Mauve aligner without SML files

Hi!

I am trying to use mauve via command line for whole genome alignment;

./mauveAligner --weight=300 --output-alignment=fifty_isolates.alignment Autumn2013_ALT_17.gbk 1.gbk.sml  Spring2012_ALT_27.gbk 2.gbk.sml --id-matrix= id_matrix.txt

I get this error:

Error: Each sequence file must have a corresponding SML file specified.

Indeed the sml files are non existent, however, and I quote the manual:

Each sequence must have a corresponding Sorted Mer List (SML) file name given. If the SML file does not exist, mauveAligner will create it.

Nothing in the options is related to SML file creation, what's the catch?!

next-gen alignment

• 3,316 views • link

updated 4.3 years ago by Ram

• written 11.5 years ago by norhanmahfouz •

problem solved!

• 0 views • link

written 11.4 years ago by norhanmahfouz •

Hey, I realize this was a long time ago, but I'm having the same problem and keep running into roadblocks. How did you solve it?

• 0 views • link

written 10.8 years ago by Pryce Michener •

Erm OK...mind saying how you solved the problem?

• 0 views • link

written 8.7 years ago by Thomas

0 answers

No answers yet.

More posts like this

Help with mauve
written 2.4 years ago by reachedahead225 •

Hi I have downloaded my genomes and they wont work it comes as error and there is a gap in the alignment I will put …
masurca invalid forward file for PE library
written 2.6 years ago by m.t.lorenc •

Hi, I ran into the following problem: ``` > singularity run --bind /scratch/masurca/:/data /pkg/containers/masurca_4.1.0.sif masurca /data/NRotund.cfg Error line 17 of configuration file '/data/NRotund.cfg': invalid forward …
error in Genome Mepping by BWA tools in Linux
written 3.3 years ago by drkuldeepbiotech •

$ gmap_build -D:\btau8refflat.gtf Unknown option: D:btau8refflat.gtf -k flag not specified, so building main hash table with default 15-mers -j flag not specified, so building regional …
Trying to make a Mauve alignment with 2 sequences and keep getting error code 3
written 3.4 years ago by jblac83 •

I'm trying to create an alignment with two sequences in Mauve (Windows) and keep getting error code 3. I tried using different formats for my …
Masurca hybrid assembly throwing Error correction of PE reads failed error
written 5.5 years ago by Pac314 •

I am trying to run my first hybrid assembly with MaSuRCA 3.2.7 with the following config file: DATA PE= pe 350 50 /fullpath/R1.fastq.gz /fullpath/R2.fastq.gz #JUMP= …
Masurca genome kunitg not finishing
written 6.1 years ago by olivier_armant •

Dear all, I am trying to use masurca to assembl a large vertebrate genome (estimated 4 to 5Gb) from illumina PE (coverage near 100X), MP …
masurca runCA failed
written 7.4 years ago by mariachiaracascarano •

Hi everybody still a newbie in bioinformatics, stuck on masurca 3.3.0... any help will be more than welcome. I am trying to assemble a bacterial …
Mauve on Ubuntu 16
written 9.8 years ago by marongiu.luigi

Dear all, I installed Mauve with the following: apt-get install mauve-aligner and then I ran it with the following: mauveAligner --output=ery.mauve --output-alignment=ery.alignment ery_multiseq.fasta where ery_multiseq.fasta …
Tutorial: InsideDNA: Analysing raw sequencing reads with FASTQC for quality control and filtering
written 10.2 years ago by shilparaopradeep •

Quality control and filtering of sequencing reads is one of the most important steps in the pre-processing of sequencing reads. However, it is not always …
Mauvealigner Error
written 13.1 years ago by HG

<p>Dear All, I used MIRA for genome assembly and i got contigfile " Ecoli-1_out.unpadded.fasta". Now i want to do alignment with this contig with another …