Mugsy Error: Can't find delta file....
So I dug out this aligner called Mugsy. I followed the instructions here and got the following error:
~~$ mugsy --directory mugsy_alignment/ --prefix mygenomes spombe_mugsy.fasta scaff2/full/alignment3/scaff2.final.scaffolds.fasta
Parsing sequences for spombe_mugsy num_seqs:3
Parsing sequences for scaff2 num_seqs:513
2 genomes
Starting Nucmer: Tue Nov 24 12:21:35 CST 2015
sh: mugsy_alignment/mygenomes.spombe_mugsy.queries.fsa: No such file or directory
.sh: mugsy_alignment/mygenomes.spombe_mugsy.filt.delta: No such file or directory
Nucmer search failed. Can't find delta file mugsy_alignment/mygenomes.spombe_mugsy.filt.delta at /home/software/mugsy_x86-64-v1r2.3/mugsy line 839.
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1 answer
Hi rajeha,
I had the same problem but when looking at mugsy --help I found that --directory must be an absolute path. This solved the problem for me.
Phil
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