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From: Bruna P. S. <bru...@em...> - 2024-05-17 12:31:56
|
Please, I got some results using "nucmer" comparing 2 fungus nucmer -o -p output /home/bruna/Downloads/TrireR....fasta /home/bruna/Downloads/GCA_00331..fna and the results just showed me 4 "TAGS" >80% of identity. [S1] [E1] | [S2] [E2] | [LEN 1] [LEN 2] | [% IDY] | [TAGS] ===================================================================================== 132933 133217 | 545 803 | 285 259 | 83.86 | scaffold_36 QMFI01009651.1 311581 311663 | 21556 21474 | 83 83 | 98.80 | scaffold_7 QMFI01002420.1 311582 311663 | 21573 21492 | 82 82 | 98.78 | scaffold_7 QMFI01002420.1 153258 153397 | 5177 5038 | 140 140 | 87.32 | scaffold_8 QMFI01000981.1 Should I interpret that both genomes have *only *those "pieces" in common? I mean, what's statistics tells me about the *general idea* of homology/similarity between both? Running mummer -b -mumreference stdout repeat-match <ref 1> <ref2> I also did not understand what number would tell me this. Many thanks! Nice project! *Bruna Pena Sollero* Zootecnista, M.S., D.Sc. Pesquisadora A Laboratório de Bioinformática (LBI) Embrapa Recursos Genéticos e Biotecnologia -- Empresa Brasileira de Pesquisa Agropecuária - Embrapa Parque Estação Biológica - PqEB s/nº. Brasília, DF - Brasil - CEP 70770-901 -- __________________________ Aviso de confidencialidade Esta mensagem da Empresa Brasileira de Pesquisa Agropecuaria (Embrapa), empresa publica federal regida pelo disposto na Lei Federal no. 5.851, de 7 de dezembro de 1972, e enviada exclusivamente a seu destinatario e pode conter informacoes confidenciais, protegidas por sigilo profissional. Sua utilizacao desautorizada e ilegal e sujeita o infrator as penas da lei. Se voce a recebeu indevidamente, queira, por gentileza, reenvia-la ao emitente, esclarecendo o equivoco. Confidentiality note This message from Empresa Brasileira de Pesquisa Agropecuaria (Embrapa), a government company established under Brazilian law (5.851/72), is directed exclusively to its addressee and may contain confidential data, protected under professional secrecy rules. Its unauthorized use is illegal and may subject the transgressor to the law's penalties. If you are not the addressee, please send it back, elucidating the failure. |
From: Luigi M. <mar...@gm...> - 2024-01-23 13:59:54
|
Hello, I just installed MUMMER4 on Ubuntu 22. I generated the alignment with nucmer and wrote the file nucmer.accords after running show-coords -r ref.delta > qry.coords. I had to change the shebang of mummer/scripts/mapview.pl to `#!/usr/bin/env perl` otherwise it woul dnot launch in the first place. Afterward, I obtained an additional error: ``` $ perl ~/src/mummer/scripts/mapview.pl qry.coords Can't locate Foundation.pm in @INC (you may need to install the Foundation module) (@INC contains: @ /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl) at .../mummer/scripts/mapview.pl line 4. BEGIN failed--compilation aborted at ...mummer/scripts/mapview.pl line 4. ``` I cant' find any fundation package for perl. How can I run mapview on ubuntu? Thank you |
From: Adam P. <aph...@gm...> - 2022-09-28 19:56:50
|
Hi Poonam, There is a README in the install directory that gives a description of the column headers for the show-snps output (the .snps suffix) and the show-diff output (the *diff suffixes). In the docs/ directory, there is a dnadiff.README file that gives some description of the .report file. Best, -Adam On Wed, Sep 28, 2022 at 3:22 PM Poonam Chitale <pc...@gs...> wrote: > Hi, > > I am interested in using dnadiff to compare 2 highly similar strains of > Mycobacterium tuberculosis. > I was hoping someone could help me better understand the column > descriptions/headers of the out.snp file generated by DNAdiff? > > Please see attached for an example file that was generated when I ran > DNAdiff across 2 samples. > > Any help would be greatly appreciated! > > Thanks, > Poonam > > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > |
