant core file in the Mauve windows GUI? When I try to do this the program says it is reading the sequences but nothing ever appears on the screen. -Susan From: Aaron Darling [mailto:aar...@ut...] Sent: Sunday, January 24, 2016 7:58 PM To: mau...@li... Subject: Re: [Mauve-users] stripsubsetLCBs error Hi Susan, what operating system are you using, and what operating system was the alignment done with? Have you tried moving the sequence files, alignment file, and .bbcols to be located in the same directory? If done carefully, it should be possible to do a total search & replace on pathnames to strip them out of the XMFA (e.g. to replace the directory name with nothing), which might help if there are some troublesome characters in the path names. It might also help us help you if you were to copy & paste the paths involved into the next email. The suggestion to improve the error message about which file failed to open is a good one, I agree it's unfortunately generic and vague. Chances are high that it's failing on the first sequence file in your alignment. One last question, did you run the original alignment from a single multifasta, or with each genome sequence in its own file? Best, -Aaron On Fri, 2016-01-22 at 18:53 +0000, Susan Beth Fogelson wrote: Hello, I am attempting to extract the LCBs from my genome alignment and I am getting the common error message: Exception FileNotOpened thrown from Unknown() in gnFileSource.cpp 67 Called by Unknown() Read 28814 backbone entries seq_count is: 0 From previous post this means that one of the paths in my xmfa file is not correct so the files cannot be opened. I have been through the file 5 times now and cannot find an abnormality in the paths to my files. Is there a way to get more information about which file the program can’t open just to give me a more focused search for the error in my file? Thank you for your time -Susan ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 _______________________________________________ Mauve-users mailing list Mau...@li...<mailto: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...> - 2016-01-25 00:58:52
|
Hi Susan, what operating system are you using, and what operating system was the alignment done with? Have you tried moving the sequence files, alignment file, and .bbcols to be located in the same directory? If done carefully, it should be possible to do a total search & replace on pathnames to strip them out of the XMFA (e.g. to replace the directory name with nothing), which might help if there are some troublesome characters in the path names. It might also help us help you if you were to copy & paste the paths involved into the next email. The suggestion to improve the error message about which file failed to open is a good one, I agree it's unfortunately generic and vague. Chances are high that it's failing on the first sequence file in your alignment. One last question, did you run the original alignment from a single multifasta, or with each genome sequence in its own file? Best, -Aaron On Fri, 2016-01-22 at 18:53 +0000, Susan Beth Fogelson wrote: > Hello, > > > > I am attempting to extract the LCBs from my genome alignment and I am > getting the common error message: > > Exception FileNotOpened thrown from > > Unknown() in gnFileSource.cpp 67 > > Called by Unknown() > > Read 28814 backbone entries > > seq_count is: 0 > > > > From previous post this means that one of the paths in my xmfa file is > not correct so the files cannot be opened. I have been through the > file 5 times now and cannot find an abnormality in the paths to my > files. Is there a way to get more information about which file the > program can’t open just to give me a more focused search for the error > in my file? Thank you for your time > > > > -Susan > > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > 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: Susan B. F. <fo...@ug...> - 2016-01-22 19:09:00
|
Hello, I am attempting to extract the LCBs from my genome alignment and I am getting the common error message: Exception FileNotOpened thrown from Unknown() in gnFileSource.cpp 67 Called by Unknown() Read 28814 backbone entries seq_count is: 0 >From previous post this means that one of the paths in my xmfa file is not correct so the files cannot be opened. I have been through the file 5 times now and cannot find an abnormality in the paths to my files. Is there a way to get more information about which file the program can't open just to give me a more focused search for the error in my file? Thank you for your time -Susan |
From: Aaron D. <aar...@ut...> - 2016-01-19 19:32:42
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I can imagine there would be consistency between guide tree groups and serotype in some or even most cases but, if you want to group by serotype I am not sure the guide tree is a good proxy. But I know little about serotypes and how they work in various organisms. On Tue, 2016-01-19 at 10:02 -0500, Amarin Cogburn wrote: > Aaron, > > > > Could the guide tree be used to group samples within a serotype or > would that too be a misinterpretation? > > > -Amarin > > > On Tue, Dec 8, 2015 at 4:41 PM, Aaron Darling > <aar...@ut...> wrote: > > Hi Susan, > > On Tue, 2015-12-08 at 20:05 +0000, Susan Beth Fogelson wrote: > > > Thank you for all of your helpful responses. I guess at > > this point my question changes. I would like to build a > > phylogenetic tree of this alignment and I assume I need to > > convert the XMFA file to another format to complete this > > task. Has anyone had experience with file conversion and > > what program would you recommend for phylogenetic tree > > reconstruction? At present I am using MEGA6 but I think > > these files are too big for that program to run effectively. > > > There are many ways to build phylogenies from Mauve alignments > and hopefully others on the list will chime in with > suggestions. Once you have an initial tree, you might consider > ClonalFrameML as a way to help reduce the impact of historical > recombination events on tree inference: > https://github.com/xavierdidelot/clonalframeml/wiki > > Best, > -Aaron > -- > 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. > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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. |