Hello, I am working with the GenomicFeatures package to create the txdb file needed for downstream analyses but am encountering a number of warnings and am unable to successfully create a txdb file. From my online searchers I have not been able to find a remedy and wonder if anyone might had advice on how best to move forward? Thanks in advance!
The command I am running is: txdb <- makeTxDbFromGFF("GCF_000002285.3_CanFam3.1_genomic.gff", format = "gff")
With the output and Warning messages:
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Error in extension_load(db@ptr, lib_path, "sqlite3_math_init") :
object '_RSQLite_extension_load' not found
In addition: Warning messages:
1: In for (i in seq_len(n)) { :
closing unused connection 3 (C:/Users/Cara N Love/Dropbox (Personal)/A-UGA/Belarus/RNAseq/Canids/Reference/Salmon/GCF_000002285.3_CanFam3.1_genomic.gff)
2: call dbDisconnect() when finished working with a connection
3: In .extract_exons_from_GRanges(exon_IDX, gr, mcols0, tx_IDX, feature = "exon", :
414 exons couldn't be linked to a transcript so were dropped (showing only the first 6):
seqid start end strand ID Name Parent Parent_type
1 NC_006590.3 2210548 2210701 + id254068 id254068 id254067 <na>
2 NC_006590.3 2210867 2211297 + id254069 id254069 id254067 <na>
3 NC_006590.3 2233270 2233690 + id254071 id254071 id254070 <na>
4 NC_006590.3 2233883 2234387 + id254072 id254072 id254070 <na>
5 NC_006590.3 2264472 2264475 + id254075 id254075 id254074 <na>
6 NC_006590.3 2264792 2264917 + id254076 id254076 id254074 <na>
4: In .extract_exons_from_GRanges(cds_IDX, gr, mcols0, tx_IDX, feature = "cds", :
410 CDS couldn't be linked to a transcript so were dropped (showing only the first 6):
seqid start end strand ID Name Parent Parent_type
1 NC_006590.3 2210650 2210701 + cds16766 <na> id254067 <na>
2 NC_006590.3 2210867 2211297 + cds16766 <na> id254067 <na>
3 NC_006590.3 2233501 2233690 + cds16767 <na> id254070 <na>
4 NC_006590.3 2233883 2234310 + cds16767 <na> id254070 <na>
5 NC_006590.3 2264472 2264475 + cds16768 <na> id254074 <na>
6 NC_006590.3 2264792 2264917 + cds16768 <na> id254074 <na>
5: In .find_exon_cds(exons, cds) :
The following transcripts have exons that contain more than one CDS (only the first CDS was kept for each
exon): rna40274, rna47965, rna54836, rna71421
6: Couldn't set synchronous mode: Not compatible with requested type: [type=builtin; target=logical].
Use synchronous = NULL to turn off this warning.
As an additinal note: I have attempted adding synchronous = NULL to furn off the final warning and this is also unsuccessful.
Thanks for any help!
