Question: please someone help me with running mirdeep2
1
gravatar for Angel
3.0 years ago by
Angel3.5k
Angel3.5k wrote:

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

mirdeep2 perl software error • 2.4k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Angel3.5k
2

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

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax71k
1

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]$

:( :( :(

ADD REPLYlink modified 3.0 years ago by genomax71k • written 3.0 years ago by Angel3.5k

cpan Font::TTF

ADD REPLYlink written 3.0 years ago by Devon Ryan91k
1

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]$

ADD REPLYlink written 3.0 years ago by Angel3.5k

one dependency not OK (IO::String)

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

ADD REPLYlink written 3.0 years ago by Devon Ryan91k

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

ADD REPLYlink written 3.0 years ago by genomax71k
1

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!

ADD REPLYlink written 3.0 years ago by Angel3.5k
1

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]$

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Angel3.5k

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

ADD REPLYlink written 3.0 years ago by genomax71k
1

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]$

ADD REPLYlink written 3.0 years ago by Angel3.5k
1

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.

ADD REPLYlink written 3.0 years ago by genomax71k
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