Question: MITE hunter stops after step 2
gravatar for danielke
13 days ago by
danielke10 wrote:

Hey everyone,

I started working with MITE hunter and for some reason it stops running after step 2, error showing is:

sh: 1: /home/my-user/MITE_hunter/mdust/: Permission denied
Use of uninitialized value $Seq in split at /home/my-user/MITE_hunter/MITE_hunter_2011/ line 70.
Use of uninitialized value $Len in division (/) at /home/my-user/MITE_hunter/MITE_hunter_2011/ line 86.
Illegal division by zero at /home/my-user/MITE_hunter/MITE_hunter_2011/ line 86.
No such file or directory

This is the code I used:

/home/bariah/MITE_hunter/MITE_hunter_2011# perl -i /home/bariah/Genomes/Chromosome_files/tau_chr/tau_d1.fasta -g tau_d1 -c 95 -f 100 -L 50 -2 12345678

The last files created are: tau_d1_Step2.fa and tau_d1_Step2.fa.dusted (which is empty)

What can be the problem ?

Thank you!

ADD COMMENTlink modified 13 days ago by WouterDeCoster26k • written 13 days ago by danielke10

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ADD REPLYlink written 13 days ago by WouterDeCoster26k

Have you indexed the genome you are giving after -i option. Try this after indexing.

Else- You can try to change the privilege to mdust.

You can also try to install folllowing way:

download and install

Download from “”

Unzip and change folder and subfolder names (replace space with "_")

cd ./MITE_Hunter-11-2011/MITE_Hunter perl -d


/home/user/repeats/MITE_Hunter-11-2011/MITE_Hunter/ -f /usr/bin/formatdb -b /usr/bin/blastall -m /usr/bin/mdust -M /usr/bin/muscle

ADD REPLYlink written 12 days ago by Puli Chandramouli Reddy150

What do you mean index the genome? it is done by the RepeatMasker, if I'm not wrong..

What do you mean change the privilege to mdust? what should i do?

Thanks for your help :)

ADD REPLYlink written 11 days ago by danielke10

If you have indexed genome in the same folder then it may not be the cause for error. change permissions to the folder using "sudo chmod 777 -R /home/my-user/MITE_hunter/mdust/

If these things do not work then the problem could be with the installation.


ADD REPLYlink written 11 days ago by Puli Chandramouli Reddy150

OK so I've tried it and still the same problem. What could be the problem with installation?

This is what I do to run MITE_hunter after installation. Might it be the first error ?

perl -i /home/my_user/MITE_hunter/tau/tau_d1.fasta -g tau_d1 -c 95 -f 200 -L 50 -n 20 -S 12345678 &
[2] 4086

my_user@my_computer:~/MITE_hunter/MITE_Hunter_2011$ formating database ...
Can't exec "/home/my_user/MITE_hunter/ncbi-blast-2.2.28+/bin/": Permission denied at /home/my_user/MITE_hunter/MITE_Hunter_2011/ line 87.
ADD REPLYlink modified 10 days ago • written 10 days ago by danielke10

Can you check that blastall program can be called globally or you can export the the blasall to your path. Basically all the required program paths (complete) should have been given correctly while installing. I suggest once again try to install as I have mentioned in earlier reply. Best.

ADD REPLYlink written 9 days ago by Puli Chandramouli Reddy150
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