Greetings, The relevant part of the error does not appear in the excerpt, but it is available in the full log[1] and looks like:
Usage: kalign-avx2 -i <seq file> -o <out aln>
Modes:
(default) : Consistency anchors + VSM (best general-purpose)
--fast : VSM only, no consistency (fastest)
--precise : Ensemble(3) + VSM + realign (highest precision)
Options:
--format : Output format. [Fasta]
--type : Alignment type (rna, dna, internal). [rna]
Options: protein, divergent (protein)
rna, dna, internal (nuc).
--gpo : Gap open penalty. []
--gpe : Gap extension penalty. []
--tgpe : Terminal gap extension penalty. []
--refine : Refinement mode. [none]
Options: none, all, confident
-n/--nthreads : Number of threads. [auto: N-1, max 16]
Ensemble options:
--ensemble : Number of ensemble runs. [off; 5 if no value
given]
--ensemble-seed : RNG seed for ensemble. [42]
--min-support : Explicit consensus threshold. [auto]
--save-poar : Save POAR table to file. [off]
--load-poar : Load POAR table for re-threshold. [off]
Advanced (usually managed by modes):
--consistency : Anchor consistency (K anchors). [5]
--consistency-weight: Consistency anchor weight. [2.0]
--realign : Alignment-guided tree rebuild iters. [0]
--vsm-amax : VSM amplitude (0 to disable). [auto]
--adaptive-budget : Scale refinement trials by uncertainty. [off]
--version (-V/-v) : Prints version. [NA]
Examples:
Passing sequences via stdin:
cat input.fa | kalign -i - -f fasta > out.afa
Combining multiple input files:
kalign seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa
not ok 5
Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 3/7 subtests
I also happen to reproduce it on an avx2-capable equipment. It
could be that the encoded invocation of kalign in bioperl-run is
going to require an update. Upstream repository[2] has been
inactive in the past few years, so it seems that we're going to
be on our own here.
[1]:
https://people.debian.org/~sanvila/build-logs/202603/bioperl-run_1.7.3-13_amd64-20260305T171652.100Z
[2]: https://github.com/bioperl/bioperl-run/
In hope this helps,
--
.''`. Étienne Mollier <[email protected]>
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`. `' sent from /dev/pts/2, please excuse my verbosity
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