Fatal error when indexing with star

[RacheliHadjez]

Hello, I am trying to run star this is my command:

!/bin/bash

PBS -q huchond

PBS -o out_StarIndex

PBS -e err_StarIndex

PBS -l select=1:ncpus=150

PBS -r y

module load STAR-2.7/STAR-2.7.5c

STAR --runThreadN 4 \ --runMode genomeGenerate \ --genomeSAindexNbases 12 \ --genomeDir /dorotheeh/hadjez/genome_index/ \ --genomeFastaFiles /dorotheeh/hadjez/NextDenovo_pilon.fasta \ --sjdbGTFfile /dorotheeh/hadjez/genomic.gtf

The error I am receiving is: Fatal INPUT FILE error, no valid exon lines in the GTF file: /dorotheeh/hadjez/genomic.gtf Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.

My question is how am I supposed to change the chromosome naming between the GTF and the fasta file if the chromosome names are different? for example in my fasta file I have

ctg000000_pilon CAAATAATGCATAAGCCATTTGCAAGAAA..... but also: ctg000010_pilon TAAGATTTTCAGATGTTACAAATAAAGGAA..... on my GTF file the names are SGJC01000001.1 but other places are SGJC01000002.1 So I don't know how to change the names if there are not the same throughout the file.

Thank you in advance!

[alexdobin]

Hi @RacheliHadjez

The chromosome names in GTF and FASTA files have to be exactly the same. If they are different, the GTF and FASTA files are incompatible, and you need to look for others.