update

README.md

@@ -11,5 +11,14 @@ Metadata (including isolated country and date) were extracted from genbank using
 ## Nextstrain build
 Hadfield et al.,[Nextstrain](https://nextstrain.org/) real-time tracking of pathogen evolution, Bioinformatics (2018)
 
+Reference sequences were list as follow:
+Dataset	Source	Accession
+rsv_A_F	Genbank	 LC377911
+rsv_A_G	Genbank	KP164507
+rsv_A_WGS	Refseq	NC038235
+rsv_B_F	Genbank	KY296706
+rsv_B_G	Genbank	KC283036
+rsv_B_WGS	Refseq	NC001781
+
 NC_038235(RSV-A) and NC_001781(RSV-B) from Refseq were used as references sequences.
 For Full instructions on how to set up nextstrain visit: https://nextstrain.org/

rsv_A_F/.snakemake/log/2019-07-29T155209.825847.snakemake.log

@@ -0,0 +1,58 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	align
+	1	all
+	1	ancestral
+	1	export
+	1	filter
+	1	refine
+	1	traits
+	1	translate
+	1	tree
+	9
+
+Job 8: 
+        Filtering to
+          - 200 sequence(s) per country year month
+          - from 1950 onwards
+
+
+
+        augur filter             --sequences data/sequences.fasta             --metadata data/metadata.tsv             --output results/filtered.fasta             --group-by country year month             --sequences-per-group 200             --min-date 1950
+
+Finished job 8.
+1 of 9 steps (11%) done
+
+Job 7: 
+        Aligning sequences to config/rsv_A_F_outgroup.gb
+          - filling gaps with N
+
+
+
+        augur align             --sequences results/filtered.fasta             --reference-sequence config/rsv_A_F_outgroup.gb             --output results/aligned.fasta             --fill-gaps
+
+Finished job 7.
+2 of 9 steps (22%) done
+
+Job 6: Building tree
+
+
+        augur tree             --alignment results/aligned.fasta             --output results/tree_raw.nwk
+
+    Error in rule tree:
+        jobid: 6
+        output: results/tree_raw.nwk
+
+RuleException:
+CalledProcessError in line 71 of /nextstrain/build/Snakefile:
+Command ' set -euo pipefail;  
+        augur tree             --alignment results/aligned.fasta             --output results/tree_raw.nwk ' returned non-zero exit status 1.
+  File "/nextstrain/build/Snakefile", line 71, in __rule_tree
+  File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run
+Shutting down, this might take some time.
+Exiting because a job execution failed. Look above for error message
+Complete log: /nextstrain/build/.snakemake/log/2019-07-29T155209.825847.snakemake.log

rsv_A_F/.snakemake/log/2019-07-29T155740.751420.snakemake.log

@@ -0,0 +1,15 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	clean
+	1
+
+Job 0: Removing directories: results  auspice
+
+rm -rfv results  auspice
+Finished job 0.
+1 of 1 steps (100%) done
+Complete log: /nextstrain/build/.snakemake/log/2019-07-29T155740.751420.snakemake.log

rsv_A_F/.snakemake/log/2019-07-29T155757.457440.snakemake.log

@@ -0,0 +1,58 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	align
+	1	all
+	1	ancestral
+	1	export
+	1	filter
+	1	refine
+	1	traits
+	1	translate
+	1	tree
+	9
+
+Job 8: 
+        Filtering to
+          - 200 sequence(s) per country year month
+          - from 1950 onwards
+
+
+
+        augur filter             --sequences data/sequences.fasta             --metadata data/metadata.tsv             --output results/filtered.fasta             --group-by country year month             --sequences-per-group 200             --min-date 1950
+
+Finished job 8.
+1 of 9 steps (11%) done
+
+Job 6: 
+        Aligning sequences to config/rsv_A_F_outgroup.gb
+          - filling gaps with N
+
+
+
+        augur align             --sequences results/filtered.fasta             --reference-sequence config/rsv_A_F_outgroup.gb             --output results/aligned.fasta             --fill-gaps
+
+Finished job 6.
+2 of 9 steps (22%) done
+
+Job 7: Building tree
+
+
+        augur tree             --alignment results/aligned.fasta             --output results/tree_raw.nwk
+
+    Error in rule tree:
+        jobid: 7
+        output: results/tree_raw.nwk
+
+RuleException:
+CalledProcessError in line 71 of /nextstrain/build/Snakefile:
+Command ' set -euo pipefail;  
+        augur tree             --alignment results/aligned.fasta             --output results/tree_raw.nwk ' returned non-zero exit status 1.
+  File "/nextstrain/build/Snakefile", line 71, in __rule_tree
+  File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run
+Shutting down, this might take some time.
+Exiting because a job execution failed. Look above for error message
+Complete log: /nextstrain/build/.snakemake/log/2019-07-29T155757.457440.snakemake.log