From: Poonam C. <pc...@gs...> - 2022-09-28 19:21:28
|
Hi, I am interested in using dnadiff to compare 2 highly similar strains of Mycobacterium tuberculosis. I was hoping someone could help me better understand the column descriptions/headers of the out.snp file generated by DNAdiff? Please see attached for an example file that was generated when I ran DNAdiff across 2 samples. Any help would be greatly appreciated! Thanks, Poonam |
From: babru s. <ba...@ya...> - 2022-03-29 22:51:31
|
MUMmer plot error at line 884. Could Adam or any one else help us to eliminate this problem? It is impossible for me at least to edit and change the script written in C++ to fix this. Thanks Babru There are many early reports of this error https://www.google.com/search?q=mummerplot+errors+884&ei=AoxDYpPUBd-eytMPo7Wp4Aw&ved=0ahUKEwiT3ev4suz2AhVfj3IEHaNaCswQ4dUDCA4&uact=5&oq=mummerplot+errors+884&gs_lcp=Cgxnd3Mtd2l6LXNlcnAQAzIFCCEQoAEyBQghEKABMgUIIRCgATIFCCEQoAE6BwgAEEcQsANKBAhBGABKBAhGGABQswdY3RZg1hpoAXABeACAAUiIAfkBkgEBNJgBAKABAcgBCMABAQ&sclient=gws-wiz-serp |
From: NOUR M. M. <nmm...@sc...> - 2022-03-14 12:39:34
|
Hello! I'm using MUMmer for the first time, and I'm running it on Ubuntu WSL, in case this information is relevant. I'm following the steps listed on your examples tutorial website<http://mummer.sourceforge.net/examples/#promer> using the following files: ecoli.fna and baumannii.fna I'm currently stuck at this step: 2.4.3. Running show-aligns To view all the pairwise alignments between two of the input sequences, we need to run the promer.delta file through the show-coords utility. show-aligns promer.delta "D_melanogaster_2Rslice" "3214968" > promer.aligns This command will print all of the pairwise alignments stored in the promer.delta file for the sequences "D_melanogaster_2Rslice" and "3214968". Output is to stdout, so we have redirected it into the file, promer.aligns. If the alignments do not fit within your screen width, or you would like them to be printed on longer lines, the screen width can be adjusted with the -w option. Since show-aligns only displays the alignments between two sequences, it will have to be run separately for each desired pair of sequences. >From what I've understood, the names between the double quotation marks are supposed to be the ref ID and the qry ID, but I have no idea where the number "3214968" came from in the command line on your website. and I have no idea what it's supposed to represent. In earlier steps, the file names used were D_melanogaster_2Rslice.fasta D_pseudoobscura_contigs.fasta so I can see where the D_melanogaster_2Rslice came from. I tried running the following codes, alongside all permutations of the sequence lengths and the names of the file: show-aligns promer.delta "ecoli" "baumanmnii" > promer.aligns show-aligns promer.delta "baumanmnii" "ecoli" > promer.aligns show-aligns promer.delta "baumanmnii" "9283306" > promer.aligns etc., etc., What confuses me even more, is that the step before it <http://mummer.sourceforge.net/examples/#:~:text=2.4.2.%20Running%20show%2Dcoords> (2.4.2) doesn't show the coordinates unless I delete the "> promer.coords" part and even when I do, the 2.4.3 step doesn't work. I would appreciate any input on what I'm meant to do now as I am very confused. If there are any other resources you could direct me to I would also be much obliged. Thank you in advance. Regards, Nour Mustafa |
From: Brook M. <br...@nm...> - 2021-06-18 22:08:05
|
