FASTQC issue

[Anna Eymann]

Hi,

I reinstall Ubuntu from the beginning and start using miARma but it is giving me this error

FASTQC ERROR :: system args failed: 34304 (mkdir -p Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ ; fastqc -f fastq -t 2 Examples/basic_examples/miRNAs/reads//SRR873382.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873383.fq.gz Examples/basic_examples/miRNAs/reads//SRR873384.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873385.fq.gz Examples/basic_examples/miRNAs/reads//SRR873386.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873387.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873388.fastq.gz Examples/basic_examples/miRNAs/reads//SRR873389.fastq.gz -o Examples/basic_examples/miRNAs/Known_miRNAs/results//Pre_fastqc_results/ >> Examples/basic_examples/miRNAs/Known_miRNAs/results//miARma_logfile.19863.log 2>&1) at lib/CbBio/RNASeq/Quality.pm line 146.

[Eduardo Andres Leon]

Dear Anna, Although miARma has no prerequisites in tense of "biological" softwares, it needs some general programs to run properly, for instance: java, make gcc and so on.

You can install all of them using the following commands:

sudo echo "deb http://cran.r-project.org/bin/linux/ubuntu/ trusty/" >> /etc/apt/sources.list
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 51716619E084DAB9
sudo apt-get update -y 
sudo apt-get -y install vim make gcc openjdk-8-jdk r-base tar bzip2 pkg-config libxml2-dev libcurl4-gnutls-dev

Once these software is installed, you will need to include bioconductor within your R installation. So you will need to execute:

R
source("http://www.bioconductor.org/biocLite.R")
biocLite()
q()

Please let me know

[Eduardo Andres Leon]

Issue #105 was marked as a duplicate of this issue.

[Eduardo Andres Leon]

Hi Anna, Did you manage to run the fastqc step ?