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pplacer hanging on osx-arm64 with sepp test case

Open dslarm opened this issue 4 months ago • 3 comments

I'm trying to make the osx-arm64 bioconda package of sepp available - but it hangs during the test phase, with a pplacer invocation that succeeds on linux-aarch64 but that hangs on osx-arm64, for the same input files.

The linux-aarch64 package for pplacer is built from source, and the osx-arm64 package is a straight binary install from the pplacer downloads.

With the attached input files, run thus:

pplacer -j 1 -r backbone.fasta.txt -s raxml-bl.info.txt -t fzh.tre.txt extended.fasta.txt

on osx-arm64 I get the hang after baseball.

Running pplacer dev analysis on extended.fasta...
Didn't find any reference sequences in given alignment file. Using supplied reference alignment.
Warning: using a statistics file directly is now deprecated. We suggest using a reference package. If you already are, then please use the latest version of taxtastic.
WARNING: your stats file is from RAxML 8.1.24; RAxML has been tested with the following versions: 7.0.4; 7.2.3; 7.2.5; 7.2.6; 7.2.7
I'm going to try parsing as if this was version 7.2.3Pre-masking sequences... sequence length cut from 1287 to 125.
Determining figs... figs disabled.
Allocating memory for internal nodes... done.
Caching likelihood information on reference tree... done.
Pulling exponents... done.
Preparing the edges for baseball... done.
^C

backbone.fasta.txt extended.fasta.txt fzh.tre.txt raxml-bl.info.txt

On linux-aarch64, the successful output is:

pplacer -j 1 -r backbone.fasta.txt-s raxml-bl.info.txt  -t fzh.tre.txt extended.fasta.txt 
Running pplacer dev analysis on extended.fasta.txt...
Didn't find any reference sequences in given alignment file. Using supplied reference alignment.
Warning: using a statistics file directly is now deprecated. We suggest using a reference package. If you already are, then please use the latest version of taxtastic.
WARNING: your stats file is from RAxML 8.1.24; RAxML has been tested with the following versions: 7.0.4; 7.2.3; 7.2.5; 7.2.6; 7.2.7
I'm going to try parsing as if this was version 7.2.3Pre-masking sequences... sequence length cut from 1287 to 125.
Determining figs... figs disabled.
Allocating memory for internal nodes... done.
Caching likelihood information on reference tree... done.
Pulling exponents... done.
Preparing the edges for baseball... done.
working on testseqf (10/10)...

dslarm avatar Aug 20 '25 22:08 dslarm