RSEM error preparing index file with mouse mm10 genome reference files and Refseq
I got the error preparing index file of refseq with RSEM.
GCF_000001635.26_GRCm38.p6_genomic.fna
GCF_000001635.26_GRCm38.p6_genomic.gff
Dose anyone have idea why Im getting error under?
rsem-refseq-extract-primary-assembly GCF_000001635.26_GRCm38.p6_genomic.fna GCF_000001635.26_GRCm38.p6_genomic.primary_assembly.fna
rsem-prepare-reference --gff3 GCF_000001635.26_GRCm38.p6_genomic.gff --trusted-sources BestRefSeq --bowtie GCF_000001635.26_GRCm38.p6_genomic.primary_assembly.fna ref/mouse_refseq
rsem-gff3-to-gtf GCF_000001635.26_GRCm38.p6_genomic.gff ref/mouse.gtf
Loaded 100000 lines
Loaded 200000 lines
...
Loaded 2200000 lines
Loaded 2300000 lines
Cannot recognize transcript rna200's parent rna199, a gene feature might be missing.
"rsem-gff3-to-gtf GCF_000001635.26_GRCm38.p6_genomic.gff ref/mouse.gtf" failed! Plase check if you provide correct parameters/options for the pipeline!
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torihikitorti •
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