PASTA fails when running UPP

[luisas]

Using the current bioconda recipe (v 4.5.5) I get the following error when running UPP:

Input file:
test_fasta.txt

Here the command line:
run_upp.py -m amino -x 4 -s test_fasta.txt -d . -o test_DEFAULT-args-default_UPP-args-default -p ./upp-temporary

Error message:

PASTA failed because one of the programs it tried to run failed.

`[10:28:52] config.py (line 371): INFO: Seed number: 297834
[10:28:52] algorithm.py (line 153): INFO: UPP version 4.5.5 used with HMMER version 3.4
[10:28:52] algorithm.py (line 155): INFO: Will user HMMER located at /home/luisasantus/Desktop/multiplesequencealign/work/conda/env-15824eade792dfc0-152242b464c7b9383ba46dc81f6c5f4d/bin/hmmbuild
[10:28:52] algorithm.py (line 157): INFO: All options: Namespace(pplacer=Namespace(path='/home/luisasantus/Desktop/multiplesequencealign/work/conda/env-15824eade792dfc0-152242b464c7b9383ba46dc81f6c5f4d/bin/pplacer'), hmmalign=Namespace(path='/home/luisasantus/Desktop/multiplesequencealign/work/conda/env-15824eade792dfc0-152242b464c7b9383ba46dc81f6c5f4d/bin/hmmalign'), hmmsearch=Namespace(path='/home/luisasantus/Desktop/multiplesequencealign/work/conda/env-15824eade792dfc0-152242b464c7b9383ba46dc81f6c5f4d/bin/hmmsearch', piped='False', elim='10000', filters='True'), hmmbuild=Namespace(path='/home/luisasantus/Desktop/multiplesequencealign/work/conda/env-15824eade792dfc0-152242b464c7b9383ba46dc81f6c5f4d/bin/hmmbuild'), jsonmerger=Namespace(path='/home/luisasantus/Desktop/multiplesequencealign/work/conda/env-15824eade792dfc0-152242b464c7b9383ba46dc81f6c5f4d/bin/seppJsonMerger.jar'), exhaustive=Namespace(strategy='centroid', minsubsetsize='2', placementminsubsetsizefacotr='4', placer='pplacer', weight_placement_by_alignment='True'), pasta=Namespace(path='run_pasta.py', user_options='--max-mem-mb=2000'), max_chunk_size=20000, distance=1, maxDiam=None, tempdir='/home/luisasantus/Desktop/multiplesequencealign/work/fd/cfb23c26d810b32a5ca6cc675d1193/upp-temporary', remtemp=False, output='test_DEFAULT-args-default_UPP-args-default', outdir='/home/luisasantus/Desktop/multiplesequencealign/work/fd/cfb23c26d810b32a5ca6cc675d1193', molecule='amino', ignore_overlap=False, cpu=8, checkpoint=<sepp.checkpointing.CheckPointManager object at 0x7fa0f1335570>, checkpoint_interval=3600, seed=297834, alignment_size=10, full_length_range=None, median_full_length=None, backbone_threshold=0.25, backbone_size=None, decomp_strategy='hierarchical', sequence_file=<_io.TextIOWrapper name='test.fa' mode='r' encoding='UTF-8'>, config_file=None, tree_file=None, alignment_file=None, backtranslation_sequence_file=None, long_branch_filter=None, placement_size=None, info_file=None, fragment_file=None)
[10:28:52] exhaustive_upp.py (line 70): INFO: Reading input sequences: <_io.TextIOWrapper name='test.fa' mode='r' encoding='UTF-8'>
[10:28:52] exhaustive_upp.py (line 117): INFO: Backbone size set to: 110
[10:28:52] exhaustive_upp.py (line 126): INFO: Writing backbone set.
[10:28:52] filemgr.py (line 129): INFO: Root temp directory built: /home/luisasantus/Desktop/multiplesequencealign/work/fd/cfb23c26d810b32a5ca6cc675d1193/upp-temporary/test_DEFAULT-args-default_UPP-args-default.vlhondzx
[10:28:52] exhaustive_upp.py (line 130): INFO: Generating pasta backbone alignment and tree.
Traceback (most recent call last):
File "/home/luisasantus/Desktop/multiplesequencealign/work/conda/env-15824eade792dfc0-152242b464c7b9383ba46dc81f6c5f4d/lib/python3.10/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
run_pasta.py --num-cpus=8 -i /home/luisasantus/Desktop/multiplesequencealign/work/fd/cfb23c26d810b32a5ca6cc675d1193/upp-temporary/test_DEFAULT-args-default_UPP-args-default.vlhondzx/backbone/backbonedavamk0b.fas --datatype=protein --temporaries=/home/luisasantus/Desktop/multiplesequencealign/work/fd/cfb23c26d810b32a5ca6cc675d1193/upp-temporary/test_DEFAULT-args-default_UPP-args-default.vlhondzx/pastaout/ -j pastajob --output-directory=/home/luisasantus/Desktop/multiplesequencealign/work/fd/cfb23c26d810b32a5ca6cc675d1193/upp-temporary/test_DEFAULT-args-default_UPP-args-default.vlhondzx/pastaout/ --max-mem-mb=2000
PASTA failed because one of the programs it tried to run failed.
The invocation that failed was:
"/home/luisasantus/Desktop/multiplesequencealign/work/conda/env-15824eade792dfc0-152242b464c7b9383ba46dc81f6c5f4d/bin/hmmeralign" "/home/luisasantus/Desktop/multiplesequencealign/work/fd/cfb23c26d810b32a5ca6cc675d1193/upp-temporary/test_DEFAULT-args-default_UPP-args-default.vlhondzx/pastaout/pastajob/temp_dkbtzna/init_aln/temphmmeralignvbsm3qa5/input.fasta" "/home/luisasantus/Desktop/multiplesequencealign/work/fd/cfb23c26d810b32a5ca6cc675d1193/upp-temporary/test_DEFAULT-args-default_UPP-args-default.vlhondzx/pastaout/pastajob/temp_dkbtzna/init_aln/query-0.fasta" "/home/luisasantus/Desktop/multiplesequencealign/work/fd/cfb23c26d810b32a5ca6cc675d1193/upp-temporary/test_DEFAULT-args-default_UPP-args-default.vlhondzx/pastaout/pastajob/temp_dkbtzna/init_aln/temphmmeralignvbsm3qa5/input.aligned" "amino"

`