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alexdobin / STAR

RNA-seq aligner
MIT License
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RNA-seq using STAR #1779

Open PratitiA opened 1 year ago

PratitiA commented 1 year ago

Hello,

I am using STAR for alignment, and I am facing an issue while I run my file on LINUX.

Could you please assist me.

This is what I get as an error when I ran STAR.

/usr/lib/rna-star/bin/STAR-avx2 --genomeDir /mnt/c/Users/pra4003/Documents/Pratiti/LIP_ESCs/ESC_5-8_2il_p3_and_p15/esc-2il-p15/ --runThreadN 6 --readFilesIn trimmed_R1_combined_fastq trimmed_R2_combined_fastq --outFileNamePrefix /mnt/c/Users/pra4003/Documents/Pratiti/LIP_ESCs/ESC_5-8_2il_p3_and_p15/esc-2il-p15 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard STAR version: 2.7.10a compiled: 2022-01-16T16:35:44+00:00 Mar 06 13:10:42 ..... started STAR run Mar 06 13:10:42 ..... loading genome

EXITING because of FATAL ERROR: could not open genome file /mnt/c/Users/pra4003/Documents/Pratiti/LIP_ESCs/ESC_5-8_2il_p3_and_p15/esc-2il-p15//genomeParameters.txt SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions

Mar 06 13:10:42 ...... FATAL ERROR, exiting

Could you please help to resolve this error.

Thanks, Pratiti

alexdobin commented 1 year ago

Hi Pratiti,

as the message states, STAR cannot read from genomeParameters.txt in the --genomeDir directory. Please check the genome indexing completed successfully.