rsv_A_F/.snakemake/log/2019-07-29T160237.533345.snakemake.log

@@ -0,0 +1,15 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	clean
+	1
+
+Job 0: Removing directories: results  auspice
+
+rm -rfv results  auspice
+Finished job 0.
+1 of 1 steps (100%) done
+Complete log: /nextstrain/build/.snakemake/log/2019-07-29T160237.533345.snakemake.log

rsv_A_F/.snakemake/log/2019-07-29T161656.234787.snakemake.log

@@ -0,0 +1,87 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	align
+	1	all
+	1	ancestral
+	1	export
+	1	refine
+	1	traits
+	1	translate
+	1	tree
+	8
+
+Job 7: 
+        Aligning sequences to config/rsv_A_F_outgroup.gb
+          - filling gaps with N
+
+
+
+        augur align             --sequences results/filtered.fasta             --reference-sequence config/rsv_A_F_outgroup.gb             --output results/aligned.fasta             --fill-gaps
+
+Finished job 7.
+1 of 8 steps (12%) done
+
+Job 6: Building tree
+
+
+        augur tree             --alignment results/aligned.fasta             --output results/tree_raw.nwk
+
+Finished job 6.
+2 of 8 steps (25%) done
+
+Job 2: 
+        Refining tree
+          - estimate timetree
+          - use opt coalescent timescale
+          - estimate marginal node dates
+          - filter tips more than 4 IQDs from clock expectation
+
+
+
+        augur refine             --tree results/tree_raw.nwk             --alignment results/aligned.fasta             --metadata data/metadata.tsv             --output-tree results/tree.nwk             --output-node-data results/branch_lengths.json             --timetree             --coalescent opt             --date-confidence             --date-inference marginal             --clock-filter-iqd 4
+
+Finished job 2.
+3 of 8 steps (38%) done
+
+Job 3: Reconstructing ancestral sequences and mutations
+
+
+        augur ancestral             --tree results/tree.nwk             --alignment results/aligned.fasta             --output results/nt_muts.json             --inference joint
+
+Finished job 3.
+4 of 8 steps (50%) done
+
+Job 5: Translating amino acid sequences
+
+
+        augur translate             --tree results/tree.nwk             --ancestral-sequences results/nt_muts.json             --reference-sequence config/rsv_A_F_outgroup.gb             --output results/aa_muts.json         
+Finished job 5.
+5 of 8 steps (62%) done
+
+Job 4: Inferring ancestral traits for region country
+
+
+        augur traits             --tree results/tree.nwk             --metadata data/metadata.tsv             --output results/traits.json             --columns region country             --confidence
+
+Finished job 4.
+6 of 8 steps (75%) done
+
+Job 1: Exporting data files for for auspice
+
+
+        augur export             --tree results/tree.nwk             --metadata data/metadata.tsv             --node-data results/branch_lengths.json results/traits.json results/nt_muts.json results/aa_muts.json             --colors config/colors.tsv             --lat-longs config/lat_longs.tsv             --auspice-config config/auspice_config.json             --output-tree auspice/rsv_A_F_tree.json             --output-meta auspice/rsv_A_F_meta.json
+
+Finished job 1.
+7 of 8 steps (88%) done
+
+localrule all:
+    input: auspice/rsv_A_F_tree.json, auspice/rsv_A_F_meta.json
+    jobid: 0
+
+Finished job 0.
+8 of 8 steps (100%) done
+Complete log: /nextstrain/build/.snakemake/log/2019-07-29T161656.234787.snakemake.log

rsv_A_F/.snakemake/log/2019-07-29T175801.529534.snakemake.log

@@ -0,0 +1,15 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	clean
+	1
+
+Job 0: Removing directories: results  auspice
+
+rm -rfv results  auspice
+Finished job 0.
+1 of 1 steps (100%) done
+Complete log: /nextstrain/build/.snakemake/log/2019-07-29T175801.529534.snakemake.log

