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I have installed mugsy in order to create a multiple genome alignment and a phylogenetic tree of several species of nematodes. The following command successfully pulls out the help:

output/software/mugsy_x86-64-v1r2.3/mugsy -h

To test that the software is installed correctly and that I am using it correctly, I ran the following alignment between the Wormbase sequence and the Ensembl sequence of the C. elegans genome:

output/software/mugsy_x86-64-v1r2.3/mugsy  --directory /.../project/output/software/mugsy_x86-64-v1r2.3/ --prefix mygenomes output/genome/celegans/ref/wormbase/seq/c_elegans.PRJNA13758.WS263.genomic.fa output/genome/celegans/ref/ensembl/seq/celegans.fa

I get the following output:

Parsing sequences for c_elegans  num_seqs:7
Parsing sequences for celegans  num_seqs:1
Can't find species II dna at output/software/mugsy_x86-64-v1r2.3/mugsy line 501.

The headers of the wormbase sequences are:

>I
>II
>III
>IV
>V
>X
>MtDNA

and the headers of the ensembl sequences are:

>I dna:chromosome chromosome:WBcel235:I:1:15072434:1 REF
>II dna:chromosome chromosome:WBcel235:II:1:15279421:1 REF
>III dna:chromosome chromosome:WBcel235:III:1:13783801:1 REF
>IV dna:chromosome chromosome:WBcel235:IV:1:17493829:1 REF
>MtDNA dna:chromosome chromosome:WBcel235:MtDNA:1:13794:1 REF
>V dna:chromosome chromosome:WBcel235:V:1:20924180:1 REF
>X dna:chromosome chromosome:WBcel235:X:1:17718942:1 REF

Maybe this line: Parsing sequences for celegans num_seqs:1 should make me worry. Why does mugsy think there is only one sequence in that genome? Why do I get the following error and how can I fix it?:

Can't find species II dna at output/software/mugsy_x86-64-v1r2.3/mugsy line 501.

I am working on a GNU/Linux platform.

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