ERROR MESSAGE: Fasta index file

Question

[granecious]

Good day

Can someone please assist me with the following. I am new to GATK(3.8), and I want to run the RealignerTargetCreator command according to what is specified on the GATK website.

This is my specific command:

>singularity exec /tools/containers/gatk/gatk-3.8--py36_4.simg java -jar GenomeAnalysisTK.jar \
-T RealignerTargetCreator \
-R ~/Analysis_data/GATK/refs/ref.fa \
-known ~/Analysis_data/GATK/Mills_and_1000G_gold_standard.indels.hg38.vcf \
-known ~/Analysis_data/GATK/Homo_sapiens_assembly38.known_indels.vcf \
-I marked_dup.bam \
-o forIndelRealigner.intervals

but I get the following error message:

> ERROR MESSAGE: Fasta index file /usr/people/sfernol/Analysis_data/GATK/refs/ref.fasta.fai.fai for reference /usr/people/sfernol/Analysis_data/GATK/refs/ref.fasta.fai does not exist.

I read up on similar problems and I tried putting the different reference files in the same location, but i still get the same error.

I used Picard for creating the .dict file and samtools for indexing my reference genome file, so i have those two files and the original fasta file in the same folder.

I am not sure what I am doing wrong, please help?

Answer 1

[Pierre Lindenbaum]

samtools faidx  ~/Analysis_data/GATK/refs/ref.fa

https://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference

We use the faidx command in samtools to prepare the fasta index file. This file describes byte offsets in the fasta file for each contig, allowing us to compute exactly where a particular reference base at contig:pos is in the fasta file.

[granecious]

Hi

I managed to solve my problem. I had to rename my sam indexed file to correspond to my ref.fa, since my file formats were different GATK could not pick up my index file.

I renamed my index file from ref.fasta.fai to ref.fa.fai and it worked.

Answer 2

[Jahad Soorni]

We had same error. When we re-create the dict file with no ".fa.dict" suffix, but only ".dcit" suffix, it work correctly.

Answer 3

[Azhar Jameel]

we have the same error; The specified fasta file doesn't exist, renamed according to the given suggestion above, and run multiple times still the same issue. is there any suggestion please. thanks