ORG.Annotate issueshttps://git.metabarcoding.org/org-asm/org-annotate/-/issues2018-08-25T11:39:05Zhttps://git.metabarcoding.org/org-asm/org-annotate/-/issues/18Add an header to the generated embl file2018-08-25T11:39:05ZEric CoissacAdd an header to the generated embl file```
ID XXX; XXX; circular; genomic DNA; XXX; XXX; ### BP.
XX
AC XXX;
XX
DE {organism} plastid, complete genome.
XX
``````
ID XXX; XXX; circular; genomic DNA; XXX; XXX; ### BP.
XX
AC XXX;
XX
DE {organism} plastid, complete genome.
XX
```https://git.metabarcoding.org/org-asm/org-annotate/-/issues/15tRNAs with intron are longer than expected2018-08-25T11:39:06ZMartí BoledatRNAs with intron are longer than expectedtRNa with an intron are around 110 nt long instead of 70-85. Usually one exon has the correct length (30-40 nt) and the other one is about 70-85 nt.[Arabidopsis_thaliana_NC_000932.embl](https://git.metabarcoding.org/org-asm/org-annotate/uploads/4d7dda030f1337dec1dfd3eb1f460b00/Arabidopsis_thaliana_NC_000932.embl)
tRNa with an intron are around 110 nt long instead of 70-85. Usually one exon has the correct length (30-40 nt) and the other one is about 70-85 nt.[Arabidopsis_thaliana_NC_000932.embl](https://git.metabarcoding.org/org-asm/org-annotate/uploads/4d7dda030f1337dec1dfd3eb1f460b00/Arabidopsis_thaliana_NC_000932.embl)
https://git.metabarcoding.org/org-asm/org-annotate/-/issues/13how about adding gawk/awk in Org binaries2018-08-25T11:39:06ZAlain Viarihow about adding gawk/awk in Org binariesI'm considering adding the proper version of gawk/awk (4.0.1) in the ORG.annot binaries
(the distro is already in src/_unix_tools_ but not installed by default)
this will require a bit more time during compilation but this is a breeze
by comparison to exonerate libraries ;-)
what about this ?
I'm considering adding the proper version of gawk/awk (4.0.1) in the ORG.annot binaries
(the distro is already in src/_unix_tools_ but not installed by default)
this will require a bit more time during compilation but this is a breeze
by comparison to exonerate libraries ;-)
what about this ?
Alain ViariAlain Viarihttps://git.metabarcoding.org/org-asm/org-annotate/-/issues/12Perhaps too many partial CDS2018-08-25T11:39:06ZEric CoissacPerhaps too many partial CDSMany CDS as partial mapping (with locations including '<' and/or '>').
Perhaps the rule is too stringent.
Example of Picea abies: -> no full CDS
```
FT CDS complement(<938..>1168)
FT CDS complement(<5338..>5748)
FT CDS complement(<5760..>7235)
FT CDS join(<6912..6937,10074..10345,10382..>10959)
FT CDS <7943..>9367
FT CDS <11547..>11654
FT CDS <12224..>12775
FT CDS <13614..>14396
FT CDS <14625..>15617
FT CDS complement(<16636..>16755)
FT CDS complement(<16877..>16990)
FT CDS complement(<17027..>17143)
FT CDS complement(<17156..>17404)
FT CDS <18645..>18830
FT CDS <18938..>19048
FT CDS <19786..>19911
FT CDS <20231..>20434
FT CDS <20561..>20839
FT CDS complement(<21105..>21461)
FT CDS complement(<22459..>23046)
FT CDS <23912..>24052
FT CDS complement(<24184..>24309)
FT CDS complement(<24783..>24959)
FT CDS <28739..>30283
FT CDS <30974..>32032
FT CDS <32815..>39192
FT CDS complement(<41560..>42024)
FT CDS <45623..>45832
FT CDS <47379..>48338
FT CDS complement(<50285..>50527)
FT CDS complement(<51893..>52156)
FT CDS complement(<52492..>57822)
FT CDS <71679..>72737
FT CDS <72688..>74106
FT CDS <74681..>74866
FT CDS complement(<75512..>75808)
FT CDS complement(<75961..>78162)
FT CDS complement(<78191..>80440)
FT CDS complement(join(<78209..78541,78575..>80347))
FT CDS complement(join(<81069..81221,81933..82158,82874..>83004))
FT CDS complement(<84100..>84702)
FT CDS complement(<86950..>87447)
FT CDS <88719..>88991
FT CDS join(<89021..89414,90092..>90525)
FT CDS <90583..>90858
FT CDS <90892..>91317
FT CDS <91305..>91958
FT CDS <92911..>93327
FT CDS <93448..>93813
FT CDS <93962..>94357
FT CDS <94498..>94731
FT CDS <94837..>94947
FT CDS <95033..>95422
FT CDS <95485..>96492
FT CDS complement(<96607..>97134)
FT CDS complement(<98056..>98754)
FT CDS complement(<99667..>99891)
FT CDS <99971..>100099
FT CDS complement(<100187..>100291)
FT CDS complement(<100369..>101892)
FT CDS complement(<104101..>105621)
FT CDS complement(join(<105668..106069,106841..>106990))
FT CDS complement(<107323..>107565)
FT CDS complement(<108258..>109001)
FT CDS complement(<109301..>110047)
FT CDS complement(<110208..>113861)
FT CDS complement(join(<113958..115613,116294..>116725))
FT CDS complement(<116751..>119978)
FT CDS <120782..>120877
FT CDS complement(<121780..>121983)
FT CDS <123650..>123775
```
Many CDS as partial mapping (with locations including '<' and/or '>').
