henan.jiang posted a comment on discussion Help

Hi, I used nucmer to align two maize genomes and generated a delta file about 2G. I then used delta-filter to filter out desired alignment with command: delta-filter -r -q delta.file, this command has run a week without output and error message. I tried to use this command with smaller bacterial genomes and it can generate the output. Has anyone encountered the same problem and how do you solve it?

Manoj Kumar posted a comment on discussion Help

Hi, I am trying to identify repeat regions in the reference sequence and masked using Mummer. I tried the following command at Mummer. However, it gives the regions in a text file. Please let me know how to get the fasta file after masking the repeats so I can use these masked fasta file for Smalt software. repeat-match ref_seq.fasta > ref_seq.repeats Output file:: Start1 Start2 Length 906850 1399638r 72 184976 1399638r 72 351538 1399638r 72

TATIANA posted a comment on ticket #1

I got a mummer error. I ran mummer for two weeks, and it crashed due to low memory last night. One chromosome was left to be processed. Is it possible to run the mummer only on the remaining chromosome and combine the outputs?

Blue cookies strain modified a comment on discussion Open Discussion

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james modified a comment on discussion Open Discussion

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james posted a comment on discussion Open Discussion

Hi, what will be the best possibility to get the best choice of, i am very curios to know about the facts and figures to know more about the best mvp development company i am tried your projects its awesom no doubt, but now i want to explore myself. Thanks

james modified a comment on discussion Open Discussion

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james posted a comment on discussion Open Discussion

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james modified a comment on discussion Open Discussion

Hi, Many Thanks for asking, I knew its a tool late but i want to help you with my all. So I recommend you to please read these guidelines step by step and i am sure this will surely helps you alot to solve your problem.

james posted a comment on discussion Open Discussion

Hi, Many Thanks for asking, I knew its a tool late but i want to help you with my all. So I recommend you to please read these guidelines step by step and i am sure this will surely helps you alot to solve your problem.

ambika Pokhrel posted a comment on discussion Help

Hello everyone, I am following one paper https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2486-8 in order to distinguish the core and accessory chromosomes of several genomes that I am working with. For this I did PROmer alignment, and generated the output files (delta and coords files). From the paper they say that the scaffolds with >=30% of their length covered by unique promer matches to core chromosomes of reference genome were considered core chromosomes and the rest as accessory...

Juliana M K C Perseguini posted a comment on discussion Help

Hi everyone. I'm starting my bioinformatics analysis. I have never worked with Linux, so I have some difficulties. My goal is to compare a nitrogen fixing bacterium genome with the reference genome of this same bacterium. I used the following commands: mummer -mum -b -c B_SEMIA_5080.fasta Bradycontig.fasta > BradyM.mums To build the graph I used the command: mummer --postscript --prefix=BradyM BradyM.mums But Linux returns me with the following message: Can't use 'defined(%hash)' (Maybe you should...

Tom2021 posted a comment on discussion Help

Steps to reproduce the issue [root@centos8 spack-src]# run-mummer1 docs/web/examples/data/B_anthracis_contigs.fasta docs/web/examples/data/B_anthracis_Mslice.fasta out.align -r Find MUMs tail: cannot open '+2' for reading: No such file or directory # reading input file "docs/web/examples/data/B_anthracis_contigs.fasta" of length 308869 # construct suffix tree for sequence of length 308869 # (maximum reference length is 536870908) # (maximum query length is 4294967295) # process 3088 characters per...

Fernando Cruz created ticket #3

[MUMMER/4.0.0beta2] nucmer4 --genome option and segmentation fault

Jonathan Gonzalez posted a comment on discussion Help

I found that the issue is in the R script DotPlotly. This problem results when DotPlotly -m is set to 5kb or higher.

Jonathan Gonzalez posted a comment on discussion Help

Hello, I am excited to use Mummer/Nucmer, and am running an alignment between a couple of small datasets and comparing this to the output from a Mauve alignment (same data). My ref dataset has 3 contigs, my query dataset has 4. For some reason, a large portion of one of the contigs in the query dataset appears to have moved to a different contig. The query contigs (C4s12 and C4s13) are of nearly the same length, but in the Nucmer alignment, C4s12 is much shorter, and the missing region appears to...

Aaron posted a comment on discussion Help

Hello, I downloaded the Mummergpu 2.0 package ，make，and then run “mummergpu ecoli.fa r1.fa” . There is an "Unknow Error" in the function of CUDA_SAFE_CALL, so i change the function to cudaError_t,but i get error about "stack smashing detected". Anyone could help me? Thanks Best regards.

Emily Crantell posted a comment on discussion Help

Hello everyone, I am brand new to this software and I will need a little help to align two sequences. I have downloaded the files in FASTA format and I know that the usage is the following: mummer -mum -b -c ref.fasta qry.fasta > ref_qry.mums but can someone please show me how this is done with a real example, step by step. Also, I am not sure where to find the query that is required and how do I save it in .mums format. I appreciate your help and support!

