Rabies Slurm Job Evidence: ginsi-gappyout

summary

variant: ginsi-gappyout

status: succeeded

selected model: TPM2u+F+G4

runtime seconds: 4.358954

output files: 14

warnings: 4

serious conflicts: 8

rooted RF: 0

artifacts

task-log: task.log
workflow-manifest: ../../rabies-method-sensitivity.manifest.json
execution-record: ../../rabies-method-sensitivity-panel.run.json
alignment-manifest: alignment.manifest.json
trimming-manifest: trimming.manifest.json
inference-comparison-manifest: inference-comparison.manifest.json
model-selection-manifest: model-selection.manifest.json
iqtree-support-manifest: iqtree-support.manifest.json
fasttree-manifest: fasttree.manifest.json

job

variant_id: ginsi-gappyout
label: MAFFT ginsi plus trimAl gappyout
status: succeeded
partition_id: compact-mafft-ginsi-elevated
array_index: 1
execution_mode: parallel
script_path: slurm-arrays/compact-mafft-ginsi-elevated.sbatch

configuration

alignment_mode: ginsi
trimming_mode: gappyout
trim_gap_threshold: 0.1
selected_model: TPM2u+F+G4
alignment_length: 1353
trimmed_alignment_length: 1353

commands

alignment: /opt/homebrew/bin/mafft --globalpair --maxiterate 1000 /Users/bijan/bijux/bijux-phylogenetics/packages/bijux-phylogenetics/src/bijux_phylogenetics/resources/datasets/pathogens/rabies_method_sensitivity_panel/sequences.fasta
trimming: /opt/homebrew/bin/trimal -in /private/var/folders/n8/vnvrbrx950b17b93f4xx47k80000gn/T/rabies-method-sensitivity-h_1dgk8y/variants/ginsi-gappyout/ginsi-gappyout.aln -out /private/var/folders/n8/vnvrbrx950b17b93f4xx47k80000gn/T/rabies-method-sensitivity-h_1dgk8y/variants/ginsi-gappyout/ginsi-gappyout.trimmed.aln -gappyout
model_selection: /opt/homebrew/bin/iqtree2 -s /private/var/folders/n8/vnvrbrx950b17b93f4xx47k80000gn/T/rabies-method-sensitivity-h_1dgk8y/variants/ginsi-gappyout/ginsi-gappyout.trimmed.aln -st DNA -seed 1 -nt 1 -m MF -pre /private/var/folders/n8/vnvrbrx950b17b93f4xx47k80000gn/T/rabies-method-sensitivity-h_1dgk8y/variants/ginsi-gappyout/engine-comparison/engine-artifacts/ginsi-gappyout/model-selection/model-selection
iqtree_support: /opt/homebrew/bin/iqtree2 -s /private/var/folders/n8/vnvrbrx950b17b93f4xx47k80000gn/T/rabies-method-sensitivity-h_1dgk8y/variants/ginsi-gappyout/ginsi-gappyout.trimmed.aln -st DNA -seed 1 -nt 1 -m TPM2u+F+G4 -bb 1000 -wbt -pre /private/var/folders/n8/vnvrbrx950b17b93f4xx47k80000gn/T/rabies-method-sensitivity-h_1dgk8y/variants/ginsi-gappyout/engine-comparison/engine-artifacts/ginsi-gappyout/bootstrap-support/bootstrap-support
fasttree: /opt/homebrew/bin/FastTree -gtr -nt /private/var/folders/n8/vnvrbrx950b17b93f4xx47k80000gn/T/rabies-method-sensitivity-h_1dgk8y/variants/ginsi-gappyout/ginsi-gappyout.trimmed.aln

runtime-and-findings

total_runtime_seconds: 4.358954
model_selection_runtime_seconds: 0.264384
iqtree_support_runtime_seconds: 0.7237
fasttree_runtime_seconds: 0.104754
serious_conflict_count: 8
rooted_engine_rf_distance: 0
rooted_same_taxa_different_rooting: false

warnings

inferred topologies differ across compared workflows
compared workflows agree on unrooted splits but differ in rooting
one or more internal nodes did not expose parsable FastTree local support labels
FastTree is an approximately maximum-likelihood workflow and its SH-like local support values should be reviewed as approximate evidence

output-inventory

fasttree.nwk: 442 bytes 0e11e0785b1a2a577da5e43b7ed4b3ec44ef7a4fc3f75cfb8727d1a9dd4795b6
ginsi-gappyout.aln: 12610 bytes a0dc6dbfd24155e76906e156bfe85bb6e6dcdfede66af54fc6aea1dba725b4d8
ginsi-gappyout.trimmed.aln: 12610 bytes a0dc6dbfd24155e76906e156bfe85bb6e6dcdfede66af54fc6aea1dba725b4d8
iqtree-support.nwk: 442 bytes 07fc4128f6d2901158464a774caea4616e0f91b14ae856dc21c277678afdff8e
rooted-engine-comparison.tsv: 3554 bytes d277d85f85161baa6279056698c3c783d77e761002be1fe982f6350729ee108b
rooted-fasttree.nwk: 437 bytes 44c9f49562a4a93b9714b880f4aa91f1300a885edf6308cdce6e309de9e6e0fa
rooted-iqtree-support.nwk: 438 bytes 3de589f226f6595c90467bba0695a541a1c97673ae2be4e48a52d4db77dc847a
rooting-summary.tsv: 223 bytes 7bf3311777083acae725e051a2ef6a80de0c457fee369d7eec0351c0b376628e
unrooted-comparison.tsv: 3423 bytes f769b731d4f51d1124fee13b6cd7498e57b88ca67a14c152ba2118b1183f1ba5
unrooted-conclusions.tsv: 2761 bytes 5d3bbe3638e32946dfeacf72e8ee667ed0f2ffe0b5fd44c90d78121b32a59d5e
unrooted-conflicting-clades.tsv: 1928 bytes f84ad8972d76103c2381662e1ccfdbc3c28540197038296fcd82665bc2f386f2
unrooted-shared-clades.tsv: 436 bytes e31182b4fccc6827b951f63471a886f1620cf0766b26ed9d98ca3cd78a2e2a9b
unrooted-stability-summary.tsv: 480 bytes c7811c0846687032b73a77e125e3ea280aedcb876ad96cfc44fa0e848cfac021
unrooted-support-weighted-conflicts.tsv: 2281 bytes 3bb2a2a9f86d95864d5989dab6ca5d36fd889ba178d9fd1278d87970732d9c4f