I would like to offer a suggestion/patch for the mummer scripts/Makefile. Currently, you use the make variable BIN_DIR for two distinct purposes: - The location of various files within the source tree that you are manipulating with sed, and - The location of installed files that gets embedded within the scripts. If the files are moved, as they are by any packaging system, the embedded paths will be incorrect. As a result, it seems important to have separate make variables for the installed paths. The attached patch accomplishes this by adding make variables, for example, INSTALL_BIN_DIR, to use in the sed replacements. It should also achieve exactly the same thing as your current Makefile does, because the definitions of the new variables correspond to those of the variables they replace. Ideally these makefiles would use ${PREFIX} to create variables for installation purposes as many other projects do, but in the meantime this would be a helpful step forward. I hope you will consider committing this patch for the next release. Thank you very much. Cheers, Brook |
From: NOAH M. <na...@sc...> - 2021-04-03 21:14:24
|
Hi, I am trying to add my MUMmer path (/Users/noahmac/Documents/MUMmer3.23 ) to my system path (/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin)by PATH=/ When I use another directory to execute the scripts I still get the following error: no such file or directory: /nucmer. Thank you and I look forward to hearing from you as to what I need to do. -- V/r Noah Mac |
From: Daniel <dan...@pr...> - 2020-12-03 05:05:24
|
My third year comp sci friend got me this far, I hope you guys can help me with the last inch! For the record, I have practically no coding experience. I am using the 3.9.4 alpha version of MUMmer. Here is the manual I have been following: http://mummer.sourceforge.net/examples/ I am at part 2.2.2 Running the Mummer plot, and I type in the final line to generate the plot. I receive some sort of error (pictured below). [Mummer.jpg] After this I went to the line '884' in the program code and saw this. [Capture.JPG] I really dont know what the issue is. How can I generate the plot? I dont have enough coding experience to figure this out on my own. Best, Daniel |
From: Maia M. <mm...@yo...> - 2020-11-11 12:52:00
|
Hi there, I'm trying to run nucmer and compare a reference genome with a genome I assembled using this code: nucmer --maxmatch -l 100 -c 500 reference.fasta asm.fa I am running MUMmer 4.0.0beta2 and I am getting the following error: terminate called after throwing an instance of 'std::runtime_error' what(): First character must be a '>', got '' Aborted I have looked this error up and nothing seems to come up in relation to mummer, do you have any idea what might be causing this? I'd appreciate any suggestions. Many thanks, Maia Munteanu |
From: Adam P. <aph...@gm...> - 2020-07-13 14:35:38
|
Hi Adriana, I'm not familiar with the conda package, but it looks like it failed to find the right shell and so left it blank. That run-mummer1 script is very old and is a C-shell script. '#!/bin/csh -f' should work if you have it on your system. Best, -Adam On Tue, Jun 23, 2020 at 12:10 PM adriana gallego < adr...@gm...> wrote: > > Cordial greeting. Thank you so much for developing MuMmer, this is an > excellent tool. > > Currently I'm facing an issue which has not been discussed yet. When I run > run-mummer1 or exact-tandems, the next error comes out > > bash: /home/adriana/miniconda3/envs/mummer_env/bin/run-mummer1: -f bad > interpreter: No such file or directory > > I think this is related with the first line of the run-mummer1 and exact > tandems files which says > > #! -f > > I tested #!/usr/bin/perl, but it did not work > > Thanks for the help > > -- > *Adriana María Gallego Rúa* > *Investigadora **Laboratorio de Biotecnología* > *Universidad de Antioquia* > > *ColombiaMedellín-2020* > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > |
From: adriana g. <adr...@gm...> - 2020-06-23 16:10:24
|
