diff --git a/nextclade/resources/all-clades/clades.tsv b/nextclade/resources/all-clades/clades.tsv index a8a5c3f..4ebd146 100644 --- a/nextclade/resources/all-clades/clades.tsv +++ b/nextclade/resources/all-clades/clades.tsv @@ -73,6 +73,19 @@ C.1.1 clade C.1 C.1.1 nuc 21062 T C.1.1 nuc 149963 T +E.1 clade C.1.1 +E.1 nuc 13563 A +E.1 nuc 121394 T +E.1 nuc 162280 A + +E.2 clade C.1.1 +E.2 nuc 13563 A +E.2 nuc 151847 A +E.2 nuc 37738 T + +E.3 clade C.1.1 +E.3 nuc 142797 T + B.1.4 clade B.1 B.1.4 nuc 34308 A @@ -82,6 +95,12 @@ B.1.5 nuc 70780 T B.1.6 clade B.1 B.1.6 nuc 111029 A +D.1 clade B.1.6 +D.1 nuc 10945 A +D.1 nuc 39515 A +D.1 nuc 44627 T +D.1 nuc 56276 A + B.1.7 clade B.1 B.1.7 nuc 25644 T @@ -136,6 +155,37 @@ B.1.20 nuc 53326 A B.1.20 nuc 164385 T B.1.20 nuc 187620 T +F.1 clade B.1.20 +F.1 nuc 11668 A +F.1 nuc 35132 A +F.1 nuc 70414 T +F.1 nuc 70666 T +F.1 nuc 96938 T + +F.2 clade B.1.20 +F.2 nuc 161629 A +F.2 nuc 22167 T + +F.3 clade B.1.20 +F.3 nuc 174050 T +F.3 nuc 180618 T + +F.4 clade B.1.20 +F.4 nuc 34277 T +F.4 nuc 92382 T +F.4 nuc 122551 T +F.4 nuc 126919 A +F.4 nuc 176643 A + +F.5 clade B.1.20 +F.5 nuc 150831 T +F.5 nuc 126169 A + +F.6 clade B.1.20 +F.6 nuc 146690 A +F.6 nuc 159608 T +F.6 nuc 168964 A + B.1.21 clade B.1 B.1.21 nuc 22415 A B.1.21 nuc 132698 T @@ -143,3 +193,8 @@ B.1.21 nuc 132698 T B.1.22 clade B.1 B.1.22 nuc 34784 T B.1.22 nuc 101418 T + +B.1.23 clade B.1 +B.1.23 nuc 27935 A +B.1.23 nuc 64171 G +B.1.23 nuc 73235 T \ No newline at end of file diff --git a/nextclade/resources/all-clades/include_accessions.txt b/nextclade/resources/all-clades/include_accessions.txt index 4153924..c3d4d62 100644 --- a/nextclade/resources/all-clades/include_accessions.txt +++ b/nextclade/resources/all-clades/include_accessions.txt @@ -7,6 +7,7 @@ MK783033 #reference for A.3 ON674051 #reference for A.2 ON676707 #reference for A.2 ON675438 #reference for A.2 +OP612690 #reference for A.2 ON676707 #reference for A.2.3 OP555515 #reference for A.2.3 OP450997 #reference for A.2.2 diff --git a/nextclade/resources/clade-iib/clades.tsv b/nextclade/resources/clade-iib/clades.tsv index 710fec3..664b4b8 100644 --- a/nextclade/resources/clade-iib/clades.tsv +++ b/nextclade/resources/clade-iib/clades.tsv @@ -56,6 +56,19 @@ C.1.1 clade C.1 C.1.1 nuc 21062 T C.1.1 nuc 149963 T +E.1 clade C.1.1 +E.1 nuc 13563 A +E.1 nuc 121394 T +E.1 nuc 162280 A + +E.2 clade C.1.1 +E.2 nuc 13563 A +E.2 nuc 151847 A +E.2 nuc 37738 T + +E.3 clade C.1.1 +E.3 nuc 142797 T + B.1.4 clade B.1 B.1.4 nuc 34308 A @@ -65,6 +78,12 @@ B.1.5 nuc 70780 T B.1.6 clade B.1 B.1.6 nuc 111029 A +D.1 clade B.1.6 +D.1 nuc 10945 A +D.1 nuc 39515 A +D.1 nuc 44627 T +D.1 nuc 56276 A + B.1.7 clade B.1 B.1.7 nuc 25644 T @@ -119,6 +138,37 @@ B.1.20 nuc 53326 A B.1.20 nuc 164385 T B.1.20 nuc 187620 T +F.1 clade B.1.20 +F.1 nuc 11668 A +F.1 nuc 35132 A +F.1 nuc 70414 T +F.1 nuc 70666 T +F.1 nuc 96938 T + +F.2 clade B.1.20 +F.2 nuc 161629 A +F.2 nuc 22167 T + +F.3 clade B.1.20 +F.3 nuc 174050 T +F.3 nuc 180618 T + +F.4 clade B.1.20 +F.4 nuc 34277 T +F.4 nuc 92382 T +F.4 nuc 122551 T +F.4 nuc 126919 A +F.4 nuc 176643 A + +F.5 clade B.1.20 +F.5 nuc 150831 T +F.5 nuc 126169 A + +F.6 clade B.1.20 +F.6 nuc 146690 A +F.6 nuc 159608 T +F.6 nuc 168964 A + B.1.21 clade B.1 B.1.21 nuc 22415 A B.1.21 nuc 132698 T @@ -126,3 +176,8 @@ B.1.21 nuc 132698 T B.1.22 clade B.1 B.1.22 nuc 34784 T B.1.22 nuc 101418 T + +B.1.23 clade B.1 +B.1.23 nuc 27935 A +B.1.23 nuc 64171 G +B.1.23 nuc 73235 T \ No newline at end of file diff --git a/nextclade/resources/clade-iib/include_accessions.txt b/nextclade/resources/clade-iib/include_accessions.txt index 9400b2d..593d3f7 100644 --- a/nextclade/resources/clade-iib/include_accessions.txt +++ b/nextclade/resources/clade-iib/include_accessions.txt @@ -8,6 +8,7 @@ MK783033 #reference for A.3 ON674051 #reference for A.2 ON676707 #reference for A.2 ON675438 #reference for A.2 +OP612690 #reference for A.2 ON676707 #reference for A.2.3 OP555515 #reference for A.2.3 OP450997 #reference for A.2.2 diff --git a/nextclade/resources/color_ordering.tsv b/nextclade/resources/color_ordering.tsv index f41f1f2..08b3dbe 100644 --- a/nextclade/resources/color_ordering.tsv +++ b/nextclade/resources/color_ordering.tsv @@ -239,9 +239,13 @@ lineage B.1.2 lineage B.1.3 lineage C.1 lineage C.1.1 +lineage E.1 +lineage E.2 +lineage E.3 lineage B.1.4 lineage B.1.5 lineage B.1.6 +lineage D.1 lineage B.1.7 lineage B.1.8 lineage B.1.9 @@ -256,8 +260,15 @@ lineage B.1.17 lineage B.1.18 lineage B.1.19 lineage B.1.20 +lineage F.1 +lineage F.2 +lineage F.3 +lineage F.4 +lineage F.5 +lineage F.6 lineage B.1.21 lineage B.1.22 +lineage B.1.23 lineage A.2 lineage A.2.1 lineage A.2.2 diff --git a/nextclade/resources/include_accessions.txt b/nextclade/resources/include_accessions.txt index fa4165b..7eee759 100644 --- a/nextclade/resources/include_accessions.txt +++ b/nextclade/resources/include_accessions.txt @@ -28,6 +28,20 @@ OQ320441 #reference for B.1.20 OP539939 #reference for B.1.21 OQ773522 #reference for B.1.22 OR095023 #reference for B.1.22 +PP754993 #reference for B.1.23 +PQ036000 #reference for B.1.23 LC753968 #reference for C.1 LC753968 #reference for C.1.1 OR643705 #reference for C.1.1 +OR804476 #reference for C.1.1 +OQ503831 #reference for D.1 +OR804499 #reference for E.1 +OR487983 #reference for E.2 +OR326991 #reference for E.3 +PP533295 #reference for F.1 +PQ160003 #reference for F.2 +OR473623 #reference for F.3 +PP556326 #reference for F.4 +PQ160004 #reference for F.5 +PP533312 #reference for F.5 +OR665162 #reference for F.6 diff --git a/nextclade/resources/lineage-b.1/clades.tsv b/nextclade/resources/lineage-b.1/clades.tsv index 505aac9..4be0318 100644 --- a/nextclade/resources/lineage-b.1/clades.tsv +++ b/nextclade/resources/lineage-b.1/clades.tsv @@ -28,6 +28,19 @@ C.1.1 clade C.1 C.1.1 nuc 21062 T C.1.1 nuc 149963 T +E.1 clade C.1.1 +E.1 nuc 13563 A +E.1 nuc 121394 T +E.1 nuc 162280 A + +E.2 clade C.1.1 +E.2 nuc 13563 A +E.2 nuc 151847 A +E.2 nuc 37738 T + +E.3 clade