Can you try the version v184.108.40.206 (from https://github.com/iqtree/iqtree2/releases) and see whether the issue still exists? Thanks.
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Because you would like to do bootstrapping, you should use "MFP" instead of "MF".
MFP: "Find best partition scheme followed by tree inference and bootstrap"
That means your syntax should be: iqtree2.exe -s Russula.fas -spp Partition.nex –m MFP+MERGE -bb 1000
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By the way, when I copied and pasted your command, it didn't work. However, it worked when I typed the command again (exactly, but changed to MF to MFP). I guess there were some hidden characters.
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The issue should have been addressed in the later version. Can you try the latest version, say v220.127.116.11, at https://github.com/iqtree/iqtree2/releases ?
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