Non IUPAC error on hg38 GATK FASTA

Question

[win]

hi all, i downloaded the Homo_sapiens_assembly38.fasta from GATK cloud including all the indices.

when i try to run GATK TargetRealignerCreator I am getting error, non IUPAC code found in reference: 70

what does this mean? I have not manipulated the reference FASTA in any way.

also i have tried dos2unix Homo_sapiens_assembly38.fasta and it not make any difference.

any ideas anyone?

[Pierre Lindenbaum]

output of

$ file Homo_sapiens_assembly38.fasta
$ grep -v '>' Homo_sapiens_assembly38.fasta | tr -d "\n\r ATGCNatgcn"

?

[win]

The first commands output is ASCII Text The second commands output is FMRY@RFYWYYKWMRYWBYYWB@FYRYSYRYYURRRYWMWWYMKYYWYKKMYRRRWRRYYBRRRRKWRS@YYMOYKYRRSKYWYYRYRYKMMRRWYRYYYRSW

what does this mean and how may it be removed?

[Pierre Lindenbaum]

it's not a fasta file. I would say it's just a FASTQ file.

what is the output of

$ head Homo_sapiens_assembly38.fasta

[win]

    >chr1  AC:CM000663.2  gi:568336023  LN:248956422  rl:Chromosome  M5:6aef897c3d6ff0c78aff06ac189178dd  AS:GRCh38
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

[Cricket]

@win -- did you find a solution to your issue?