ERROR MESSAGE: Fasta index file
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3.1 years ago
granecious • 0

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.

genome • 5.0k views
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3.1 years ago
samtools faidx  ~/Analysis_data/GATK/refs/ref.fa


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.

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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.

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6 months ago

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

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11 weeks ago

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