miARmaseq results problem

Issue #108 resolved
Maurizio Polano created an issue

I use the docker version of miARmaseq:

./miARma --version
?[3;J
#########################################################################   
#   miARma, miRNA and RNASeq Multiprocess Analysis          #
#                miARma v 1.7.2 (Dec-2017)                              #
#                                                           #
#   Created at Computational Biology and Bioinformatics Group (CbBio)   #
#   Institute of Biomedicine of Seville. IBIS (Spain)                   #
#   Modified and Updated at Bioinformatics Unit at IPBLN-CSIC       #
#   Institue for Parasitology and Biomedicine Lopez-Neyra (IPBLN-CSIC). #
#   Granada (Spain)                                     #
#   Copyright (c) 2017 IBIS & IPBLN. All rights reserved.               #
#   mail : miARma-devel@cbbio.es                                        #
#########################################################################

Usage:

  perl ./miARma file.ini [options]

Options:

If I use the example no error I found but If I use my data I always have this error:

[Tue Apr 17 13:35:13 2018] Post Quality Analysis finished.
[Tue Apr 17 13:35:14 2018] Starting a "Bowtie1" Alignment Analysis
[Tue Apr 17 13:47:04 2018] "Bowtie1" Alignment Analysis finished
[Tue Apr 17 13:47:04 2018] Starting a Readcount Analysis
[Tue Apr 17 13:49:04 2018] Readcount Analysis finished.
[Tue Apr 17 13:49:04 2018] Starting a differential expression analysis using EdgeR software(s)
Problem while running this R command:
print(resultsfiles)

Error:
print(resultsfiles) : object 'resultsfiles' not found
Execution halted
root@499f12d281cb:/home/miARma/miARma# 

all the R package are intalled becauese the example works

#target samplename GaspID type f21.fastq R4 TP f11.fastq R1 TP f3.fastq R6 NP f211.fastq R5 NP

#contrast "GaspID" "Confronto2=NP-TP" on the scitpt uyou can see th this error

source("./lib/CbBio/RNASeq/R-Scripts/QC_EdgeR.R") Error in file(filename, "r", encoding = encoding) : cannot open the connection

Comments (3)

  1. Eduardo Andres Leon

    Could you attach the targets and contrast txt files ? As you have written I can't see the problem. You can use eduardo.andres at csic.es instead

    E

  2. Log in to comment