Cordial greeting. Thank you so much for developing MuMmer, this is an excellent tool. Currently I'm facing an issue which has not been discussed yet. When I run run-mummer1 or exact-tandems, the next error comes out bash: /home/adriana/miniconda3/envs/mummer_env/bin/run-mummer1: -f bad interpreter: No such file or directory I think this is related with the first line of the run-mummer1 and exact tandems files which says #! -f I tested #!/usr/bin/perl, but it did not work Thanks for the help -- *Adriana María Gallego Rúa* *Investigadora **Laboratorio de Biotecnología* *Universidad de Antioquia* *ColombiaMedellín-2020* |
From: adriana g. <adr...@gm...> - 2020-06-16 17:23:02
|
Cordial greeting Im getting next issue when I try to run exact-tandems in Mummer (I used miniconda to install mummer) I dont know what -f means bash: /home/adriana/miniconda3/envs/mummer_env/bin/exact-tandems: -f: wrong interpreter: No file or directory exist Thanks Adriana |
From: Adam P. <aph...@gm...> - 2020-03-25 17:54:56
|
Hi, Is this mummer3 or mummer4? If you update to mummer4, large reference genomes shouldn't cause such errors. Best, -Adam On Wed, Mar 25, 2020 at 1:49 PM Hanschen, Erik Richard via MUMmer-help < mum...@li...> wrote: > > > Hi, > > > > I’m getting the following error when attempting to run Nucmer. I’m running > it on 1 core with plenty (500G) of memory available. > > > > $ nucmer --maxmatch --prefix="test" REF.fna CONTIGS.fna > > > > > > Output: > > 1: PREPARING DATA > > 2,3: RUNNING mummer AND CREATING CLUSTERS > > # reading input file "REF.ntref" of length 535387449 > > # construct suffix tree for sequence of length 535387449 > > # (maximum reference length is 536870908) > > # (maximum query length is 4294967295) > > # process 5353874 characters per dot > > #......................................................................ERROR: > mummer and/or mgaps returned non-zero > > ERROR: Could not parse delta file, test.delta > > error no: 400 > > Loading reference REF.fna ... > > Loading query CONTIGS.fna... > > > > I’ve read on the help forums that this is likely due to too large of > multi-fasta sequences and splitting the file into two. However, is > splitting the reference or contig file preferred? Should splitting be done > based on even number of sequences or even length of sequences? > > Thanks, > Erik > > > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > |
From: Hanschen, E. R. <han...@la...> - 2020-03-25 17:48:59
|
Hi, I’m getting the following error when attempting to run Nucmer. I’m running it on 1 core with plenty (500G) of memory available. $ nucmer --maxmatch --prefix="test" REF.fna CONTIGS.fna Output: 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS # reading input file "REF.ntref" of length 535387449 # construct suffix tree for sequence of length 535387449 # (maximum reference length is 536870908) # (maximum query length is 4294967295) # process 5353874 characters per dot #......................................................................ERROR: mummer and/or mgaps returned non-zero ERROR: Could not parse delta file, test.delta error no: 400 Loading reference REF.fna ... Loading query CONTIGS.fna... I’ve read on the help forums that this is likely due to too large of multi-fasta sequences and splitting the file into two. However, is splitting the reference or contig file preferred? Should splitting be done based on even number of sequences or even length of sequences? Thanks, Erik |
From: Begum, N. <nee...@kc...> - 2020-01-15 15:34:45
|
Dear all, I desperately require some help. For some reason my nucmer is giving me error. 1: PREPARING DATA 2,3: RUNNING mummer AND CREATING CLUSTERS # reading input file nucmer_output/ba_vs_ca.ntref" of length 2975538 # construct suffix tree for sequence of length 2975538 # (maximum reference length is 536870908) # (maximum query length is 4294967295) # process 29755 characters per dot #....................................... 4: FINISHING DATA ERROR: Could not parse delta file, error no: 400 Could you help me in correcting this error? Regards N |