Perhaps the rule is too stringent.
Example of Picea abies: -> no full CDS
```
FT CDS complement(<938..>1168)
FT CDS complement(<5338..>5748)
FT CDS complement(<5760..>7235)
FT CDS join(<6912..6937,10074..10345,10382..>10959)
FT CDS <7943..>9367
FT CDS <11547..>11654
FT CDS <12224..>12775
FT CDS <13614..>14396
FT CDS <14625..>15617
FT CDS complement(<16636..>16755)
FT CDS complement(<16877..>16990)
FT CDS complement(<17027..>17143)
FT CDS complement(<17156..>17404)
FT CDS <18645..>18830
FT CDS <18938..>19048
FT CDS <19786..>19911
FT CDS <20231..>20434
FT CDS <20561..>20839
FT CDS complement(<21105..>21461)
FT CDS complement(<22459..>23046)
FT CDS <23912..>24052
FT CDS complement(<24184..>24309)
FT CDS complement(<24783..>24959)
FT CDS <28739..>30283
FT CDS <30974..>32032
FT CDS <32815..>39192
FT CDS complement(<41560..>42024)
FT CDS <45623..>45832
FT CDS <47379..>48338
FT CDS complement(<50285..>50527)
FT CDS complement(<51893..>52156)
FT CDS complement(<52492..>57822)
FT CDS <71679..>72737
FT CDS <72688..>74106
FT CDS <74681..>74866
FT CDS complement(<75512..>75808)
FT CDS complement(<75961..>78162)
FT CDS complement(<78191..>80440)
FT CDS complement(join(<78209..78541,78575..>80347))
FT CDS complement(join(<81069..81221,81933..82158,82874..>83004))
FT CDS complement(<84100..>84702)
FT CDS complement(<86950..>87447)
FT CDS <88719..>88991
FT CDS join(<89021..89414,90092..>90525)
FT CDS <90583..>90858
FT CDS <90892..>91317
FT CDS <91305..>91958
FT CDS <92911..>93327
FT CDS <93448..>93813
FT CDS <93962..>94357
FT CDS <94498..>94731
FT CDS <94837..>94947
FT CDS <95033..>95422
FT CDS <95485..>96492
FT CDS complement(<96607..>97134)
FT CDS complement(<98056..>98754)
FT CDS complement(<99667..>99891)
FT CDS <99971..>100099
FT CDS complement(<100187..>100291)
FT CDS complement(<100369..>101892)
FT CDS complement(<104101..>105621)
FT CDS complement(join(<105668..106069,106841..>106990))
FT CDS complement(<107323..>107565)
FT CDS complement(<108258..>109001)
FT CDS complement(<109301..>110047)
FT CDS complement(<110208..>113861)
FT CDS complement(join(<113958..115613,116294..>116725))
FT CDS complement(<116751..>119978)
FT CDS <120782..>120877
FT CDS complement(<121780..>121983)
FT CDS <123650..>123775
```
Alain ViariAlain Viarihttps://git.metabarcoding.org/org-asm/org-annotate/-/issues/10Small and Large single copies seems to be exchanged in the annotation2018-08-25T11:39:06ZMartí BoledaSmall and Large single copies seems to be exchanged in the annotationhttps://git.metabarcoding.org/org-asm/org-annotate/-/issues/9Perhaps we have to enforce static linking for binaries2018-08-25T11:39:06ZEric CoissacPerhaps we have to enforce static linking for binariesWhen I am compiling organist on our cluster, I get trouble because of the multiple version of glib2. Perhaps that if we switch to static linking, this will ensure that our installer will be portable.When I am compiling organist on our cluster, I get trouble because of the multiple version of glib2. Perhaps that if we switch to static linking, this will ensure that our installer will be portable.https://git.metabarcoding.org/org-asm/org-annotate/-/issues/6Reordering of feature has a bug2018-08-25T11:39:06ZEric CoissacReordering of feature has a bugShould be related to several features at the same coordinates
