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Star error #2

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sscien opened this issue Jan 13, 2022 · 1 comment
Open

Star error #2

sscien opened this issue Jan 13, 2022 · 1 comment

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@sscien
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sscien commented Jan 13, 2022

EXITING because of FATAL ERROR: could not open genome file /diskmnt/Projects/Users/dcui/Projects/Fusion_hg38/Integrate_dependencies/STAR//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
@sscien
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sscien commented Jan 13, 2022

Solution:

Update the dependencies path and also update the dependencies since we updated STAR from 2.7.2 to 2.7.8a

Update genomeDir in fusion_pipeline_ris_v1.sh

STAR --runThreadN 80 --genomeDir /storage1/fs1/dinglab/Active/Projects/PECGS/PECGS_pipeline/Fusion/STAR-Fusion_dependencies/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --readFilesCommand zcat --readFilesIn ../${fq_1} ../${fq_2} --outSAMtype BAM Unsorted --outFileNamePrefix star --chimSegmentMin 18 --chimOutType WithinBAM --outSAMunmapped Within 1> ../logs/star.out 2> ../logs/star.err

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@sscien