- edited description
miARmaseq results problem
Issue #108
resolved
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)
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reporter -
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
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