Question: Mugsy multi alignment errors
0
gravatar for teresa.noviello89
4.7 years ago by
Italy
teresa.noviello890 wrote:

Hi. I'm trying to align 3 genomes using mugsy but I have some problems, expecially with delta files

./mugsy_x86-64-v1r2.1/mugsy --directory /home/.../prova hg38.fa mm10.fa danRer7.fa
3 genomes
Starting Nucmer: mar 22 dic 2015, 17.03.54, CET
.sh: ./mugsy_x86-64-v1r2.1/MUMmer3.20/delta-filter: No such file or directory
sh: ./mugsy_x86-64-v1r2.1/MUMmer3.20/delta2maf: No such file or directory
sh: ./mugsy_x86-64-v1r2.1/fixMAFnames.pl: No such file or directory
.sh: ./mugsy_x86-64-v1r2.1/MUMmer3.20/delta-filter: No such file or directory
sh: ./mugsy_x86-64-v1r2.1/MUMmer3.20/delta2maf: No such file or directory
sh: ./mugsy_x86-64-v1r2.1/fixMAFnames.pl: No such file or directory

Finished Nucmer mar 22 dic 2015, 17.04.08, CET
Starting MUGSYWGA: mar 22 dic 2015, 17.04.08, CET
sh: ./mugsy_x86-64-v1r2.1/maf2fasta.pl: No such file or directory
sh: ./mugsy_x86-64-v1r2.1/maf2fasta.pl: No such file or directory
Final output (MAF format): /home/.../prova/tmp.maf
Finished mar 22 dic 2015, 17.06.03, CET

Can you help me?

thanks

linux mugsy alignment • 2.1k views
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by teresa.noviello890

The error messages are quite explicit: you're missing scripts that come with mugsy. Either you didn't install them or they can't be found by the main program. Did you change the MUGSY_INSTALL variable in the script mugsyenv.sh before sourcing it ? And did you source this file before running mugsy ?

ADD REPLYlink written 4.7 years ago by Jean-Karim Heriche23k

Hi. Thanks for your answer. Yes I installed all the required scripts and added the variable mugsyenv.sh as indicated in the reference page but the errors remain.

ADD REPLYlink modified 9 months ago by RamRS30k • written 4.7 years ago by teresa.noviello890

But did you source the mugsyenv.sh file before running mugsy (in the same terminal) ?

ADD REPLYlink written 4.7 years ago by Jean-Karim Heriche23k

Yes of course. Here the steps that I do after the download of the new version

export MUGSY_INSTALL=$HOME/mugsy_x86-64-v1r2.3
source mugsy_x86-64-v1r2.3/mugsyenv.sh

(when I printenv I obtain MUGSY_INSTALL=./mugsy_x86-64-v1r2.3)

then I run mugsy

mugsy --directory /home/noviello/prova/ 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: mer 23 dic 2015, 10.37.31, CET
.sh: ./mugsy_x86-64-v1r2.3/MUMmer3.20/delta-filter: No such file or directory
sh: ./mugsy_x86-64-v1r2.3/MUMmer3.20/delta2maf: No such file or directory
sh: ./mugsy_x86-64-v1r2.3/fixMAFnames.pl: No such file or directory
.sh: ./mugsy_x86-64-v1r2.3/MUMmer3.20/delta-filter: No such file or directory
sh: ./mugsy_x86-64-v1r2.3/MUMmer3.20/delta2maf: No such file or directory
sh: ./mugsy_x86-64-v1r2.3/fixMAFnames.pl: No such file or directory

Finished Nucmer mer 23 dic 2015, 10.37.42, CET
Starting MUGSYWGA: mer 23 dic 2015, 10.37.42, CET
sh: ./mugsy_x86-64-v1r2.3/maf2fasta.pl: No such file or directory
sh: ./mugsy_x86-64-v1r2.3/maf2fasta.pl: No such file or directory
Final output (MAF format): /home/noviello/prova/tmp.maf
Finished mer 23 dic 2015, 10.39.16, CET

The parsing step is now running but the error with delta files still remains

ADD REPLYlink modified 9 months ago by RamRS30k • written 4.7 years ago by teresa.noviello890

Not sure if you're still having an issue, but I had this problem as well. Are you running on macOS by chance? if so you need to follow the instructions on the mugsy website for machines that do not have pre-compiled binaries. That is to say, you need to download mugsy_trunk and compile the binaries for yourself. This resolved the problems for me, but now I have new issues.

ADD REPLYlink modified 9 months ago by RamRS30k • written 3.7 years ago by patrick.j.abeli0

Patrick- Did you ever figure out your other problems? I'm using Mac as well.. and I think I'm having the same ones.

ADD REPLYlink written 3.5 years ago by hillary.figler0

Could be a problem with the paths?

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by teresa.noviello890

Is your $HOME defined in the terminal you're running things in ? In any case, MUGSY_INSTALL should contain an absolute path and in your case it doesn't: MUGSY_INSTALL=./mugsy_x86-64-v1r2.3

ADD REPLYlink modified 9 months ago by RamRS30k • written 4.7 years ago by Jean-Karim Heriche23k

Ok thanks for your usefull help. I changed as you suggested with the absolute path and even if now with the printenv I obtain MUGSY_INSTALL= ./mugsy_x86-64-v1r2.3/MUMmer3.20 the errors remain the same. Any other hint?

ADD REPLYlink modified 9 months ago by RamRS30k • written 4.7 years ago by teresa.noviello890
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