error in star

Question

[yueli7]

Hello,

When I ran STAR, it happens like this:

Anyone has suggestion?

Thanks in advance for great help!

yue

administrator@ACB-HuangLab-Ubuntu:~/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

[GenoMax]

Hello yueli7!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=82060

This is typically not recommended as it runs the risk of annoying people in both communities.

[yueli7]

Thank you for reminding me!

Answer 1

[GenoMax]

You can't use wrong type of file. /home/administrator/human/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna is a fasta format sequence file. You need a GTF format file for the --sjdbGTFfile option.