I am using the tool seqret from emboss to transform an annotation file in GFF3 format and a FASTA file into an EMBL file because Wormbase does not supply an EMBL file with annotation and sequence together. I am running it on Mac OS X. I got the gff3 and fasta files from Wormbase. I installed emboss using conda from the bioconda channel. I use the following command:
seqret -sequence c_elegans.PRJNA13758.WS263.genomic.fa -feature -fformat gff -fopenfile c_elegans.PRJNA13758.WS263.annotations.gff3 -osformat embl -auto -outseq c_elegans.PRJNA13758.WS263.embl
It fails with the following error:
/Users/me/anaconda/bin/seqret`: line 7: 54774 Killed: 9 _seqret "$@"
/Users/me/anaconda/bin/seqret
is a short file that indeed contains _seqret "$@"
on line 7:
#!/bin/sh
BIN_DIR=$(dirname $(which seqret))
export EMBOSS_ACDROOT=$BIN_DIR/../share/EMBOSS/acd/
export EMBOSS_DATA=$BIN_DIR/../share/EMBOSS/data/
export PLPLOT_LIB=$BIN_DIR/../share/EMBOSS/
_seqret "$@"
I tried to erase it but that did not help.
I also tried EMBLmyGFF3 in a Python 2 environment:
EMBLmyGFF3 c_elegans.PRJNA13758.WS263.annotations.gff3 c_elegans.PRJNA13758.WS263.genomic.fa --topology linear --molecule_type 'genomic DNA' --transl_table 1 --species 'Caenorhabditis elegans' --locus_tag CELE --project_id PRJNA13758 -o c_elegans.PRJNA13758.WS263.annotations.embl
but I just had this message on display for hours:
#############################################################################
# NBIS 2016 - Sweden #
# Authors: Martin Norling, Niclas Jareborg, Jacques Dainat #
# Please visit https://github.com/NBISweden/EMBLmyGFF3 for more information #
#############################################################################
Update 11th March:
I started EMBLmyGFF3 yesterday at 5 pm and this morning it started outputting messages such as:
08:22:08 ERROR feature: >>inverted_repeat<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:22:08 ERROR feature: >>assembly_component<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:22:08 WARNING feature: Unknown qualifier 'genbank' - skipped
08:22:08 ERROR feature: >>tandem_duplication<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:22:08 WARNING feature: Unknown qualifier 'public_name' - skipped
08:22:08 WARNING feature: Unknown qualifier 'polymorphism' - skipped
08:22:08 WARNING feature: Unknown qualifier 'other_name' - skipped
08:22:08 WARNING feature: Unknown qualifier 'consequence' - skipped
08:22:08 WARNING feature: Unknown qualifier 'variation' - skipped
08:22:08 ERROR feature: >>biological_region<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:22:08 WARNING feature: Unknown qualifier 'balancer_type' - skipped
08:22:08 WARNING feature: Unknown qualifier 'balancer' - skipped
08:22:08 ERROR feature: >>protein_match<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:22:08 ERROR feature: >>transcript_region<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:22:08 ERROR feature: >>transcribed_fragment<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
...
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:45:36 ERROR feature: >>piRNA<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:46:00 ERROR feature: >>pseudogenic_tRNA<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:47:59 ERROR feature: >>antisense_RNA<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:47:59 ERROR feature: >>lincRNA<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:48:03 ERROR feature: >>pre_miRNA<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:48:03 ERROR feature: >>miRNA<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
08:50:37 ERROR feature: >>snRNA<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
09:04:00 ERROR feature: >>miRNA_primary_transcript<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
For some of these features, it seems OK to not report them. But for others, such as piRNA, I need to find a solution. C. elegans has got 1000s of piRNAs, it would be nice to have them in the EMBL file. I need to find a list of valid EMBL feature types.
Update + ~ 24h computation:
...
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
12:21:19 ERROR feature: >>scRNA<< is not a valid EMBL feature type. You can ignore this message if you don't need it.
Otherwise tell me which EMBL feature it corresponds to by adding the information within the json mapping file.
Conversion done
My EMBL file is only 1.19 GB compared to the GFF3 3.34 GB, so I probably lost a lot of annotation that is not supported by EMBL.