Question: error in star
0
gravatar for yueli7
2.2 years ago by
yueli7140
China
yueli7140 wrote:

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
rna-seq • 1.1k views
ADD COMMENTlink modified 2.2 years ago by genomax85k • written 2.2 years ago by yueli7140

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.

ADD REPLYlink written 2.2 years ago by genomax85k

Thank you for reminding me!

ADD REPLYlink written 2.2 years ago by yueli7140
2
gravatar for genomax
2.2 years ago by
genomax85k
United States
genomax85k wrote:

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.

ADD COMMENTlink written 2.2 years ago by genomax85k
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