please someone help me with running mirdeep2

Question

[zizigolu]

hi,

long time I am trying many ways and googling to run mirdeep2 but always error :( :( :(

[izadi@lbox200 mirdeep2_0_0_8]$ install.pl

Installing PDF-API2 now

Warning: prerequisite Font::TTF 0 not found.

RNAfold was/is not installed properly

pdf was/is not installed properly

ttf was/is not installed properly

randfold was/is not installed properly

bowtie was/is not installed properly

Please run the install.pl script again to check if everything is properly installed.

[izadi@lbox200 mirdeep2_0_0_8]$ [izadi@lbox200 mirdeep2_0_0_8]$

please someone help me and save me from this confusion

[GenoMax]

Lots of things appear to be missing from your system.

Since you can't get the install.pl to work why don't you use the instructions in part 2 of the README file included in the package. Install the packages individually.

without the install mirdeep script follow the instructions given in Sample Installation

[zizigolu]

sorry may you please read my errors

based on Sample Installation I downloaded RNAfold, bowtie, Vienna, SQUID and Perl package PDF::API2

after unziping I tried one by one

tar xvvzf ViennaRNA-1.8.4.tar.gz

configure --prefix=/usr/data/nfs6/izadi/ViennaRNA-2.2.10/

telling

checking for perl... /usr/bin/perl

checking for perl module ExtUtils::Embed... no

configure: error: Require ExtUtils::Embed to proceed

[izadi@lbox200 ViennaRNA-2.2.10]$

for fixing error i tried

wget http://files1.directadmin.com/services/all/perl_modules/ExtUtils-Embed-1.14.tar.gz

tar xvzf ExtUtils-Embed-1.14.tar.gz

cd ExtUtils-Embed-1.14

perl Makefile.PL

share/perl5 .) at ../genmake line 5.

BEGIN failed--compilation aborted at ../genmake line 5.

Warning: NAME must be a package name

Generating a Unix-style Makefile

Writing Makefile for ExtUtils-Embed

Writing MYMETA.yml and MYMETA.json

[izadi@lbox200 ExtUtils-Embed-1.14]$

[izadi@lbox200 mirdeep2_0_0_8]$ configure --prefix=/usr/data/nfs6/izadi/mirdeep2_0_0_8/essentials/ViennaRNA-1.8.4/install_dir/

but

Makefile.perl:338: recipe for target 'RNA_wrap.o' failed

make[3]: *** [RNA_wrap.o] Error 1

make[3]: Leaving directory '/usr/data/nfs6/izadi/mirdeep2_0_0_8/essentials/ViennaRNA-1.8.4/Perl'

Makefile:342: recipe for target 'all-local' failed

make[2]: *** [all-local] Error 2\

make[2]: Leaving directory '/usr/data/nfs6/izadi/mirdeep2_0_0_8/essentials/ViennaRNA-1.8.4/Perl'

Makefile:323: recipe for target 'all-recursive' failed

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory '/usr/data/nfs6/izadi/mirdeep2_0_0_8/essentials/ViennaRNA-1.8.4'

Makefile:239: recipe for target 'all' failed

make: *** [all] Error 2

then I tried

[izadi@lbox200 home]$ cd /usr/data/nfs6/izadi/randfold-2.0.1/

[izadi@lbox200 randfold-2.0.1]$ emacs Makefile

Fatal error 11: Segmentation fault

Backtrace:

emacs[0x50ad9c]

emacs[0x4f124c]

emacs[0x50955e]

emacs[0x509789]

emacs[0x5097ef]

/lib64/libpthread.so.0(+0x10c30)[0x2af91f604c30]

/usr/lib64/nvidia/libGL.so.1(+0xbd79d)[0x2af922df079d]

Segmentation fault (core dumped)

[izadi@lbox200 randfold-2.0.1]$

even

[izadi@lbox200 PDF-API2-2.028]$ perl Makefile.PL PREFIX=/usr/data/nfs6/izadi/mirdeep2_0_0_8/ 
LIB=/usr/data/nfs6/izadi/mirdeep2_0_0_8/lib/

Warning: prerequisite Font::TTF 0 not found.

Generating a Unix-style Makefile

Writing Makefile for PDF::API2

Writing MYMETA.yml and MYMETA.json

[izadi@lbox200 PDF-API2-2.028]$

:( :( :(

[Devon Ryan]

cpan Font::TTF

[zizigolu]

thank you Devon

t/ttfcopy.t (Wstat: 512 Tests: 0 Failed: 0)

Non-zero exit status: 2

Parse errors: Bad plan. You planned 4 tests but ran 0.

Files=3, Tests=6, 0 wallclock secs ( 0.01 usr 0.01 sys + 0.08 cusr 0.01 csys = 0.11 CPU)

Result: FAIL

Failed 1/3 test programs. 0/6 subtests failed.

