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broadinstitute / gtex-pipeline

GTEx & TOPMed data production and analysis pipelines
BSD 3-Clause "New" or "Revised" License
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Could not open genomeFastaFile:/data/Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta #55

Closed xiyasong closed 3 years ago

xiyasong commented 3 years ago

Hi: I am very new to Docker and GTEx, and I am trying to use GTEx pipeline to my own RNA-seq data. However, I have stocked on the first step: build the STAR index, because it returns the following error:

Feb 10 21:14:11 ..... started STAR run Feb 10 21:14:11 ... starting to generate Genome files

EXITING because of INPUT ERROR: could not open genomeFastaFile: /data/Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta

My genemoe fasta file works good on my server's STAR, so it should be a good fasta file. So I guess I have problem in my code using: docker run --rm -v /Users/mstermo/Degree_project:/data -t broadinstitute/gtex_rnaseq:V8 /bin/bash -c "STAR \ --runMode genomeGenerate \ --genomeDir /data/star_index_oh100 \ --genomeFastaFiles /data/Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta \ --sjdbGTFfile /data/gencode.v26.annotation.gtf \ --sjdbOverhang 100 \ --runThreadN 4"

I got confused on how to exactly substitute my own path and parameter in the command line in this pipeline? And I am not sure about my understanding of the substitution of $path_to_references:/data is correct or not. So I guess maybe that cause the problem. I make a folder called 'data' and put all the things inside.

My path is like this: data$pwd /Users/mstermo/Degree_project/data

data$ll total 17537740 -rw-r--r--@ 1 mstermo staff 8.0K Feb 10 21:58 .DS_Store -rw-r--r-- 1 mstermo staff 25M Feb 3 11:11 .Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta.swp -rwxr-xr-x 1 mstermo staff 13G Jan 25 2019 EGAR00001121490_ccRCC-1-tumor_RNAseq.bam -rw-r--r--@ 1 mstermo staff 45K Jun 8 2017 Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.dict -rw-r--r--@ 1 mstermo staff 2.9G Jun 8 2017 Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta -rw-r--r--@ 1 mstermo staff 11K Jun 8 2017 Homo_sapiens_assembly38_noALT_noHLA_noDecoy_ERCC.fasta.fai -rwxr-xr-x@ 1 mstermo staff 59K Feb 2 14:00 _README.TXT -rwxr-xr-x 1 mstermo staff 1.1G Feb 2 13:44 gencode.v26.annotation.gtf drwxr-xr-x 3 mstermo staff 96B Feb 10 21:54 star_index_oh100/ -rw-r--r-- 1 mstermo staff 394B Feb 10 22:15 test.sh

Thanks for your read and hoping for your help!

francois-a commented 3 years ago

Hi,

It looks like in the command

docker run --rm -v /Users/mstermo/Degree_project:/data -t broadinstitute/gtex_rnaseq:V8 /bin/bash -c ...

the path needs to be -v /Users/mstermo/Degree_project/data:/data

xiyasong commented 3 years ago

Thank you very much ! It worked.