C.1.1 +E.3 nuc 142797 T + B.1.4 clade B.1 B.1.4 nuc 34308 A @@ -37,6 +50,12 @@ B.1.5 nuc 70780 T B.1.6 clade B.1 B.1.6 nuc 111029 A +D.1 clade B.1.6 +D.1 nuc 10945 A +D.1 nuc 39515 A +D.1 nuc 44627 T +D.1 nuc 56276 A + B.1.7 clade B.1 B.1.7 nuc 25644 T @@ -91,6 +110,37 @@ B.1.20 nuc 53326 A B.1.20 nuc 164385 T B.1.20 nuc 187620 T +F.1 clade B.1.20 +F.1 nuc 11668 A +F.1 nuc 35132 A +F.1 nuc 70414 T +F.1 nuc 70666 T +F.1 nuc 96938 T + +F.2 clade B.1.20 +F.2 nuc 161629 A +F.2 nuc 22167 T + +F.3 clade B.1.20 +F.3 nuc 174050 T +F.3 nuc 180618 T + +F.4 clade B.1.20 +F.4 nuc 34277 T +F.4 nuc 92382 T +F.4 nuc 122551 T +F.4 nuc 126919 A +F.4 nuc 176643 A + +F.5 clade B.1.20 +F.5 nuc 150831 T +F.5 nuc 126169 A + +F.6 clade B.1.20 +F.6 nuc 146690 A +F.6 nuc 159608 T +F.6 nuc 168964 A + B.1.21 clade B.1 B.1.21 nuc 22415 A B.1.21 nuc 132698 T @@ -98,3 +148,8 @@ B.1.21 nuc 132698 T B.1.22 clade B.1 B.1.22 nuc 34784 T B.1.22 nuc 101418 T + +B.1.23 clade B.1 +B.1.23 nuc 27935 A +B.1.23 nuc 64171 G +B.1.23 nuc 73235 T \ No newline at end of file diff --git a/phylogenetic/build-configs/ci/config.yaml b/phylogenetic/build-configs/ci/config.yaml index 7010b1f..f58e32f 100644 --- a/phylogenetic/build-configs/ci/config.yaml +++ b/phylogenetic/build-configs/ci/config.yaml @@ -36,9 +36,15 @@ subsample: - B.1.1 - B.1.2 - B.1.3 + - C.1 + - C.1.1 + - E.1 + - E.2 + - E.3 - B.1.4 - B.1.5 - B.1.6 + - D.1 - B.1.7 - B.1.8 - B.1.9 @@ -53,10 +59,15 @@ subsample: - B.1.18 - B.1.19 - B.1.20 + - F.1 + - F.2 + - F.3 + - F.4 + - F.5 + - F.6 - B.1.21 - B.1.22 - - C.1 - - C.1.1 + - B.1.23 b1: group_by: "--group-by country year" sequences_per_group: "--subsample-max-sequences 100" diff --git a/phylogenetic/defaults/clades.tsv b/phylogenetic/defaults/clades.tsv index 11857c9..5851db4 100644 --- a/phylogenetic/defaults/clades.tsv +++ b/phylogenetic/defaults/clades.tsv @@ -73,6 +73,19 @@ C.1.1 clade C.1 C.1.1 nuc 21062 T C.1.1 nuc 149963 T +E.1 clade C.1.1 +E.1 nuc 13563 A +E.1 nuc 121394 T +E.1 nuc 162280 A + +E.2 clade C.1.1 +E.2 nuc 13563 A +E.2 nuc 151847 A +E.2 nuc 37738 T + +E.3 clade C.1.1 +E.3 nuc 142797 T + B.1.4 clade B.1 B.1.4 nuc 34308 A @@ -82,6 +95,12 @@ B.1.5 nuc 70780 T B.1.6 clade B.1 B.1.6 nuc 111029 A +D.1 clade B.1.6 +D.1 nuc 10945 A +D.1 nuc 39515 A +D.1 nuc 44627 T +D.1 nuc 56276 A + B.1.7 clade B.1 B.1.7 nuc 25644 T @@ -136,6 +155,37 @@ B.1.20 nuc 53326 A B.1.20 nuc 164385 T B.1.20 nuc 187620 T +F.1 clade B.1.20 +F.1 nuc 11668 A +F.1 nuc 35132 A +F.1 nuc 70414 T +F.1 nuc 70666 T +F.1 nuc 96938 T + +F.2 clade B.1.20 +F.2 nuc 161629 A +F.2 nuc 22167 T + +F.3 clade B.1.20 +F.3 nuc 174050 T +F.3 nuc 180618 T + +F.4 clade B.1.20 +F.4 nuc 34277 T +F.4 nuc 92382 T +F.4 nuc 122551 T +F.4 nuc 126919 A +F.4 nuc 176643 A + +F.5 clade B.1.20 +F.5 nuc 150831 T +F.5 nuc 126169 A + +F.6 clade B.1.20 +F.6 nuc 146690 A +F.6 nuc 159608 T +F.6 nuc 168964 A + B.1.21 clade B.1 B.1.21 nuc 22415 A B.1.21 nuc 132698 T @@ -143,3 +193,8 @@ B.1.21 nuc 132698 T B.1.22 clade B.1 B.1.22 nuc 34784 T B.1.22 