what does this error mean?

Question

[zizigolu]

sorry guys,

how knows what does this error mean and could be solved?

miRDeep ERROR :: system args failed: 65280 (mkdir -p

Examples/basic_examples/miRNAs/DeNovo_miRNAs/results//miRDeep_results/ ; export PERL5LIB=./lib/Perl/;miRDeep2.pl

[GenoMax]

What other text is there around this error? What command are you getting this error from?

[zizigolu]

thank you

I was trying miarma with its own example data

[izadi@lbox200 cbbio-miarma-d7ecf5d38145]$ miARma

Examples/basic_examples/miRNAs/DeNovo_miRNAs/miARma_miRNAs_DeNovo.ini

#########################################################################   
#   miARma, miRNA and RNASeq Multiprocess Analysis          #
#                miARma v 1.5.1 (Aug-2016)                              #
#                                                           #
#   Created at Computational Biology and Bioinformatics Group (CbBio)   #
#   Institute of Biomedicine of Seville. IBIS (Spain)                   #
#   Copyright (c) 2016 IBIS. All rights reserved.                       #
#   mail : [e-mail]                                        #
#########################################################################

[Wed Oct  5 20:05:12 2016] Starting a miARma analysis for miRNA
[Wed Oct  5 20:05:12 2016] Checking provided parameters for: Quality,DeNovo,DEAnalysis,TargetPrediction. 
[Wed Oct  5 20:05:12 2016] All parameters are correct.
[Wed Oct  5 20:05:17 2016] Starting Quality Analysis.
[Wed Oct  5 20:06:12 2016] Quality Analysis finished.
[Wed Oct  5 20:06:12 2016] Starting a De novo identification and quantification of miRNAs
miRDeep ERROR :: system args failed: 65280 (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/SRR873382.fa Genomes/Indexes/bowtie1/human/homo_sapiens19.fa Examples/basic_examples/miRNAs/DeNovo_miRNAs/results//miRDeep_results/SRR873382_vs_genome.arf Examples/basic_examples/miRNAs/data/hsa_mature_miRBase20.fasta none Examples/basic_examples/miRNAs/data/precursors_miRBase20.fasta -r SRR873382 -P -d -c -v >> Examples/basic_examples/miRNAs/DeNovo_miRNAs/results//miARma_stat.828.log 2>&1) at lib/CbBio/RNASeq/Aligner.pm line 2213.
[izadi@lbox200 cbbio-miarma-d7ecf5d38145]$

[GenoMax]

Did you manage to install miRDeep2.pl? It looks like miARma is trying to execute that and not finding it (perhaps)?

[zizigolu]

thank you,

I ran perl install.pl telling

Installing PDF-API2 now

randfold was/is not installed properly

bowtie was/is not installed properly

pdf was/is not installed properly

RNAfold 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]$

totally confused ...

[Brice Sarver]

Is that semicolon your PERL5LIB supposed to be there?

[zizigolu]

thank you but PERL5LIB was included in error