error when provided a single template with more than 12000 proteins

[irleader]

"at Stitch.PhylogeneticTree+Tree1[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]].Remodel[[System.ValueTuple2[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e],[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]], System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]](System.Func2<Tree1<System.__Canon>,System.ValueTuple2<System.__Canon,System.__Canon>>) ...... at Stitch.PhylogeneticTree+Tree1[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]].Remodel[[System.ValueTuple2[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e],[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]], System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]](System.Func2<Tree1<System.__Canon>,System.ValueTuple2<System.__Canon,System.__Canon>>)
at Stitch.PhylogeneticTree+ProteinHierarchyTree..ctor(Tree1<System.String>, System.Collections.Generic.List1<Stitch.Alignment>)
at Stitch.RunParameters.Run.g__BuildTree|20_2(Stitch.Segment)
at Stitch.RunParameters.Run+<>c.b__20_4(Stitch.Segment)
at System.Threading.Tasks.Parallel+<>c__DisplayClass44_02[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e],[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]].<PartitionerForEachWorker>b__1(System.Collections.IEnumerator ByRef, Int32, Boolean ByRef) at System.Threading.Tasks.TaskReplicator+Replica1[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]].ExecuteAction(Boolean ByRef)
at System.Threading.Tasks.TaskReplicator+Replica.Execute()
at System.Threading.Tasks.TaskReplicator+Replica+<>c.<.ctor>b__4_0(System.Object)
at System.Threading.Tasks.Task.InnerInvoke()
at System.Threading.Tasks.Task+<>c.<.cctor>b__273_0(System.Object)
at System.Threading.ExecutionContext.RunInternal(System.Threading.ExecutionContext, System.Threading.ContextCallback, System.Object)
at System.Threading.Tasks.Task.ExecuteWithThreadLocal(System.Threading.Tasks.Task ByRef, System.Threading.Thread)
at System.Threading.Tasks.Task.ExecuteEntryUnsafe(System.Threading.Thread)
at System.Threading.Tasks.ThreadPoolTaskScheduler.TryExecuteTaskInline(System.Threading.Tasks.Task, Boolean)
at System.Threading.Tasks.TaskScheduler.TryRunInline(System.Threading.Tasks.Task, Boolean)
at System.Threading.Tasks.Task.InternalRunSynchronously(System.Threading.Tasks.TaskScheduler, Boolean)
at System.Threading.Tasks.Task.RunSynchronously(System.Threading.Tasks.TaskScheduler)
at System.Threading.Tasks.TaskReplicator+Replica.Start()
at System.Threading.Tasks.TaskReplicator.Run[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]](ReplicatableUserAction1<System.__Canon>, System.Threading.Tasks.ParallelOptions, Boolean) at System.Threading.Tasks.Parallel.PartitionerForEachWorker[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e],[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]](System.Collections.Concurrent.Partitioner1<System.__Canon>, System.Threading.Tasks.ParallelOptions, System.Action1<System.__Canon>, System.Action2<System.__Canon,System.Threading.Tasks.ParallelLoopState>, System.Action3<System.__Canon,System.Threading.Tasks.ParallelLoopState,Int64>, System.Func4<System.__Canon,System.Threading.Tasks.ParallelLoopState,System.__Canon,System.__Canon>, System.Func5<System.__Canon,System.Threading.Tasks.ParallelLoopState,Int64,System.__Canon,System.__Canon>, System.Func1<System.__Canon>, System.Action1<System.__Canon>) at System.Threading.Tasks.Parallel.ForEachWorker[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e],[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]](System.Collections.Generic.IEnumerable1<System.__Canon>, System.Threading.Tasks.ParallelOptions, System.Action1<System.__Canon>, System.Action2<System.__Canon,System.Threading.Tasks.ParallelLoopState>, System.Action3<System.__Canon,System.Threading.Tasks.ParallelLoopState,Int64>, System.Func4<System.__Canon,System.Threading.Tasks.ParallelLoopState,System.__Canon,System.__Canon>, System.Func5<System.__Canon,System.Threading.Tasks.ParallelLoopState,Int64,System.__Canon,System.__Canon>, System.Func1<System.__Canon>, System.Action1<System.__Canon>) at System.Threading.Tasks.Parallel.ForEach[[System.__Canon, System.Private.CoreLib, Version=7.0.0.0, Culture=neutral, PublicKeyToken=7cec85d7bea7798e]](System.Collections.Generic.IEnumerable1<System.__Canon>, System.Threading.Tasks.ParallelOptions, System.Action`1<System.__Canon>)
at Stitch.RunParameters.Run.RunTemplateMatching()
at Stitch.RunParameters.Run.Calculate()
at Stitch.ToRunWithCommandLine.RunBatchFile(System.String, Stitch.ExtraArguments)
at Stitch.ToRunWithCommandLine.Main()"

This is the tail of the error message, the same dataset (around 1000 reads) and batchfile works well with a template of 500 proteins, when the template is replace with 12000 proteins, this error comes out. The first part of the message keeps repeating, I only paste 2 repeats here.

[douweschulte]

From the stacktrace I can see it crashes in the phylogenetic tree generation. Turning the tree generation off will prevent this crash, use BuildTree: False as argument in the TemplateMatching section to turn this off. Either the C# stacktrace misses the underlying issue or that issue was present earlier in the stacktrace, but from this info I will not be able to pinpoint the exact issue. Hopefully just turning off the tree is enough to make it usable for your use case.