UPP hangs with no error or info given

[aravenscraft]

Hi there,

I am trying to run UPP. I managed to get it installed and it responds correctly when I run the help (-h) option. When I try to build a phylogeny, UPP starts up and I can see pairlocalalign running in the Activity Monitor, but UPP never gets past the step where it generates the pasta backbone alignment and tree.

What should I do to troubleshoot? (When I run run_pasta.py -h, pasta responds correctly.)

Thank you! Alison

Commands I ran: conda activate py37 cd sepp/ run_upp.py --median_full_length 11600 --outdir UPP_OUTPUT_DIR --sequence_file WILD_CONCAT_seqsforUPP.fasta -cp CHCK_FILE -cpi 60

Terminal output: /Users/ravenscrafta/miniconda3/envs/py37/bin/run_upp.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html import('pkg_resources').run_script('sepp==4.5.2', 'run_upp.py') [15:01:11] config.py (line 370): INFO: Seed number: 297834 [15:01:11] exhaustive_upp.py (line 69): INFO: Reading input sequences: <_io.TextIOWrapper name='/Users/ravenscrafta/Documents/2019_ARLINGTON/2022_3 fall/PROJECTS/Lepto spatial survey MS/spatiotemporal analysis/analysis/phylogeny/UPP/WILD_CONCAT_seqsforUPP.fasta' mode='r' encoding='UTF-8'> [15:01:11] exhaustive_upp.py (line 105): INFO: Full length sequences are set to be from 8700 to 14500 character long [15:01:11] exhaustive_upp.py (line 111): INFO: Detected 381 fragmentary sequences [15:01:11] exhaustive_upp.py (line 116): INFO: Backbone size set to: 112 [15:01:11] exhaustive_upp.py (line 125): INFO: Writing backbone set. [15:01:11] filemgr.py (line 129): INFO: Root temp directory built: /var/folders/45/fjj2c9w57ygb_6zkv5fflpy00000gq/T/sepp/output.jnic_n0j [15:01:11] exhaustive_upp.py (line 129): INFO: Generating pasta backbone alignment and tree.

The CHCK_FILE is empty.