ORG.Annotate issueshttps://git.metabarcoding.org/org-asm/org-annotate/-/issues2018-08-25T11:39:06Zhttps://git.metabarcoding.org/org-asm/org-annotate/-/issues/21Problem with closely related protein genes2018-08-25T11:39:06ZEric CoissacProblem with closely related protein genesAs example psaA and psaB are two closely related proteins. Therefore the soft annotate at the *psaA* locus a *psaA* gene (that is ok) and a *psaB* gene (that is wrong) and the opposite at the *psaB* locusAs example psaA and psaB are two closely related proteins. Therefore the soft annotate at the *psaA* locus a *psaA* gene (that is ok) and a *psaB* gene (that is wrong) and the opposite at the *psaB* locushttps://git.metabarcoding.org/org-asm/org-annotate/-/issues/20Compilation error for exonerate on ubuntu 16.042018-08-25T11:39:06ZEric CoissacCompilation error for exonerate on ubuntu 16.04The library pthread is not correctly linked The library pthread is not correctly linked https://git.metabarcoding.org/org-asm/org-annotate/-/issues/16line /inference="detect pass:pass1:core"2018-08-25T11:39:06ZMartà Boledaline /inference="detect pass:pass1:core"All CDS annotated have the line /inference="detect pass:pass1:core" below /inference="similar to DNA sequence..."All CDS annotated have the line /inference="detect pass:pass1:core" below /inference="similar to DNA sequence..."https://git.metabarcoding.org/org-asm/org-annotate/-/issues/14blastx concurency issue2018-08-25T11:39:06ZAlain Viariblastx concurency issuethere is a concurency issue when running cds detector
in blastx mode (PASS1_SPEEDUP 1) on several processors
I don't know yet if it comes from the formatting step
or the blast step (I suspect the former)
until this is fixed, don't change teh default settings
(PASS1_SPEEDUP 0)
there is a concurency issue when running cds detector
in blastx mode (PASS1_SPEEDUP 1) on several processors
I don't know yet if it comes from the formatting step
or the blast step (I suspect the former)
until this is fixed, don't change teh default settings
(PASS1_SPEEDUP 0)
Alain ViariAlain Viarihttps://git.metabarcoding.org/org-asm/org-annotate/-/issues/8Exon numbering and reordering is (sometimes) wrong2018-08-25T11:39:06ZAlain ViariExon numbering and reordering is (sometimes) wrongthis should be fixed in cds detector formatting not in org-annotate.sh
```
FT gene complement(4937..6067)
FT /gene="rps16"
FT /locus_tag=""
FT CDS complement(join(4937..5163,6028..6067))
FT /codon_start=1
FT /transl_table=11
FT /gene="rps16"
FT /locus_tag=""
FT /product="ribosomal protein S16"
FT /inference="similar to DNA sequence:NC_007898:LyesC2p087"
FT /translation="MVKLRLKRCGRKQRAVYRIVAIDVRSRREGKDLQKVGFYDPIKNQ
FT TYLNVPAILYFLEKGAQPTETVQDILKKAEVFKELRLNQPKFN"
FT exon complement(6028..6067)
FT /gene="rps16"
FT /locus_tag=""
FT /number=2
FT exon complement(4937..5163)
FT /gene="rps16"
FT /locus_tag=""
FT /number=1
```this should be fixed in cds detector formatting not in org-annotate.sh
```
FT gene complement(4937..6067)
FT /gene="rps16"
FT /locus_tag=""
FT CDS complement(join(4937..5163,6028..6067))
FT /codon_start=1
FT /transl_table=11
FT /gene="rps16"
FT /locus_tag=""
FT /product="ribosomal protein S16"
FT /inference="similar to DNA sequence:NC_007898:LyesC2p087"
FT /translation="MVKLRLKRCGRKQRAVYRIVAIDVRSRREGKDLQKVGFYDPIKNQ
FT TYLNVPAILYFLEKGAQPTETVQDILKKAEVFKELRLNQPKFN"
FT exon complement(6028..6067)
FT /gene="rps16"
FT /locus_tag=""
FT /number=2
FT exon complement(4937..5163)
FT /gene="rps16"
FT /locus_tag=""
FT /number=1
```