Hi all. I'm quite new to RNA-seq and in particular using the STAR alignment software. I have written a script to map my reads to a reference genome, but it keeps erroring out and giving me this error message:
EXITING because of fatal input ERROR: could not open readFilesIn=/dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/DT_1_read1.fastq
Essentially, it cannot seem to open my fastq files, but I cannot figure out why. Here is my script (sorry for the lengthy directory paths)
module load STAR/2.5.2a
cd /dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017
mkdir David_data1
STAR --genomeDir /dfs1/bio/dtatarak/indexes/STAR_Index --readFilesIn /dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/DT_1_read1.fastq /dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/DT_1_read2.fastq --runThreadN 8 --outFileNamePrefix "David_data1/DT_1"
Does anyone know what the problem might be? I've scoured the internet, and I can't seem to find a solution.
EXITING because of fatal input ERROR: could not open readFilesIn=/dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/DT_1_read1.fastq
Essentially, it cannot seem to open my fastq files, but I cannot figure out why. Here is my script (sorry for the lengthy directory paths)
module load STAR/2.5.2a
cd /dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017
mkdir David_data1
STAR --genomeDir /dfs1/bio/dtatarak/indexes/STAR_Index --readFilesIn /dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/DT_1_read1.fastq /dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/DT_1_read2.fastq --runThreadN 8 --outFileNamePrefix "David_data1/DT_1"
Does anyone know what the problem might be? I've scoured the internet, and I can't seem to find a solution.
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