Help with Mugsy

Question

[teresa.noviello89]

Hi. Here again another error with mugsy. I'm trying to align the genomes of human, mouse and zebrafish for a conservation analysis.

I had some problem with the installation that I have resolved but some other issues came out.

Here's the error. Can you help me? Thanks

./mugsy --directory /home/noviello/mugsy_x86-64-v1r2.3/prova/ --prefix HMZ hg38.fa mm10.fa danRer7.fa
Parsing sequences for hg38  num_seqs:455
Parsing sequences for mm10  num_seqs:66
Parsing sequences for danRer7  num_seqs:1133
3 genomes
Starting Nucmer: gio  7 gen 2016, 10.02.05, CET
..
Finished Nucmer ven  8 gen 2016, 07.26.49, CET
Starting MUGSYWGA: ven  8 gen 2016, 07.26.49, CET
sh: line 1: 27762 Abortito                /home/noviello/mugsy_x86-64-v1r2.3/mugsyWGA --outfile /home/noviello/mugsy_x86-64-v1r2.3/prova/HMZ --seq /home/noviello/mugsy_x86-64-v1r2.3/prova/HMZ.all.fsa --aln /home/noviello/mugsy_x86-64-v1r2.3/prova/HMZ.xmfa --distance 1000 --minlength 30 --unique true > /home/noviello/mugsy_x86-64-v1r2.3/prova/HMZ.mugsywga.out 2> /home/noviello/mugsy_x86-64-v1r2.3/prova/HMZ.mugsywga.stderr
system /home/noviello/mugsy_x86-64-v1r2.3/mugsyWGA --outfile /home/noviello/mugsy_x86-64-v1r2.3/prova/HMZ --seq /home/noviello/mugsy_x86-64-v1r2.3/prova/HMZ.all.fsa --aln /home/noviello/mugsy_x86-64-v1r2.3/prova/HMZ.xmfa --distance 1000 --minlength 30  --unique true  > /home/noviello/mugsy_x86-64-v1r2.3/prova/HMZ.mugsywga.out 2> /home/noviello/mugsy_x86-64-v1r2.3/prova/HMZ.mugsywga.stderr failed: 34304: at ./mugsy line 933.

[Jean-Karim Heriche]

Check what the program is trying to do when it fails i.e. check what line 933 is doing and in which context.

[hillary.figler]

Did you get Mugsy to work? I'm having the same problem.

[teresa.noviello89]

No, unfortunately I had always the same error and I let it go. Sorry if I can't help you

[terence.strobaugh]

I also have the same problem.

[Jean-Karim Heriche]

The mugsyWGA command aborted (error code 34304 / 256 = 134, signal is 134 - 128 = 6 = SIGABRT). Try to figure out why: Do you have correct permissions on all the files and directories ? Does it run out of memory ? Are the input data in the correct format ?