zipped trees seem to have issues (under error_free_files/phylogenetic_trees) about favites HOT 9 CLOSED

Are you using cat? The files are gzipped, so you need to use zcat (or equivalently gunzip -c if you're on Mac and don't have zcat), not cat

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Never mind, I found the directory you're working in (FAVITES/output/set7/output_7_1 within your home folder), and I see that the files are already unzipped. I'll investigate

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I was able to reproduce the error. It seems like an issue with merging the trees. I'll investigate and roll out an update to FAVITES when it's fixed

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Caught the issue: I forgot to update the merge function after gzipping the trees, so it was looking for files with extension .tre instead of .tre.gz. Fixing and will roll out in update later today

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Fixed in commit: 12283fb

Building updated Docker image

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You can either switch to FAVITES version 1.1.3 (which now has the merging bug fixed), or you can use the method I described in my recent email to you to manually merge the trees. Switching versions will be easier, but it will take more compute time.

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Reproducing my "manually merge trees" solution here so I can close this ticket:

While I'm fixing the bug in merging trees, here's a way you can manually merge them instead of having to rerun. First, the relevant files:

• The seed tree can be found in OUTPUT/seed_sequences/seed.txt
• For each leaf in the seed tree, the corresponding sequence can be found in OUTPUT/seed_sequences/seqgen.out
• For each leaf sequence, the file OUTPUT/seed_sequences/seed_sequences.tsv.gz has the corresponding N# root of the individual trees
• The corresponding N# SeqGen files (which include the individual trees) can be found in OUTPUT/SeqGen_output

To do the merge, you should be able to do the following:

1. Load the seed tree (OUTPUT/seed_sequences/seed.txt)
2. Map each leaf in the seed tree to an N# label (seed tree -> sequence from OUTPUT/seed_sequences/seqgen.out -> N# label from OUTPUT/seed_sequences/seed_sequences.tsv.gz)
3. For each N# label, load the corresponding tree (OUTPUT/SeqGen_output) and set the corresponding leaf in the seed tree to the root of the N# tree

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