From: Adam P. <aph...@gm...> - 2019-12-12 23:26:22
|
Hello, Those are all small repetitive alignments, which are occluding the other alignments. Try running: > delta-filter -m 191212mummer-10xNanko_oldPmref.delta > 191212mummer-10xNanko_oldPmref.mdelta > mummerplot 191212mummer-10xNanko_oldPmref.mdelta --postscript Which should clean up the plot quite a bit. Best, -Adam On Thu, Dec 12, 2019 at 9:33 AM <r00...@nt...> wrote: > Dear mummer group: > > Good evening. > > Japanese apricot (Prunus mume) is our research specie, and we > conducted 10x genomics technique making a new genome by using genomic > DNA from Japanese cultivar. > Furthermore, we would like to compare the genomic difference between > publised Prunus mume genome (chinese cultivar) with the new > 10xgenomics Prunus mume genome. > > But the result of mummerplot showed very strange from the demo picture > from the mummer tutorial website. > > The steps we used as below: > nucmer -p 191212mummer-10xNanko_oldPmref > /data/share/genome/pmum/old-with/annotation-until2018/P.mume.genome.fa > > /data/public/hsiang/10x_sequencing/190812-test1-result/output_0817_prefix.1.fasta > mummerplot 191212mummer-10xNanko_oldPmref.delta --postscript > And the output files as below: > out.ps > out.rplot > out.gp > out.fplot > 191212mummer-10xNanko_oldPmref.delta > > FILES LINK: > https://drive.google.com/open?id=1wH1Xpt8r4MiZ050UPWWu0mUkeJFpZEqH > > > Could you give me some solutions and suggestions? > > Thank you very much > > Best wishes, > > > Clarence Hsiang > > > > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > |
From: <r00...@nt...> - 2019-12-12 14:32:57
|
Dear mummer group: Good evening. Japanese apricot (Prunus mume) is our research specie, and we conducted 10x genomics technique making a new genome by using genomic DNA from Japanese cultivar. Furthermore, we would like to compare the genomic difference between publised Prunus mume genome (chinese cultivar) with the new 10xgenomics Prunus mume genome. But the result of mummerplot showed very strange from the demo picture from the mummer tutorial website. The steps we used as below: nucmer -p 191212mummer-10xNanko_oldPmref /data/share/genome/pmum/old-with/annotation-until2018/P.mume.genome.fa /data/public/hsiang/10x_sequencing/190812-test1-result/output_0817_prefix.1.fasta mummerplot 191212mummer-10xNanko_oldPmref.delta --postscript And the output files as below: out.ps out.rplot out.gp out.fplot 191212mummer-10xNanko_oldPmref.delta FILES LINK: https://drive.google.com/open?id=1wH1Xpt8r4MiZ050UPWWu0mUkeJFpZEqH Could you give me some solutions and suggestions? Thank you very much Best wishes, Clarence Hsiang |
From: Uzma B. K. <Kh...@ca...> - 2019-04-23 20:45:08
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Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Uzma Basit Khan Sent: Tuesday, April 23, 2019 6:41:52 PM To: mum...@li... Subject: Help needed in running promer Hi trhere Happy Easter . Wishing you a bright and shining Easter filled with family and friends. I need your help in running a program PROMER given as a utility of MUmmer tool. Actually some of my contigs need to be ordered and oriented according to their alignment to strain 2603V/R by using PROMER (1). Ordered matching contigs needs to be pasted together into a pseudochromosome, and nonmatching contigs needs to be tacked on the end in random order. In the pseudochromosome, contigs will be separated by the sequence NNNNNCATTCCATTCATTAATTAATTAATGAATGAATGNNNNN, which (i) generates a stop codon in all six reading frames so that no gene is predicted across junctions and (ii) provides a start site in all frames, pointing toward contigs to predict incomplete genes at their extremities. I also need to use GLIMMER gene prediction to predict ORFs and annotate by using an automated pipeline that combines GLIMMER gene prediction (2,3). 