GATK "We encountered a non-standard non-IUPAC base in the provided reference: '13"

Question

[Phismil]

Hello Team,

I am trying to run GATK

java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R reference.fasta -I header.bam -o realigned.intervals

My reference is a trinity assembled genome with GO terms in fasta header and already indexed. I get error:

Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '13

Any idea what is going wrong?

Regards

[5heikki]

There's a non-standard non-IUPAC base in your reference.fasta? Output of:

grep -v '^>' reference.fasta | sed 's/[a,A,g,G,c,C,t,T,u,U]//g'

?

Alternatively, it could be related to the encoding of your file, in which case e.g. dos2unix could be a solution. Google knows a lot about your problem..

[Devon Ryan]

This will be due to a \r (ascii 13), so you nailed it with dos2unix.

[Phismil]

Thanks for your suggestions !

[skdv2522]

same issue. how can i resolve it. kindly give me the suggestion

[skdv2522]

Command

sudo java -jar gatk-package-4.5.0.0-local.jar HaplotypeCaller -R /home/user/Downloads/STEVIA_GENOME/Stevia\ rebaudiana_genome.fasta -I /home/data/transcriptome_combine_stress_stevia/37_added_sorted.bam -O C_L15_2.vcf -ERC GVCF

[25 September 2024 at 2:23:52 pm IST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 9.33 minutes.
Runtime.totalMemory()=4395630592
***********************************************************************

A USER ERROR has occurred: Bad input: We encountered a non-standard non-IUPAC base in the provided input sequence: '45'

Above is the error I got

[GenoMax]

Did you try the commands noted above?

[skdv2522]

which command you are talking about

[GenoMax]

Click here --> GATK "We encountered a non-standard non-IUPAC base in the provided reference: '13"

[skdv2522]

i have gone through this but couldn't tackle the problem. could you please explain a little

[skdv2522]

9:42:57.242 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0
19:42:57.242 INFO  SmithWatermanAligner - Total compute time in native Smith-Waterman : 0.00 sec
19:42:57.244 INFO  HaplotypeCaller - Shutting down engine
[4 October 2024 at 7:42:57 pm IST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 7.75 minutes.
Runtime.totalMemory()=2717908992
***********************************************************************

A USER ERROR has occurred: Bad input: We encountered a non-standard non-IUPAC base in the provided input sequence: '45'

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

get error while running gatk snp calling