Moritz Blumer posted a comment on discussion Help

Hello, I am trying to figure out a way to adress the following problem: I have a eukaryotic genome assembly that is split up into two FASTA files: (1) The first file contains a reference assembly with numerous scaffolds; (2) the second file features scaffolds that carry allelic versions of genes that also appear in (1). I am interested in detecting those allelic gene versions that differ from their equivalent in file (1) by short indels (frameshifts, especially premature stop codons). Would Nucmer...

LIYY posted a comment on ticket #9

Dear Adam: I have this trouble, too.I got the reason,but How to solve ? Split my sequence?OR change Makerfile?How to change? Thanks, LIYY

Jessika Nordin posted a comment on discussion Help

Hi, I'm trying to get a dot-plot with mummerplot. When I run mummerplot mega.tiling there is no problems at all. But when I try to run mummerplot with a delta file I get the following error no matter which parameters I include (mummerplot mega.delta -R canFam3.1.fa -Q Mischka.megabubbles.fasta -filter -layout or mummerplot mega.delta or any combination): "out.gp", line 3376: integer overflow; change to floating point WARNING: Unable to run 'gnuplot -geometry 500x500+0+0 -title mummerplot out.gp',...

Juliana Eschholz posted a comment on discussion Help

Hi I uploaded the MUmmer, did the make check and then make install and everything is correct. But I was using another program (Mix) and when I put the command: serv@Serv:~/MIX-master$/preprocessing.py nucmer --maxmatch -c 30 -l 30 -banded -prefix=alignments /home/serv/MIX-master/contigs.fa Usage: preprocessing.py [options] preprocessing.py: error: no such option: --maxmatch I got problems. Soon I took the Nucmer again and put the command to test if it was working, command: sudo apt-get install nucmer...

Stephen Williams posted a comment on discussion Help

I have a filtered delta file that is making a 12x12 comparison. I am successful when plotting the filtered file but the strongest alignments are not on the diagonal when using the -layout preference. I thought it might be because one of my .fasta files uses "chr" and the other uses "Chr". When I change the header from chr ->Chr everything falls apart. mummer returns an error seem below. Here are my two trials Successful: delta-filter -l 150 -i 95 -u 95 -r results.delta.fasta > results.filter.delta.fast...

Stefano Romano modified a comment on discussion Help

I have a multi fasta containing 100s of gene clusters. I would like to align them...

Stefano Romano posted a comment on discussion Help

I have a multi fasta containing 100s of gene clusters. I would like to align them...

ebioman posted a comment on discussion Help

Hello You could compile it with make CPPFLAGS="-O3 -DSIXTYFOURBITS" Which will allow...

Kamil S Jaron posted a comment on discussion Help

Hi, I facing the same problem. I have investigated bit further. It is a segementation...

Kamil S Jaron created ticket #19

code dumped for no obvious reson

Anthony Bayega posted a comment on discussion Help

Hi, I need some help here. I was trying to obtain a mummer plot using; mummerplot...

Nithya .K V modified a comment on discussion Open Discussion

Hi all, I am very new to the tool MUMMER. I tried to create MUMMERplot using one...

Nithya .K V posted a comment on discussion Open Discussion

Nithya .K V Nithya .K V 1 hour ago Hi all, I am very new to the tool MUMMER. I tried...

Nithya .K V posted a comment on discussion Help

Hi all, I am very new to the tool MUMMER. I tried to create MUMMERplot using one...

Mahul Chakraborty posted a comment on discussion Help

Hi, I am using mummer (nucmer) to create a dotplot between the genome assemblies...

Adam Phillippy created ticket #18

Unnecessary mouse format option in mummerplot

Won Cheol Yim created ticket #17

Nucmer generated core dump.

MUMmer released /OldFiles/4th_brochure.pdf

Enzo posted a comment on discussion Help

Hi all, I am doing alignment between wheat sequences (query) and rice reference genome....

Milo created ticket #2

nucmer - postnuc hang on step 4 FINISHING DATA

stredger modified a comment on discussion Help

Yea, so shells don't like spaces in paths! The makefile is trying to perform the...

stredger posted a comment on discussion Help

Yea, so shells don't like spaces in paths! The makefile is trying to perform the...

Peter posted a comment on discussion Help

Hi, I have basically the same problem. I use mummer as a part of the quast package....

Muhammad posted a comment on discussion Help

HI We are looking for lateral gene transfer between insect and bacterial and for...

Muhammad posted a comment on discussion Help

Hi, I am trying to compare two genomes (of insect and bacteria) I did run with nucmer...

Leighton Pritchard created ticket #16

nucmer fails on FASTA input with no line-wrapping