Question: Help with Mugsy
0
gravatar for teresa.noviello89
3.8 years ago by
Italy
teresa.noviello890 wrote:

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 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.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by teresa.noviello890

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

ADD REPLYlink written 3.8 years ago by Jean-Karim Heriche21k

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

ADD REPLYlink written 2.7 years ago by hillary.figler0

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

ADD REPLYlink written 2.7 years ago by teresa.noviello890

I also have the same problem.

ADD REPLYlink written 2.5 years ago by terence.strobaugh0

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 ?

ADD REPLYlink written 2.5 years ago by Jean-Karim Heriche21k
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