could not open file pGe.sjdbGTFfile

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Niharika Singh

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Feb 17, 2023, 2:25:04 PM2/17/23
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Hi everyone,

I am trying to create a reference library using the following code:

STAR \
--runMode genomeGenerate \
--runThreadN 8 \
--genomeDir /scratch/c.c22019143/R256/fastq/Mapping/STAR/ \
--genomeFastaFiles /scratch/c.c22019143/R256/fastq/Mapping/STAR/Mus_musculus.GRCm39.dna_sm.primary_assembly.fa \
--sjdbGTFfile /scratch/c.c22019143/R256/fastq/Mapping/STAR/Mus_musculus.GRCm39.108.gtf

But I keep getting this error:

FATAL error, could not open file pGe.sjdbGTFfile=/scratch/c.c22019143/R256/fastq/Mapping/STAR/Mus_musculus.GRCm39.108.gtf

I downloaded the .gtf file from ensembl thrice to ensure I get the correct file. Could you please help? 

Many thanks,
Niharika. 

Alexander Dobin

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Feb 22, 2023, 11:42:29 AM2/22/23
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Hi Niharika,

it seems STAR cannot see the file. Please check the permissions with
ls -l /scratch/c.c22019143/R256/fastq/Mapping/STAR/Mus_musculus.GRCm39.108.gtf

Cheers
Alex

QIQI GUO

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Apr 17, 2023, 4:09:53 PM4/17/23
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Hi Niharika,

I’m sorry to bother you.

my name is Qiqi Guo and I'm a postdoctoral researcher at UCLA. I came across your question about the error message "could not open file pGe.sjdbGTFfile" on Google Groups, and I am experiencing a similar issue. I was wondering if you have found a solution to this problem. I would greatly appreciate it if you could provide me with any information or advice on how to resolve this issue.

Thank you so much and have a nice day.

Best regards
Qiqi
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