MITE hunter stops after step 2

Question

[danielke]

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/low_complexity_filter.pl line 70.
Use of uninitialized value $Len in division (/) at /home/my-user/MITE_hunter/MITE_hunter_2011/low_complexity_filter.pl line 86.
Illegal division by zero at /home/my-user/MITE_hunter/MITE_hunter_2011/low_complexity_filter.pl line 86.
No such file or directory

This is the code I used:

/home/bariah/MITE_hunter/MITE_hunter_2011# perl MITE_Hunter_manager.pl -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!

[WouterDeCoster]

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[Puli Chandramouli Reddy]

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 “http://target.iplantcollaborative.org/mite_hunter/MITE%20Hunter-11-2011.zip”

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

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

install

/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

[danielke]

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 :)

[Puli Chandramouli Reddy]

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.

Best

[danielke]

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 MITE_Hunter_manager.pl -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/blast_formatdb_index.pl line 87.
16403/328040

[Puli Chandramouli Reddy]

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.

[bch930129]

I’ve met the same problem in step 2,it is said that sh: /share_bio/Buchh/MITEs/mdust/mdust/mdust.c: Permission denied . Did you solve this problem ?

Answer 1

[Colaptes]

I had the same problem with the same permission denied error message. In my case it turned out I did not have write permissions on the genome sequence I was analyzing. No idea if it is the same problem you had, but I fixed mine by copy-pasting the fasta file that was owned by another user to create a copy where I had read-write privileges.