Snakefile

rule tree:
    message: "Building tree"
    input:
        alignment = rules.align.output.alignment
    output:
        tree = "results/tree_raw.nwk"
    shell:
        """
        # Remove any prior RAxML outputs which didn't get cleaned up
        rm -v RAxML_*.* 2>/dev/null || true

        augur tree \
            --alignment {input.alignment} \
            --output {output.tree} \
            --method raxml \
            --tree-builder-args '-m GTRCAT -p $RANDOM -f a -x $RANDOM -N 1000' \
            --override-default-args \
        || (
            echo "WARNING: augur tree failed because of known issues with bootstrapping <https://github.com/nextstrain/augur/pull/1127>; trying to copy tree manually" >&2
            cp -v RAxML_bipartitions.* {output.tree}
            rm -v RAxML_*.*
        )
        """

workaround.diff

diff --git a/Snakefile b/Snakefile
index a60e8e9..cefc567 100644
--- a/Snakefile
+++ b/Snakefile
@@ -86,12 +86,20 @@ rule tree:
         tree = "results/tree_raw.nwk"
     shell:
         """
+        # Remove any prior RAxML outputs which didn't get cleaned up
+        rm -v RAxML_*.* 2>/dev/null || true
+
         augur tree \
             --alignment {input.alignment} \
             --output {output.tree} \
             --method raxml \
             --tree-builder-args '-m GTRCAT -p $RANDOM -f a -x $RANDOM -N 1000' \
-            --override-default-args
+            --override-default-args \
+        || (
+            echo "WARNING: augur tree failed because of known issues with bootstrapping <https://github.com/nextstrain/augur/pull/1127>; trying to copy tree manually" >&2
+            cp -v RAxML_bipartitions.* {output.tree}
+            rm -v RAxML_*.*
+        )
         """