Issue loading GTF

[EglantineMB]

Hi,

I am trying to load a gtf file but run into an error I could not solve using the importGTF function:

Step 1 of 10: Checking data... Step 2 of 10: Obtaining annotation... importing GTF (this may take a while)... Error in $<-.data.frame(*tmp*, "cumSum", value = c(0, 1064, 0, 1061, : replacement has 2 rows, data has 6

I managed to identify the gene that was in cause, and apparently I managed to load the file only when I remove one of their exon. Howver, I am particularly interested in this gene and would need to be able to load the whole file. I included below a subset of the gtf file I tried to load unsucessfully.

Thank you for any help that will be given!

GTF file :

000018F PacBio exon 1793400 1794072 . - . transcript_id "PB.4856.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1794134 1794417 . - . transcript_id "PB.4856.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1795099 1795268 . - . transcript_id "PB.4856.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1795345 1795770 . - . transcript_id "PB.4856.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1793963 1794072 . - 2 transcript_id "PB.4856.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1793963 1794072 . - 2 transcript_id "PB.4856.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1794134 1794417 . - 1 transcript_id "PB.4856.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1795099 1795268 . - 0 transcript_id "PB.4856.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1795345 1795434 . - 0 transcript_id "PB.4856.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1793475 1795770 . - . transcript_id "PB.4856.2"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1793475 1794072 . - . transcript_id "PB.4316.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1794134 1794417 . - . transcript_id "PB.4316.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1795099 1795268 . - . transcript_id "PB.4316.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1795345 1795772 . - . transcript_id "PB.4316.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1793963 1794072 . - 2 transcript_id "PB.4316.1"; gene_id "maker-000018F-augustus-gene-17.59"; 00018F PacBio CDS 1794134 1794417 . - 1 transcript_id "PB.4316.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1795099 1795268 . - 0 transcript_id "PB.4316.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1795345 1795434 . - 0 transcript_id "PB.4316.1"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1793925 1794072 . - . transcript_id "PB.4856.3"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1794134 1794417 . - . transcript_id "PB.4856.3"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1795099 1795268 . - . transcript_id "PB.4856.3"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio exon 1795345 1795770 . - . transcript_id "PB.4856.3"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1793963 1794072 . - 2 transcript_id "PB.4856.3"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1794134 1794417 . - 1 transcript_id "PB.4856.3"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1795099 1795268 . - 0 transcript_id "PB.4856.3"; gene_id "maker-000018F-augustus-gene-17.59"; 000018F PacBio CDS 1795345 1795434 . - 0 transcript_id "PB.4856.3"; gene_id "maker-000018F-august

[kvittingseerup]

Could you highlight the problematic exon?

[EglantineMB]

Actually when I remove any of the exon the file can load, so I don't know which one is faulty.