EXITING: because of fatal INPUT file error: could not open read file

[abeedhakhan]

Hi Alex,

I have built the genome index using the prebuilt binary version of star and it worked fine. However, when I try to align my read files, it continuously shows this error of sometimes not being able to read the files and other times not been able to read the files in the genome directory in which the built index is. I have tried to change permissions to my files but not working. And, I don't understand why the permission error because I haven't done anything to the files.

Here's the command I run along with the error:

(base) akhan@IITNBTLM001 adapter_trimmed_reads % ./STAR --runThreadN 16
--genomeDir /Users/akhan/Documents/Projects/Giulia_INs/transfer_219628_files_30cd539e/genomeDir
--readFilesCommand zcat
--readFilesIn /Users/akhan/Documents/Projects/Giulia_INs/transfer_219628_files_30cd539e/adapter_trimmed_reads/L2_paired1.fq.gz,/Users/akhan/Documents/Projects/Giulia_INs/transfer_219628_files_30cd539e/adapter_trimmed_reads/L2_paired2.fq.gz
--outFileNamePrefix /Users/akhan/Documents/Projects/Giulia_INs/transfer_219628_files_30cd539e/adapter_trimmed_reads/L2
--sjdbOverhang 150
--outFilterScoreMinOverLread 0.1
--outFilterMatchNminOverLread 0.1

!!!!! WARNING: Could not ls /Users/akhan/Documents/Projects/Giulia_INs/transfer_219628_files_30cd539e/adapter_trimmed_reads/L2_paired1.fq.gz

EXITING: because of fatal INPUT file error: could not open read file: /Users/akhan/Documents/Projects/Giulia_INs/transfer_219628_files_30cd539e/adapter_trimmed_reads/L2_paired1.fq.gz
SOLUTION: check that this file exists and has read permision.

Apr 30 23:07:10 ...... FATAL ERROR, exiting