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pplacerException: an error was encountered while running pplacer. #620

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luwenyi111 opened this issue Jan 13, 2025 · 0 comments
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error Help required for a GTDB-Tk error.

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@luwenyi111
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When I run the command, I cannot get the classfiy result. Please give some advice. Thanks!!!
gtdbtk classify_wf --genome_dir new_reassemblebins --out_dir classify_wf2 --extension fa --prefix bin --cpus 1 --pplacer_cpus 1 --skip_ani_screen --full_tree

[2025-01-09 14:50:14] TASK: Placing 129 bacterial genomes into reference tree with pplacer using 1 CPUs (be patient).
[2025-01-09 14:50:14] INFO: pplacer version: v1.1.alpha19-0-g807f6f3
[2025-01-09 17:03:18] ERROR: Controlled exit resulting from an unrecoverable error or warning.

================================================================================
EXCEPTION: PplacerException
MESSAGE: An error was encountered while running pplacer.


Traceback (most recent call last):
File "/media/home/anaconda3/envs/gtdbtknew/lib/python3.8/site-packages/gtdbtk/main.py", line 102, in main
gt_parser.parse_options(args)
File "/media/home/anaconda3/envs/gtdbtknew/lib/python3.8/site-packages/gtdbtk/main.py", line 1182, in parse_options
self.classify(options,all_classified_ani= all_classified_ani,all_failed_prodigal=all_failed_prodigal)
File "/media/home/anaconda3/envs/gtdbtknew/lib/python3.8/site-packages/gtdbtk/main.py", line 587, in classify
reports = classify.run(genomes=genomes,
File "/media/home/anaconda3/envs/gtdbtknew/lib/python3.8/site-packages/gtdbtk/classify.py", line 682, in run
classify_tree = self.place_genomes(user_msa_file,
File "/media/home/anaconda3/envs/gtdbtknew/lib/python3.8/site-packages/gtdbtk/classify.py", line 270, in place_genomes
pplacer.run(self.pplacer_cpus, 'wag', pplacer_ref_pkg, pplacer_json_out,
File "/media/home/anaconda3/envs/gtdbtknew/lib/python3.8/site-packages/gtdbtk/external/pplacer.py", line 95, in run
raise PplacerException(
gtdbtk.exceptions.PplacerException: An error was encountered while running pplacer.

@luwenyi111 luwenyi111 added the error Help required for a GTDB-Tk error. label Jan 13, 2025
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