1) Delcher, A. L., Phillippy, A., Carlton, J. & Salzberg, S. L. (2002) Nucleic Acids Res. 30 , 2478–2483. pmid:12034836 2) Delcher, A. L., Harmon, D., Kasif, S., White, O. & Salzberg, S. L. (1999) Nucleic Acids Res. 27 ,4636–4641. pmid:10556321 3) Salzberg, S. L., Delcher, A. L., Kasif, S. & White, O. (1998) Nucleic Acids Res. 26 , 544–548.pmid:9421513 PROMER which is a part of MUMMER tool available on accra as MUMmer/3.23 genomics module. I tried to run it on my two samples PHEGBS0041 and BS-S2208 used as a multi-fasta format file (named as example.fasta) using a reference 2603VR isolate (All attached herewith) . Following command lines were used 1) promer -p promer 2603VR.fasta examples.fasta 2) Running show-coords show-coords -r -c -l -L 100 -I 50 promer.delta > promer.coords where r is reference seq c is alignment coverage l sequence length (-L) is minimum length cutoffs (-I) is minimum percent identity cutoffs 3) Running show-aligns show-aligns promer.delta "2603VR_reference" "BS-S2208" > promer.aligns It produces all outputs but as empty files. I further downloaded example files provided at http://mummer.sourceforge.net/examples/#promer 1) D_melanogaster_2Rslice.fasta 2) D_pseudoobscura_contigs.fasta But this also produced empty output files. Can you please help me in pointing out where I did wrong. Thanks much Uzma |
From: oussrir a. <ous...@gm...> - 2019-04-23 10:41:18
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hello I want to use mummer to align two eukaryotic genomes, how can I do, knowing that each species has 4 chromosomes or more |
From: Youhanna S. D. Ph.D. <ysa...@gm...> - 2019-03-07 16:11:56
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Hello, I'm trying to install the mummer 4 beta under cygwin 64. and when i do "Make" the "make Install" there are error message reported below. could anyone please help me with this? also. how would i know that software installed properly regards John make makeall-am make[1]: Entering directory '/home/mummer-4.0.0beta2' CXXsrc/tigr/tigrinc.lo *src/tigr/tigrinc.cc:*In function ‘*FILE* File_Open(const char*, const char*)*’: *src/tigr/tigrinc.cc:19:14:*error: ‘*fileno*’ was not declared in this scope if(isatty(fileno(fp))) ^~~~~~ *src/tigr/tigrinc.cc:19:14:*note: suggested alternative: ‘*mblen*’ if(isatty(fileno(fp))) ^~~~~~ mblen make[1]: *** [Makefile:1861: src/tigr/tigrinc.lo] Error 1 make[1]: Leaving directory '/home/mummer-4.0.0beta2' make: *** [Makefile:1074: all] Error 2 makeinstall-am make[1]: Entering directory '/home/mummer-4.0.0beta2' CXXsrc/tigr/tigrinc.lo *src/tigr/tigrinc.cc:*In function ‘*FILE* File_Open(const char*, const char*)*’: *src/tigr/tigrinc.cc:19:14:*error: ‘*fileno*’ was not declared in this scope if(isatty(fileno(fp))) ^~~~~~ *src/tigr/tigrinc.cc:19:14:*note: suggested alternative: ‘*mblen*’ if(isatty(fileno(fp))) ^~~~~~ mblen make[1]: *** [Makefile:1861: src/tigr/tigrinc.lo] Error 1 make[1]: Leaving directory '/home/mummer-4.0.0beta2' make: *** [Makefile:2600: install] Error 2 |
From: Deepak K. <dee...@an...> - 2019-02-11 14:34:58
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Dear Mummer Users, I am trying to run mummer on 2 phage genomes and looking to generate the mapview figure. I have generated the coords file for the 2 phages (attached), and I also prepared a cds file for the reference (attached). And, then ran command: ./mapview -n 1 -f pdf -p mapview ref_qry.coords KP010413_1.cds but I keep getting error: ERROR in the input files ! The reference seq ID can't be found in GFF files ! The first column in the GFF file should be the ID of the reference seq. The alignments file should provide the same info in the column before the last one. Here are some example records for the GFF file: gnl|FlyBase|X Dmel3 initial-exon 2155 2413 . - . X_CG3038.1 gnl|FlyBase|X Dmel3 last-exon 1182 2077 . - . X_CG3038.1 ... The fields are : <seq_ID> <source> <exon type> <start> <end> <score> <strand> <frame> <gene_name> Please let me know what is the issue here; I would really appreciate. Thanks, DK ________________________________ From: Deepak Kumar Sent: Monday, February 11, 2019 5:10 PM To: mum...