the gtf file for cow

Question

[yueli7]

Hello,

I used STAR to make index.

Pavilion-Desktop-590-p0xxx:~/STAR-2.7.0e/source$ ./STAR --runThreadN 30 --runMode genomeGenerate --genomeDir /home/li/genome/ --genomeFastaFiles /home/li/genome/UMD3.1_chromosomes.fa --sjdbGTFfile /home/li/genome/Bos_taurus.ARS-UCD1.2.98.chr.gtf --sjdbOverhang 99

Oct 12 22:50:52 ..... started STAR run

Oct 12 22:50:52 ... starting to generate Genome files

Oct 12 22:51:40 ... starting to sort Suffix Array. This may take a long time...

Oct 12 22:51:51 ... sorting Suffix Array chunks and saving them to disk...

Oct 12 23:22:15 ... loading chunks from disk, packing SA...

Oct 12 23:35:59 ... finished generating suffix array

Oct 12 23:35:59 ... generating Suffix Array index

Oct 12 23:49:34 ... completed Suffix Array index

Oct 12 23:49:34 ..... processing annotations GTF

Fatal INPUT FILE error, no valid exon lines in the GTF file: /home/li/genome/Bos_taurus.ARS-UCD1.2.98.chr.gtf Solution: check the formatting of the GTF file. Most likely cause is the difference in chromosome naming between GTF and FASTA file.

Oct 12 23:49:48 ...... FATAL ERROR, exiting

Thanks in advance for great help!

Best,

Yue

[igor]

Did you get your FASTA and GTF files from the same source?

[shoujun.gu]

' Most likely cause is the difference in chromosome naming between GTF and FASTA file.'
Just check the chr names in GTF and FASTA files first...

[yueli7]

Thanks shoujin.gu,

the names in GTF and FASTA files:

of vilion-Desktop-590-p0xxx:~/STAR-2.7.0e/source$ ./STAR --runThreadN 30 --runMode genomeGenerate --genomeDir /home/li/genome/ --genomeFastaFiles /home/li/genome/GCF_002263795.1_ARS-UCD1.2_refseq_chrids.fa --sjdbGTFfile /home/li/genome/Bos_taurus.ARS-UCD1.2.98.chr.gtf --sjdbOverhang 99

Oct 13 22:03:30 ..... started STAR run

Oct 13 22:03:31 ... starting to generate Genome files

Oct 13 22:04:19 ... starting to sort Suffix Array. This may take a long time...

Oct 13 22:04:29 ... sorting Suffix Array chunks and saving them to disk...

Oct 13 22:25:05 ... loading chunks from disk, packing SA...

Oct 13 22:38:34 ... finished generating suffix array

Oct 13 22:38:34 ... generating Suffix Array index

Oct 13 22:52:45 ... completed Suffix Array index

Oct 13 22:52:45 ..... processing annotations GTF

Oct 13 22:52:57 ..... inserting junctions into the genome indices

Oct 14 01:09:48 ... writing Genome to disk ...

Oct 14 01:13:02 ... writing Suffix Array to disk ...

Oct 14 02:44:31 ... writing SAindex to disk

Oct 14 02:44:51 ..... finished successfully

[shoujun.gu]

I mean take a look at the name of chromosome within each file.... whether they are consistent, such as all are they all like 'Chr 1'? All are they all like '1'?

[yueli7]

Hello, shoujun.gu,

Thank you for your message!

I should download the data from:

https://bovinegenome.elsiklab.missouri.edu/node/68,

GCF_002263795.1_ARS-UCD1.2_refseq_chrids.fa.gz

ftp://ftp.ensembl.org/pub/current_gtf/bos_taurus/

Bos_taurus.ARS-UCD1.2.98.chr.gtf.gz

Thank you again!

yue

[shoujun.gu]

Seems your data come from different sources, their chromosome labels maybe different. This may cause the program error. Try to download your fa and gft file from the same website.