EXITING because of fatal input ERROR: could not open readFilesIn=home/pathtofile/read1.fastq

ssa...@uic.edu

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Jan 25, 2016, 2:15:45 PM1/25/16

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Hi All,

I am very new to Star and I have been trying to run mapping. I am stuck with is error and I am not able to figure the solution to it.

I am running in on linux

STAR --runThreadN 6 --genomeDir /home/scp/Documents/GenomeDirRn5 --readFilesIn home/scp/Documents/Pandey_6RNAseq_20151127/1_ATCACG_out.fastq --sjdbGTFfile /home/scp/Downloads/Rattus_norvegicus_UCSC_rn5/Rattus_norvegicus/UCSC/rn5/Annotation/Archives/archive-2015-07-17-14-36-10/Genes/genes.gtf --outFileNamePrefix /home/scp/Documents/StarOut --sjdbGTFtagExonParentTranscript gene_id --quantMode GeneCounts

The error i get is

EXITING because of fatal input ERROR: could not open readFilesIn=home/scp/Documents/Pandey_6RNAseq_20151127/1_ATCACG_out.fastq

Jan 25 10:35:34 ...... FATAL ERROR, exiting

The files and placed in the location. Permissions given, still am not able to find why the error pops up.

Thanks in advance.

Alexander Dobin

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Jan 26, 2016, 3:40:27 PM1/26/16

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Hi @ssanth5

it looks like you are missing the "/" in front of your path:

--readFilesIn home/scp/Documents/Pandey_6RNAseq_20151127/1_ATCACG_out.fastq

shoud be

--readFilesIn /home/scp/Documents/Pandey_6RNAseq_20151127/1_ATCACG_out.fastq

Cheers

Alex

ssa...@uic.edu

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Jan 27, 2016, 11:07:43 AM1/27/16

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Thank you so much! Was a bit careless.

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