@li... Subject: Error when running mapview with cds Dear Mummer Users, I am trying to run mummer on 2 phage genomes and looking to generate the mapview figure. I have generated the coords file for the 2 phages (attached), and I also prepared a cds file for the reference (attached). And, then ran command: ./mapview -n 1 -f pdf -p mapview ref_qry.coords KP010413_1.cds but I keep getting error: ERROR in the input files ! The reference seq ID can't be found in GFF files ! The first column in the GFF file should be the ID of the reference seq. The alignments file should provide the same info in the column before the last one. Here are some example records for the GFF file: gnl|FlyBase|X Dmel3 initial-exon 2155 2413 . - . X_CG3038.1 gnl|FlyBase|X Dmel3 last-exon 1182 2077 . - . X_CG3038.1 ... The fields are : <seq_ID> <source> <exon type> <start> <end> <score> <strand> <frame> <gene_name> Please let me know what is the issue here; I would really appreciate. Thanks, DK |
From: Fatihah Y. <fat...@gm...> - 2018-11-08 02:42:49
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Hi, I am a newbie in perl and don't have much experience on this. Hope anyone could help. I managed to run “mummer" for the alignment between reference and query sequences. The problem occurred when I tried to plot using “mummerplot” following to the tutorial. mummerplot -x "[0,1000500]" -y "[0,50000000]" -postscript -p mummer mummer.mums Can't locate object method "new" via package "TIGR::Foundation" (perhaps you forgot to load "TIGR::Foundation"?) at /usr/local/bin/mummerplot line 187. I searched for any possible solution. Someone recommended to do "make clean" and "make", but it did not work either. I am using MacOS High Sierra if it could give any hint on the possible cause. Hope you could help. Thanks, Fateh |
From: Adam P. <aph...@gm...> - 2018-10-10 20:54:18
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A very rough explanation: All the alignment intervals on the reference and query are scored based on some combination of their length and identity, and a subset are marked as the "best" alignment for that region of the genome. -m keeps any alignment that is marked best on EITHER the reference OR query. -1 keeps only alignments that are marked best on BOTH the reference AND query. Another way of saying it: if there is a duplication in the query genome, -m will attempt to keep alignments from the ancestral copy in the reference to both paralogs in query. -1 will only keep the alignments between orthologs, and the duplication will remain unaligned. Both options are heuristics and don't always work perfectly, but can be helpful in reducing the number of repetitive alignments in the output. Best, -Adam On Sun, Oct 7, 2018 at 5:11 AM Arun Prasanna <aru...@gm...> wrote: > Hello, > > Can anyone please tell me the meaning of M-to-M alignments mean ? I > understood that 1-to-1 means number of unique alignments. > > Thanks, > AP > _______________________________________________ > MUMmer-help mailing list > MUM...@li... > https://lists.sourceforge.net/lists/listinfo/mummer-help > |
From: Arun P. <aru...@gm...> - 2018-10-07 09:11:05
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Hello, Can anyone please tell me the meaning of M-to-M alignments mean ? I understood that 1-to-1 means number of unique alignments. Thanks, AP |