GATK: Failed to load reference dictionary

[evonne16]

Hi,
When I use DepthOfCoverage of GATK, the error is 'Failed to load reference dictionary' .
I can't get why.
My command as below:
$java -jar GenomeAnalysisTK.jar \ -T DepthOfCoverage \ -R refall/allRef.fa \ -I mapping/DNAnew.sorted.bam \ -o mapping/dcDNA.targetCoverage

Thanks

[Heisman]

Have you used that same reference dictionary for other commands with the GATK successfully?

[me_myself_andI]

I think you might have to create the dict file manually depending on the GATK version. I see this happening every now and then as well. The extra-complication is that if (my version of) GATK can't read the dict file it will also create an empty reference index file. What works for me is the following:

Before running GATK:

1. test if the reference index (refall/allRef.fa.fai in your case) exists and if it doesn't or if it's of size zero, recreate it with 'samtools faidx'.

2. Also test wether the reference dictionary exists (refall/allRef.fa.dict in your case) and if it doesn't or if it's of size zero recreate it with Picard's CreateSequenceDictionary.

Andreas

EDIT: As pointed out by dGho 'samtools index' was meant to be 'samtools faidx'

[wangli]

Hi, Andreas

I would like to thank you for your very useful information here. I got my similar problem fixed according to your suggestions.
Actually, I have used the same dictionary for other commands of GATK successfully before. So, at first, i feel very confused why it can be used for some command but not others. Following your suggestion, I check my .dict and .fai files again, and i found their size is 0. Then i just deleted them. And type in my command. We donot need to use samtools or picard to generate these two files. The new version of GATK can generate itself. But i donot know why after running through a command, these two files turn to 0 size and we need to generate them again. That is weird. But my problem is solved. Thanks again!

[dGho]

1. test if the reference index (refall/allRef.fa.fai in your case) exists and if it doesn't or if it's of size zero, recreate it with 'samtools index'.

Your comment was very useful, but just for reference or for future readers, I believe you meant the following command to create a ref index:

samtools faidx refall/allRef.fa

[me_myself_andI]

Yes, that's right!