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Hello,

I have been having issues using the snp2go functions for my non-model organism because the output produces enriched results but does not include the number of regions associated with each significant GO term. My organism is annotated using SnpEff and Panther so I have GO term associations, I am just confused why the results are returning these objects with NAs.

Attached is a picture of my GTF:

This is a picture of the GO association file:

Here is the output of SNP2GO:

Any help will be greatly appreciated, I assume it is a formatting issue or something simple like that I just cannot figure it out!

Best,
Connor Murray

Hello,
I am trying to use SNP2GO with a gff3 annotation file. It starts reading the file (Reading Pacla8A.gff3) and crashes with error:

Error in .Call2("Rle_constructor", values, lengths, PACKAGE = "S4Vectors") : Rle of type 'list' is not supported

I tried to run the same command line with my SNP data but another "gff" and it works nicely. So the problem should come from the annotation file but I have no idea of where/what to look since everything looks fine (9 columns, "Ontology_term" etc).

I am quite lost with this annotation since it was done in another lab and this is a bit far from my skills. Any input would be very welcome.
Thank you

Here is the command line I use:

candidates <- read.delim("signif_snps.vcf",sep = " ", header=FALSE,comment.char="#")
candidates[,2] <- as.numeric(candidates[,2])

noncandidates <- read.delim("all_snps.vcf",sep = " ", header=FALSE,comment.char="#")
noncandidates[,2] <- as.numeric(noncandidates[,2])

snps_cand <- GRanges(seqnames=candidates[,1],ranges=IRanges(candidates[,2],candidates[,2]))
snps_non_cand <- GRanges(seqnames=noncandidates[,1],ranges=IRanges(noncandidates[,2],noncandidates[,2]))


x <- snp2go(gff="Pacla8A.gff3",
            candidateSNPs=snps_cand,
            noncandidateSNPs=snps_non_cand)

Here are the first lines of the gff3:

pcla8_s000007 CNAG gene 34 20855 . + . ID=Pacla8A056872;gene_type=protein_coding pcla8_s000007 CNAG transcript 34 18362 . + . ID=Pacla8A056872T1;Parent=Pacla8A056872;Name=Pacla8A056872T1;product=Pacla8A056872P1;gene_type=protein_coding;transcript_biotype=protein_coding;Description=ABC transporter G family member 21 , partial;Ontology_term=GO:0004871%2C GO:0005516%2C GO:0005524%2C GO:0005737%2C GO:0007165%2C GO:0016020%2C GO:0016887 pcla8_s000007 CNAG exon 34 72 . + . ID=Pacla8A056872T1.exon1;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 153 259 . + . ID=Pacla8A056872T1.exon2;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 464 527 . + . ID=Pacla8A056872T1.exon3;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 599 674 . + . ID=Pacla8A056872T1.exon4;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 1050 1136 . + . ID=Pacla8A056872T1.exon5;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 1261 1327 . + . ID=Pacla8A056872T1.exon6;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 3057 3186 . + . ID=Pacla8A056872T1.exon7;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 3260 3278 . + . ID=Pacla8A056872T1.exon8;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 3330 3331 . + . ID=Pacla8A056872T1.exon9;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 3438 3515 . + . ID=Pacla8A056872T1.exon10;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 3779 3781 . + . ID=Pacla8A056872T1.exon11;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 5357 5364 . + . ID=Pacla8A056872T1.exon12;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 8738 8898 . + . ID=Pacla8A056872T1.exon13;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 10123 10298 . + . ID=Pacla8A056872T1.exon14;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 10658 10714 . + . ID=Pacla8A056872T1.exon15;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 10819 10867 . + . ID=Pacla8A056872T1.exon16;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 10992 11027 . + . ID=Pacla8A056872T1.exon17;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 12131 12195 . + . ID=Pacla8A056872T1.exon18;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 12813 12974 . + . ID=Pacla8A056872T1.exon19;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 13191 13284 . + . ID=Pacla8A056872T1.exon20;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 13444 13504 . + . ID=Pacla8A056872T1.exon21;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 15295 15853 . + . ID=Pacla8A056872T1.exon22;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 16087 16170 . + . ID=Pacla8A056872T1.exon23;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 16476 16533 . + . ID=Pacla8A056872T1.exon24;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 16839 17053 . + . ID=Pacla8A056872T1.exon25;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 17585 17793 . + . ID=Pacla8A056872T1.exon26;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG exon 18176 18362 . + . ID=Pacla8A056872T1.exon27;Parent=Pacla8A056872T1;Name=Pacla8A056872T1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 34 72 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 153 259 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 464 527 . + 1 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 599 674 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 1050 1136 . + 2 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 1261 1327 . + 2 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 3057 3186 . + 1 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 3260 3278 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 3330 3331 . + 2 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 3438 3515 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 3779 3781 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 5357 5364 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 8738 8898 . + 1 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 10123 10298 . + 2 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 10658 10714 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 10819 10867 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 10992 11027 . + 2 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 12131 12195 . + 2 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 12813 12974 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 13191 13284 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 13444 13504 . + 2 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 15295 15853 . + 1 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 16087 16170 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 16476 16533 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 16839 17053 . + 2 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 17585 17793 . + 0 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG CDS 18176 18362 . + 1 ID=Pacla8A056872C1;Parent=Pacla8A056872T1;Name=Pacla8A056872C1;gene_type=protein_coding;transcript_biotype=protein_coding pcla8_s000007 CNAG transcript 8354 20855 . + . ID=Pacla8A056872T2;Parent=Pacla8A056872;Name=Pacla8A056872T2;product=Pacla8A056872P2;gene_type=protein_coding;transcript_biotype=protein_coding;Description=ABC transporter G family member 14 isoform X3;Ontology_term=GO:0005524%2C GO:0016020%2C GO:0016887