rsv_A_F/.snakemake/log/2019-07-29T175822.757253.snakemake.log

@@ -0,0 +1,39 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	align
+	1	all
+	1	ancestral
+	1	export
+	1	filter
+	1	refine
+	1	traits
+	1	translate
+	1	tree
+	9
+
+Job 8: 
+        Filtering to
+          - 200 sequence(s) per country year month
+          - from 1950 onwards
+
+
+
+        augur filter             --sequences data/sequences.fasta             --metadata data/metadata.tsv             --output results/filtered.fasta             --group-by country year month             --sequences-per-group 200             --min-date 1950
+
+    Error in rule filter:
+        jobid: 8
+        output: results/filtered.fasta
+
+RuleException:
+CalledProcessError in line 34 of /nextstrain/build/Snakefile:
+Command ' set -euo pipefail;  
+        augur filter             --sequences data/sequences.fasta             --metadata data/metadata.tsv             --output results/filtered.fasta             --group-by country year month             --sequences-per-group 200             --min-date 1950 ' returned non-zero exit status 1.
+  File "/nextstrain/build/Snakefile", line 34, in __rule_filter
+  File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run
+Shutting down, this might take some time.
+Exiting because a job execution failed. Look above for error message
+Complete log: /nextstrain/build/.snakemake/log/2019-07-29T175822.757253.snakemake.log

rsv_A_F/.snakemake/log/2019-07-29T180035.992016.snakemake.log

@@ -0,0 +1,15 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	clean
+	1
+
+Job 0: Removing directories: results  auspice
+
+rm -rfv results  auspice
+Finished job 0.
+1 of 1 steps (100%) done
+Complete log: /nextstrain/build/.snakemake/log/2019-07-29T180035.992016.snakemake.log

rsv_A_F/.snakemake/log/2019-07-29T180041.541002.snakemake.log

@@ -0,0 +1,71 @@
+Building DAG of jobs...
+Using shell: /bin/bash
+Provided cores: 1
+Rules claiming more threads will be scaled down.
+Job counts:
+	count	jobs
+	1	align
+	1	all
+	1	ancestral
+	1	export
+	1	filter
+	1	refine
+	1	traits
+	1	translate
+	1	tree
+	9
+
+Job 8: 
+        Filtering to
+          - 200 sequence(s) per country year month
+          - from 1950 onwards
+
+
+
+        augur filter             --sequences data/sequences.fasta             --metadata data/metadata.tsv             --output results/filtered.fasta             --group-by country year month             --sequences-per-group 200             --min-date 1950
+
+Finished job 8.
+1 of 9 steps (11%) done
+
+Job 6: 
+        Aligning sequences to config/rsv_A_F_outgroup.gb
+          - filling gaps with N
+
+
+
+        augur align             --sequences results/filtered.fasta             --reference-sequence config/rsv_A_F_outgroup.gb             --output results/aligned.fasta             --fill-gaps
+
+Finished job 6.
+2 of 9 steps (22%) done
+
+Job 7: Building tree
+
+
+        augur tree             --alignment results/aligned.fasta             --output results/tree_raw.nwk
+
+Finished job 7.
+3 of 9 steps (33%) done
+
+Job 2: 
+        Refining tree
+          - estimate timetree
+          - use opt coalescent timescale
+          - estimate marginal node dates
+          - filter tips more than 4 IQDs from clock expectation
+
+
+
+        augur refine             --tree results/tree_raw.nwk             --alignment results/aligned.fasta             --metadata data/metadata.tsv             --output-tree results/tree.nwk             --output-node-data results/branch_lengths.json             --timetree             --coalescent opt             --date-confidence             --date-inference marginal             --clock-filter-iqd 4
+
+    Error in rule refine:
+        jobid: 2
+        output: results/tree.nwk, results/branch_lengths.json
+
+RuleException:
+CalledProcessError in line 98 of /nextstrain/build/Snakefile:
+Command ' set -euo pipefail;  
+        augur refine             --tree results/tree_raw.nwk             --alignment results/aligned.fasta             --metadata data/metadata.tsv             --output-tree results/tree.nwk             --output-node-data results/branch_lengths.json             --timetree             --coalescent opt             --date-confidence             --date-inference marginal             --clock-filter-iqd 4 ' returned non-zero exit status 1.
+  File "/nextstrain/build/Snakefile", line 98, in __rule_refine
+  File "/usr/lib/python3.6/concurrent/futures/thread.py", line 56, in run
+Terminating processes on user request, this might take some time.
+Complete log: /nextstrain/build/.snakemake/log/2019-07-29T180041.541002.snakemake.log