```
FT CDS complement(15013..15723)
FT gene complement(15013..15723)
FT /codon_start=1
FT /gene="rps2"
FT /locus_tag=""
FT /transl_table=11
FT /gene="rps2"
FT /locus_tag=""
FT /product=ribosomal protein S2
FT /inference="similar to DNA sequence:NC_009267:OlpuCp010"
FT /translation="MTKRYWNIDLEEMMRAGVHFGHGTRKWNPRMAPYISAKRKGIHII
FT NLTRTARFLSEACDLVFDAASRGKQFLIVGTKNKAADLVSRAAIRARCHYVNKKWLGGM
FT LTNWSTTEKRLHKFRDLRTEQKTEGFNRLPKRDAAVLKRQLSRLETYLGGIKYMTGLPD
FT IVIILDQQEEYTALRECITLGIPTISLIDTNCNPDLADISIPANDDAIASIRFILNKLV
FT FAICEGRSSYIQNS"
```Should be related to several features at the same coordinates
```
FT CDS complement(15013..15723)
FT gene complement(15013..15723)
FT /codon_start=1
FT /gene="rps2"
FT /locus_tag=""
FT /transl_table=11
FT /gene="rps2"
FT /locus_tag=""
FT /product=ribosomal protein S2
FT /inference="similar to DNA sequence:NC_009267:OlpuCp010"
FT /translation="MTKRYWNIDLEEMMRAGVHFGHGTRKWNPRMAPYISAKRKGIHII
FT NLTRTARFLSEACDLVFDAASRGKQFLIVGTKNKAADLVSRAAIRARCHYVNKKWLGGM
FT LTNWSTTEKRLHKFRDLRTEQKTEGFNRLPKRDAAVLKRQLSRLETYLGGIKYMTGLPD
FT IVIILDQQEEYTALRECITLGIPTISLIDTNCNPDLADISIPANDDAIASIRFILNKLV
FT FAICEGRSSYIQNS"
```https://git.metabarcoding.org/org-asm/org-annotate/-/issues/5There is no quotes around the product qualifier:2018-08-25T11:39:06ZEric CoissacThere is no quotes around the product qualifier:Quotes are missing around the product qualifier
```
FT /locus_tag=""
FT /product=RNA polymerase beta'' subunit
FT /inference="similar to DNA sequence:NC_021102:L053_p074"
```Quotes are missing around the product qualifier
```
FT /locus_tag=""
FT /product=RNA polymerase beta'' subunit
FT /inference="similar to DNA sequence:NC_021102:L053_p074"
```https://git.metabarcoding.org/org-asm/org-annotate/-/issues/3muscle CentOS2018-08-25T11:39:06ZAlain Viarimuscle CentOS
pb compil muscle sous linux CentOS
à partir du Makefile principal
ça marche si lancé depuis le sous-directory muscle
pb compil muscle sous linux CentOS
à partir du Makefile principal
ça marche si lancé depuis le sous-directory muscleAlain ViariAlain Viarihttps://git.metabarcoding.org/org-asm/org-annotate/-/issues/2Makefile(s)2018-08-25T11:39:06ZAlain ViariMakefile(s)revoir tous les Makefile dans src
o ceux de repseek, muscle et sumatra ne répondent pas a clean/portclean
o nettoyer le makefile de repseek
o la target clean doit nettoyer localement pas effacer le port ;-)
revoir tous les Makefile dans src
o ceux de repseek, muscle et sumatra ne répondent pas a clean/portclean
o nettoyer le makefile de repseek
o la target clean doit nettoyer localement pas effacer le port ;-)
Alain ViariAlain Viarihttps://git.metabarcoding.org/org-asm/org-annotate/-/issues/1test issue2018-08-25T11:39:06ZAlain Viaritest issuetest issue org.annotatetest issue org.annotateAlain ViariAlain Viari