Makefile:1307: recipe for target 'test_dynamic' failed

make: * [test_dynamic] Error 2

BHALLISSY/Font-TTF-1.06.tar.gz

one dependency not OK (IO::String); additionally test harness failed

/usr/bin/make test -- NOT OK

//hint// to see the cpan-testers results for installing this module, try:

reports BHALLISSY/Font-TTF-1.06.tar.gz

[izadi@lbox200 PDF-API2-2.028]$

[Devon Ryan]

one dependency not OK (IO::String)

So install IO::String too. cpan is annoying to use.

[GenoMax]

Use these instructions to setup CPAN to automatically install all dependencies.

[zizigolu]

thank you

[izadi@lbox200 perl-5.24.0]$ perl -MCPAN -e 'my $c = "CPAN::HandleConfig"; $c->load(doit => 1, autoconfig => 1); $c->edit(prerequisites_policy => "follow"); $c->edit(build_requires_install_policy => "yes"); $c->commit' CPAN: File::HomeDir loaded ok (v1.00)

prerequisites_policy [follow]

Please use 'o conf commit' to make the config permanent!

build_requires_install_policy [yes]

Please use 'o conf commit' to make the config permanent!

[zizigolu]

sorry,

I even installed a new version of perl, may you please help me to run mirdeep2? my mentor has asked me to find miRNAs more than a month ago, I tried many tools.. in miARmaSeq also when de novo miRNAs identification I got an error related to mirdeep like so

izadi@lbox200 cbbio-miarma-d7ecf5d38145]$ perl miARma Examples/basic_examples/miRNAs/DeNovo_miRNAs/2.DeNovo/2.1.DeNovo.ini

[Sun Oct 2 17:14:13 2016] Starting a miARma analysis for miRNA

[Sun Oct 2 17:14:13 2016] Checking provided parameters for: DeNovo.

[Sun Oct 2 17:14:13 2016] Checking General-output_dir parameter ... Exists!

[Sun Oct 2 17:14:13 2016] The folder specified in

(output_dir=Examples/basic_examples/miRNAs/DeNovo_miRNAs/results/) already exists.

[Sun Oct 2 17:14:13 2016] Wait 5 seconds to overwrite the folder. Cancel otherwise: 0

[Sun Oct 2 17:14:19 2016] Continue.

[Sun Oct 2 17:14:19 2016] All parameters are correct.

[Sun Oct 2 17:14:19 2016] Starting a De novo identification and quantification of miRNAs

miRDeep ERROR :: system args failed: 6400 (mkdir -p Examples/basic_examples/miRNAs/DeNovo_miRNAs/results//miRDeep_results/ ; export PERL5LIB=./lib/Perl/;miRDeep2.pl

Examples/basic_examples/miRNAs/DeNovo_miRNAs/results//miRDeep_results/HsCa-Ca_1.fa

Genomes/Indexes/bowtie1/human/homo_sapiens19.fa

Examples/basic_examples/miRNAs/DeNovo_miRNAs/results//miRDeep_results/HsCa-Ca_1_vs_genome.arf

Examples/basic_examples/miRNAs/data/hsa_mature_miRBase20.fasta none

Examples/basic_examples/miRNAs/data/precursors_miRBase20.fasta -r HsCa-Ca_1 -P -d -c -v >>

Examples/basic_examples/miRNAs/DeNovo_miRNAs/results//miARma_stat.13522.log 2>&1) at

lib/CbBio/RNASeq/Aligner.pm line 2213.

[izadi@lbox200 cbbio-miarma-d7ecf5d38145]$

[izadi@lbox200 RandA.1.1.4]$ cd /usr/data/nfs6/izadi/RandA.1.1.4/pipeline/

[izadi@lbox200 pipeline]$ perl RandA_pipe.pl randa.config cluster/no-cluster

Starting Analysis.. path to pipe is /usr/data/nfs6/izadi/RandA.1.1.4/pipeline

GD::Graph::bars module not found! Will not produce histograms, proceeding.

[RandA_pipe.pl] Math::CDF module not found, cannot proceed (please see README file). Quitting...

[izadi@lbox200 pipeline]$

[izadi@lbox200 pipeline]$ Math::CDF

Math::CDF: Command not found.

[izadi@lbox200 pipeline]$

I tried

cpan Math::CDF Spreadsheet::Result: FAIL

Failed 5/8 test programs. 0/109 subtests failed.

Makefile:933: recipe for target 'test_dynamic' failed

make: * [test_dynamic] Error 2

RUZ/GDGraph-1.53.tar.gz

/usr/bin/make test -- NOT OK

//hint// to see the cpan-testers results for installing this module, try:

reports RUZ/GDGraph-1.53.tar.gz

[izadi@lbox200 pipeline]$

[GenoMax]

Install Math::CDF. Install GD::Bar::Graph.

[zizigolu]

ERROR: Can't create '/usr/local/lib64/perl5/Math' mkdir /usr/local/lib64/perl5: Permission denied at /usr/share/perl5/vendor_perl/ExtUtils/Install.pm line 477.

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! at -e line 1. Makefile:800: recipe for target 'pure_site_install' failed make: * [pure_site_install] Error 13 [izadi@lbox200 Math-CDF-0.1]$

[GenoMax]

Looks like you would need to use sudo to install that or see if you can use an alternate location that you can write to.