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Old 04-25-2018, 02:33 PM   #1
yueli
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Location: china

Join Date: May 2013
Posts: 53
Default error in STAR

Hello,

When I ran STAR, it happens like this:

Anyone has suggestion?

Thanks in advance for great help!


yue


[email protected]:~/STAR-2.6.0a/source$ ./STAR --runThreadN 30 --runMode genomeGenerate --genomeDir /home/administrator/genomeDir --genomeFastaFiles /home/administrator/human/hg38.fa --sjdbGTFfile /home/administrator/human/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna --sjdbOverhang 99
Apr 25 13:31:30 ..... started STAR run
Apr 25 13:31:31 ... starting to generate Genome files
Apr 25 13:32:52 ... starting to sort Suffix Array. This may take a long time...
Apr 25 13:33:11 ... sorting Suffix Array chunks and saving them to disk...
Apr 25 14:11:42 ... loading chunks from disk, packing SA...
Apr 25 14:17:39 ... finished generating suffix array
Apr 25 14:17:39 ... generating Suffix Array index
Apr 25 14:20:57 ... completed Suffix Array index
Apr 25 14:20:57 ..... processing annotations GTF

Fatal INPUT FILE error, no exon lines in the GTF file: /home/administrator/human/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
Solution: check the formatting of the GTF file, it must contain some lines with exon in the 3rd column.
Make sure the GTF file is unzipped.
If exons are marked with a different word, use --sjdbGTFfeatureExon .

Apr 25 14:21:22 ...... FATAL ERROR, exiting
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Old 04-26-2018, 03:39 AM   #2
GenoMax
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Join Date: Feb 2008
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Cross-posted: https://www.biostars.org/p/311462/
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