mummer plot unable to parse alignment file

powoods · 07-21-2019, 08:25 AM

Hello,

I am currently trying to make a dotplot in order to compare the sequence similarity between a reference genome and an early stage reference genome that my own lab is constructing. The software I am using to do this is called "mummer".

To get an initial feel for how the mummer software works, I aligned one chromosome of the reference genome to itself since this should in theory produce a perfect diagonal line.

The code I used for this was:
mummer Chromosome1.fasta Chromosome1.fasta > Chromosome1.mums

Then to create a dotplot of this alignment file I used the following code:
mummerplot -postscript -p OUTPUT_plot Chromosome1.mums

This code created the perfectly diagonal line dot plot as predicted.

My issue is that when I try to use the same code to align two different sequences, mummerplot is not able to parse the alignment file.

Here is the code I am using:
mummer Chromosome1.fasta Scaffold1.fasta >Chrom1_v_Scaff1.mums
mummerplot -postscript -p OUTPUT_plot Chrom1_v_Scaff1.mums

The following error appears every time I align two different sequences and try to plot the alignment:
gnuplot 5.2 patchlevel 7
Reading mummer file Chrom1_v_Scaff1.mums (use mummer -c)
ERROR: Could not parse Chrom1_v_Scaff1.mums
26869245 25 82

I have tried all the other alignment programs in mummer including "-mum", "-maxmatch" and "-nucmer" and they all give the same error.

I would really appreciate a solution to this issue if anyone has one, thank you.

jdavik · 11-05-2020, 12:27 AM

Hi,
did you ever figure out a solution here? I'm running into the same issue.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
MUMmer plot full of dots and no diagonal lines	dbob	Bioinformatics	3	02-18-2016 08:41 AM
error unable to parse known snp	litali	Bioinformatics	0	10-06-2015 05:00 AM
Alignment of assembly to reference (nuclear genome) [MUMmer]	prs321	Bioinformatics	0	09-10-2013 11:48 AM
How to use the Bioperl to parse the parse flat file of UniProtKB database?	bewlib	Bioinformatics	1	11-29-2012 05:30 PM
Global Alignment With Mummer (Parameter for Gap Extension & Opening Cost)	peveralldubois	Bioinformatics	0	03-07-2011 12:45 AM

07-21-2019, 08:25 AM	#1
powoods Junior Member Location: Colorado Join Date: Jul 2019 Posts: 1	mummer plot unable to parse alignment file Hello, I am currently trying to make a dotplot in order to compare the sequence similarity between a reference genome and an early stage reference genome that my own lab is constructing. The software I am using to do this is called "mummer". To get an initial feel for how the mummer software works, I aligned one chromosome of the reference genome to itself since this should in theory produce a perfect diagonal line. The code I used for this was: mummer Chromosome1.fasta Chromosome1.fasta > Chromosome1.mums Then to create a dotplot of this alignment file I used the following code: mummerplot -postscript -p OUTPUT_plot Chromosome1.mums This code created the perfectly diagonal line dot plot as predicted. My issue is that when I try to use the same code to align two different sequences, mummerplot is not able to parse the alignment file. Here is the code I am using: mummer Chromosome1.fasta Scaffold1.fasta >Chrom1_v_Scaff1.mums mummerplot -postscript -p OUTPUT_plot Chrom1_v_Scaff1.mums The following error appears every time I align two different sequences and try to plot the alignment: gnuplot 5.2 patchlevel 7 Reading mummer file Chrom1_v_Scaff1.mums (use mummer -c) ERROR: Could not parse Chrom1_v_Scaff1.mums 26869245 25 82 I have tried all the other alignment programs in mummer including "-mum", "-maxmatch" and "-nucmer" and they all give the same error. I would really appreciate a solution to this issue if anyone has one, thank you.

11-05-2020, 12:27 AM	#2
jdavik Junior Member Location: Norway Join Date: Nov 2020 Posts: 1	mummrplot Hi, did you ever figure out a solution here? I'm running into the same issue.