Trouble running Mugsy

Question

[merzanaeem007]

Hello, I'm new to ubuntu/linux and Mugsy. I'm supposed to use mugsy to align a few thousand viral genome (HIV1) however upon following the steps in the official Mugsy website I still had trouble running it, heres what I have done so far.

• I have downloaded and unzipped mugsy to my desktop using the commands

cd /home/user/Desktop tar xvzf mugsy_x86-64-v1r2.2.tgz

• I editted the mugsyenv.sh file by changing the export line to:

export MUGSY_INSTALL=/home/user/Desktop/mugsy_x86-64-v1r2.2

• On the terminal I typed the following:

Bash Source source /home/naeem/Desktop/mugsy_x86-64-v1r2.2/mugsyenv.sh (nothing happened)

• Then I typed

run mugsy (gave the message mugsy: command not found) mugsy (gave the message mugsy: command not found)

• I tried typing:

mugsy --directory /home/naeem/Desktop --prefix alignment HIV1_db_1.fasta HIV1_db_2.fasta (HIV1_db_1.fasta & HIV1_db_2.fasta both being in the same folder of mugsy_x86-64-v1r2.2) but still got the message mugsy: command not found

If anyone could help me understand what I'm missing/doing wrong, I would appreciate it (alooooot), thanks in advance for any effort :)

Answer 1

[zorbax]

Maybe you should try install it with conda instead. Your error is because you are adding the mugsy source folder like the installation folder in MUGSY_INSTALL variable.

Try with conda:

conda create -n Mugsy -c bioconda -y mugsy.

This instruction will create an environment with mugsy on it. Then you can use it with:

conda activate Mugsy

[merzanaeem007]

Thanks aloooooooot, it did indeed work out :)

[merzanaeem007]

I'm sorry to bother you again but if your familiar with Mugsy, I seem to encounter another error and couldn't say if its because of using conda or not. When i try to align 2 genomes, the part where it runs Nucmer gives a ".Segmentation fault (core dumped)" message.

• The command line I used is (I cd to the mugsy_testing directory):

mugsy --directory /home/naeem/Desktop/HIV1/mugsy_testing --prefix test_alignment HIV1_db_1.fasta HIV1_db_2.fasta

• The complete process log is as follows:

Parsing sequences for HIV1_db_1 num_seqs:1 Parsing sequences for HIV1_db_2 num_seqs:1 2 genomes Starting Nucmer: Fri 21 Aug 2020 13:30:19 +03 .Segmentation fault (core dumped)

Finished Nucmer Fri 21 Aug 2020 13:30:20 +03 Starting MUGSYWGA: Fri 21 Aug 2020 13:30:20 +03 Final output (MAF format): /home/naeem/Desktop/HIV1/mugsy_testing/test_alignment.maf Finished Fri 21 Aug 2020 13:30:20 +03

The .maf file is mostly empty I did some google search about it and reason seems to be memory/write permission related but couldn't fix it, any idea about ? thanks a ton again :)

[zorbax]

you need more memory, I think.

[merzanaeem007]

I find it confusing that a 4gb ram can't align two 9kbp sequences, I'll try running it on the university servers during the weekend and check the results. Thanks though :)

[merzanaeem007]

I'm updating just in case someone else might suffer from the same issue.

The issue doesn't seem to be with memory or read/write permissions, I tried aligning 2 B.subtilis genomes and they were aligned perfectly but then i added a line of gaps (-) in each genome and tried aligning them again and got the same error, so it must be something related to how Mugsy handles gaps/- . Thanks again zorbax for the effort, appreciate it :)