Mauve on Ubuntu 16

Question

[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 is the fasta file with the different sequences I want to align; each sequence has a unique name. The file is 13 Mb and the average sequence's length is 1.2 Mb. The output was:

Sequence loaded successfully.
ery_multiseq.fasta 1876490 base pairs.
Sequence loaded successfully.
ery_multiseq.fasta 1876490 base pairs.
Sequence loaded successfully.
ery_multiseq.fasta 1752910 base pairs.
Sequence loaded successfully.
ery_multiseq.fasta 1752910 base pairs.
Sequence loaded successfully.
ery_multiseq.fasta 1787941 base pairs.
Sequence loaded successfully.
ery_multiseq.fasta 1787941 base pairs.
Sequence loaded successfully.
ery_multiseq.fasta 346770 base pairs.
Sequence loaded successfully.
ery_multiseq.fasta 398993 base pairs.
Sequence loaded successfully.
ery_multiseq.fasta 454198 base pairs.
Sequence loaded successfully.
ery_multiseq.fasta 731061 base pairs.
Using 15-mers for initial seeds
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 0 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 0 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 0 seconds.
Creating sorted mer list
Create time was: 0 seconds.
0%..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%..27%..28%..29%..30%..
31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..Starting with 43306 MUMs
Eliminating overlaps yields 43767 MUMs
Multiplicity filter gives 0 MUMs

The ery.mauve file contained:

FormatVersion   4
SequenceCount   10
Sequence0File   ery_multiseq.fasta
Sequence0Length 1876490
Sequence1File   ery_multiseq.fasta
Sequence1Length 1876490
Sequence2File   ery_multiseq.fasta
Sequence2Length 1752910
Sequence3File   ery_multiseq.fasta
Sequence3Length 1752910
Sequence4File   ery_multiseq.fasta
Sequence4Length 1787941
Sequence5File   ery_multiseq.fasta
Sequence5Length 1787941
Sequence6File   ery_multiseq.fasta
Sequence6Length 346770
Sequence7File   ery_multiseq.fasta
Sequence7Length 398993
Sequence8File   ery_multiseq.fasta
Sequence8Length 454198
Sequence9File   ery_multiseq.fasta
Sequence9Length 731061
IntervalCount   0

whereas the ery.alignment was completely empty.

What did I do wrong?

Many thanks

[marongiu.luigi]

PS: launching the GUI version I got the error: "the sequences might not have any homologous regions" which silly since the sequences are from variants of the same species

Answer 1

[h.mon]

I think Mauve assumes one genome (or set of related reads) per file, so it tries to align one or more sequences from one file to one or more sequences of a second (and third, fourth, etc) file. Did you try splitting each sequence into a file and passing all files to Mauve?

mauveAligner --output=ery.mauve --output-alignment=ery.alignment ery_seq1.fasta ery_seq2.fasta ery_seqN.fasta