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Old 10-09-2017, 11:05 AM   #1
dtatarak
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Location: Irvine, CA

Join Date: Oct 2017
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Unhappy STAR error: could not open readFilesIn

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.
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Old 10-09-2017, 11:14 AM   #2
GenoMax
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Are you using a cluster to run this job (likely since you are using modules)? If so check to make sure that "/dfs1/bio/dtatarak/DT-advancement_RNAseq_stuff/RNAseq_10_4_2017/" is available on the job nodes where the job is actually running.
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Old 10-11-2017, 10:19 AM   #3
aprice67
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Location: New York

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If you are using a cluster or SGE setup, you might try to qlogin and see if you can still find the files and if the paths are correct. You might check if the permissions on those input files are correct for another process accessing them also.

If you copy and paste the command directly into the command line does it fail the same way or does it work? If it works, that means its probly a cluster submission issue, and if it fails it means you maybe messed up the path to the input file.
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