FrameDP installation issue

Question

[mforthman]

Has anyone ever encountered issues installing FrameDP on a local computer? I followed installation instructions, ran the FrameDP_check_install.pl script, and received the following errors:

Testing FrameDP Installation
/usr/local/framedp/bin/../bin/FrameDP.pl --cfg /usr/local/framedp/bin/../cfg/FrameDP.cfg --infile /usr/local/framedp/bin/../data/HuSep2007Test --outdir /usr/local/framedp/bin/../test/check_install.37245 --workingdir /usr/local/framedp/bin/../test/check_install.37245   --overwrite_repository 
Training............................................started
launched job, job ID = 37256
launched job, job ID = 37257

Now Waiting until all subprocesses are finished
Unable to read >/usr/local/framedp/bin/../test/check_install.37245/HuSep2007Test.refdb.blastx<
 at /usr/local/framedp/bin/../bin/FrameDP_train.pl line 772.
    main::_BuildSubDb('/usr/local/framedp/bin/../db/uniprot_sprot.fasta-norep', '/usr/local/framedp/bin/../test/check_install.37245/DB_subset_...', '/usr/local/framedp/bin/../test/check_install.37245/HuSep2007T...') called at /usr/local/framedp/bin/../bin/FrameDP_train.pl line 654
    main::BuildTrainingDatasetFromBlastX('ParamParser=HASH(0x7fdf78816de8)', 'Logger=HASH(0x7fdf79b84010)', '#16#06#20#15#14#47#01#') called at /usr/local/framedp/bin/../bin/FrameDP_train.pl line 114
========================================
/usr/local/framedp/bin/../bin/FrameDP.pl
========================================
Fatal error in training step

 at /usr/local/framedp/bin/../bin/FrameDP.pl line 619.
    main::ErrMsg('Fatal error in training step\x{a}') called at /usr/local/framedp/bin/../bin/FrameDP.pl line 141
==========================
./framedp_check_install.pl
==========================
Fatal error running FrameDP pipeline

 at ./framedp_check_install.pl line 214.
    main::ErrMsg('Fatal error running FrameDP pipeline\x{a}') called at ./framedp_check_install.pl line 145

FrameDP (and even all of its subdirectories) were set in my $PATH. I cannot figure out what I need to do to get this to run properly.

[GenoMax]

Unable to read /usr/local/framedp/bin/../test/check_install.37245/HuSep2007Test.refdb.blastx

Error is clear based on that message.

[mforthman]

I get that's part of the problem, and yet, it's there, so I don't know why this is an issue.

[GenoMax]

But is it readable by whichever account you are running this from?

[mforthman]

Meaning a permissions issue? I changed permissions for the entire FrameDP directory at the very beginning.

[GenoMax]

Correct. Read permissions. What does ls -l /usr/local/framedp/bin/../test/check_install.37245/HuSep2007Test.refdb.blastx show?

[mforthman]

using chmod 777:

-rwxrwxrwx  1 Forthman  admin  0 Jun 20 11:14 /usr/local/framedp/bin/../test/check_install.37245/HuSep2007Test.refdb.blastx

I also looked at FrameDP_train.pl line 772 referenced below this particular error message and here is what the line looks like:

my $f_blast = new IO::File($blastresultfile,"r") or Carp::croak("Unable to read >$blastresultfile<\n");

[GenoMax]

You shouldn't need 777 (neither should you use those as a good practice when not needed). It is possible that one of the directories higher up in the hierarchy may not have the necessary permissions.

[mforthman]

But if I applied this to the FrameDP directory itself, should this not have taken care of that issue? EDIT: I've just checked the permissions for files within several subdirectories and all are readable.

[GenoMax]

It everything is 777 from that point on it should. Are you running this validation as account Forthman?

[mforthman]

Yes and yes. I noticed that each time I attempted check_install, it would look for a test/check_install.[some_random_number] directory, with the blastx file, though with the extension .txt. I edited the script to remove that random number and eliminated the .txt entension. It is now able to read the blastx file.

But...now I am running into other issues. The first one is

Michaels-MacBook-Air-2:bin Forthman$ ./FrameDP_check_install.pl 
Testing FrameDP Installation
/usr/local/framedp/bin/../bin/FrameDP.pl --cfg /usr/local/framedp/bin/../cfg/FrameDP.cfg --infile /usr/local/framedp/bin/../data/HuSep2007Test --outdir /usr/local/framedp/bin/../test/check_install --workingdir /usr/local/framedp/bin/../test/check_install   --overwrite_repository 
Training............................................started
launched job, job ID = 37830
launched job, job ID = 37831

Now Waiting until all subprocesses are finished
/usr/local/framedp/bin/../bin/ext/ncbi-blast/bin/formatdb: /usr/local/framedp/bin/../bin/ext/ncbi-blast/bin/formatdb: cannot execute binary file

I've even cd to the directory formatdb is in and tried to execute it manually by typing ./formatdb, as well as without ./, but it states "cannot execute binary file".

[GenoMax]

DId you download FrameDP from this link? That looks like a linux only install and will not work on OS X.

What do you see if you do file formatdb ? I have a feeling that you are trying to use the software (at least parts of it like blast) on wrong OS.

[mforthman]

ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.4.1, not stripped

It must because I am using OS X

[GenoMax]

As I suspected this is not going to work. At a minimum you could try to download the OS X blast executables but you may run into some other issue with other programs that are needed.

Time to look for an alternative software.