nuc 101418 T + +B.1.23 clade B.1 +B.1.23 nuc 27935 A +B.1.23 nuc 64171 G +B.1.23 nuc 73235 T \ No newline at end of file diff --git a/phylogenetic/defaults/color_ordering.tsv b/phylogenetic/defaults/color_ordering.tsv index 5e61aa9..53b601c 100644 --- a/phylogenetic/defaults/color_ordering.tsv +++ b/phylogenetic/defaults/color_ordering.tsv @@ -16906,9 +16906,13 @@ lineage B.1.2 lineage B.1.3 lineage C.1 lineage C.1.1 +lineage E.1 +lineage E.2 +lineage E.3 lineage B.1.4 lineage B.1.5 lineage B.1.6 +lineage D.1 lineage B.1.7 lineage B.1.8 lineage B.1.9 @@ -16923,8 +16927,15 @@ lineage B.1.17 lineage B.1.18 lineage B.1.19 lineage B.1.20 +lineage F.1 +lineage F.2 +lineage F.3 +lineage F.4 +lineage F.5 +lineage F.6 lineage B.1.21 lineage B.1.22 +lineage B.1.23 lineage A.2 lineage A.2.1 lineage A.2.2 diff --git a/phylogenetic/defaults/exclude_accessions.txt b/phylogenetic/defaults/exclude_accessions.txt index 56ec682..3ee6eba 100644 --- a/phylogenetic/defaults/exclude_accessions.txt +++ b/phylogenetic/defaults/exclude_accessions.txt @@ -118,3 +118,6 @@ PP853012 # Suspicious clusters PP852987 # Suspicious clusters MG693723 # Spotty/gappy/clusters + +PP852989 # Nigerian overdiverged B.1 +OP605587 # Slovenia overdiverged B.1 diff --git a/phylogenetic/defaults/hmpxv1/config.yaml b/phylogenetic/defaults/hmpxv1/config.yaml index 4cd55da..39b29c0 100644 --- a/phylogenetic/defaults/hmpxv1/config.yaml +++ b/phylogenetic/defaults/hmpxv1/config.yaml @@ -33,9 +33,15 @@ subsample: - B.1.1 - B.1.2 - B.1.3 + - C.1 + - C.1.1 + - E.1 + - E.2 + - E.3 - B.1.4 - B.1.5 - B.1.6 + - D.1 - B.1.7 - B.1.8 - B.1.9 @@ -50,13 +56,18 @@ subsample: - B.1.18 - B.1.19 - B.1.20 + - F.1 + - F.2 + - F.3 + - F.4 + - F.5 + - F.6 - B.1.21 - B.1.22 - - C.1 - - C.1.1 + - B.1.23 b1: group_by: "--group-by country year" - sequences_per_group: "--subsample-max-sequences 100" + sequences_per_group: "--subsample-max-sequences 300" other_filters: "--exclude-where outbreak!=hMPXV-1 clade!=IIb" ## align diff --git a/phylogenetic/defaults/mpxv/config.yaml b/phylogenetic/defaults/mpxv/config.yaml index 6bd9678..73d1579 100644 --- a/phylogenetic/defaults/mpxv/config.yaml +++ b/phylogenetic/defaults/mpxv/config.yaml @@ -31,9 +31,15 @@ subsample: - B.1.1 - B.1.2 - B.1.3 + - C.1 + - C.1.1 + - E.1 + - E.2 + - E.3 - B.1.4 - B.1.5 - B.1.6 + - D.1 - B.1.7 - B.1.8 - B.1.9 @@ -48,10 +54,15 @@ subsample: - B.1.18 - B.1.19 - B.1.20 + - F.1 + - F.2 + - F.3 + - F.4 + - F.5 + - F.6 - B.1.21 - B.1.22 - - C.1 - - C.1.1 + - B.1.23 b1: group_by: "--group-by country year" sequences_per_group: "--subsample-max-sequences 100" diff --git a/phylogenetic/rules/construct_phylogeny.smk b/phylogenetic/rules/construct_phylogeny.smk index 4ce598f..c33ddeb 100644 --- a/phylogenetic/rules/construct_phylogeny.smk +++ b/phylogenetic/rules/construct_phylogeny.smk @@ -30,7 +30,6 @@ rule tree: augur tree \ --alignment {input.alignment} \ --exclude-sites {input.tree_mask} \ - --tree-builder-args="-redo" \ --output {output.tree} \ --nthreads {threads} """