gtdbtk.exceptions.PplacerException: An error was encountered while running pplacer.

[mattoslmp]

Dear, I' having the errror mensage bellow. Could you give any suggestions/tips:

[2022-08-16 22:00:57] ERROR: Controlled exit resulting from an unrecoverable error or warning.

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

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Traceback (most recent call last): File "/bio_temp/share_bio/softwares/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/site-packages/gtdbtk/main.py", line 98, in main gt_parser.parse_options(args) File "/bio_temp/share_bio/softwares/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/site-packages/gtdbtk/main.py", line 834, in parse_options self.classify(options) File "/bio_temp/share_bio/softwares/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/site-packages/gtdbtk/main.py", line 458, in classify classify.run(genomes=genomes, File "/bio_temp/share_bio/softwares/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/site-packages/gtdbtk/classify.py", line 396, in run high_classify_tree = self.place_genomes(user_msa_file, File "/bio_temp/share_bio/softwares/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/site-packages/gtdbtk/classify.py", line 261, in place_genomes pplacer.run(self.pplacer_cpus, 'wag', pplacer_ref_pkg, pplacer_json_out, File "/bio_temp/share_bio/softwares/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/site-packages/gtdbtk/external/pplacer.py", line 92, in run raise PplacerException( gtdbtk.exceptions.PplacerException: An error was encountered while running pplacer.

[aaronmussig]

Hi, how much memory do you have on the server running GTDB-Tk? This usually occurs when pplacer runs out of memory. Do you have the rest of the GTDB-Tk log above the traceback?

[pchaumeil]

Ticket closed due to inactivity.

[kunaljaani]

Hi!

I recently updated my gtdbtk installation to the latest v2.4.0 and also downloaded the associated database v220. I am running gtdbtk as a part of metaGEM pipeline w/ 128GB RAM. It was running fine before the upgrade but is now throwing this error could you please suggest a fix?

Thank you Kunal

==> Step 9 of 9: placing genome 214 of 246 (86.99%).[2024-06-26 14:40:23] INFO: Calculating RED values based on reference tree. ==> Step 9 of 9: placing genome 216 of 246 (87.80%).[2024-06-26 14:40:24] INFO: 284 out of 284 have an class assignments. Those genomes will be reclassified. [2024-06-26 14:40:24] TASK: Placing 157 bacterial genomes into class-level reference tree 3 (1/6) with pplacer using 12 CPUs (be patient). [2024-06-26 14:40:40] INFO: Calculating RED values based on reference tree. [2024-06-26 14:40:41] INFO: 246 out of 246 have an class assignments. Those genomes will be reclassified. [2024-06-26 14:40:41] TASK: Placing 155 bacterial genomes into class-level reference tree 3 (1/7) with pplacer using 12 CPUs (be patient). ==> Step 7 of 9: Preparing the edges for baseball.Process Process-67:.51/85.57 GB, 77.73%). Traceback (most recent call last): File "/home/metaGEM/workflow/envs/metagem/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/home/metaGEM/workflow/envs/metagem/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/home/metaGEM/workflow/envs/metagem/lib/python3.8/site-packages/gtdbtk/external/pplacer.py", line 127, in _worker raise PplacerException('An error was encountered while ' gtdbtk.exceptions.PplacerException: An error was encountered while running pplacer, check the log file: GTDBTk/classify/intermediate_results/pplacer/tree_3/pplacer.class_level.bac120.out ==> Step 5 of 9: Caching likelihood information on reference tree (66.76/85.57 GB, 78.02%).[2024-06-26 14:53:48] ERROR: Controlled exit resulting from an unrecoverable error or warning.

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

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Traceback (most recent call last): File "/home/metaGEM/workflow/envs/metagem/lib/python3.8/site-packages/gtdbtk/main.py", line 102, in main gt_parser.parse_options(args) File "/home/metaGEM/workflow/envs/metagem/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 "/home/metaGEM/workflow/envs/metagem/lib/python3.8/site-packages/gtdbtk/main.py", line 587, in classify reports = classify.run(genomes=genomes, File "/home/metaGEM/workflow/envs/metagem/lib/python3.8/site-packages/gtdbtk/classify.py", line 624, in run low_classify_tree, submsa_file_path = self._place_in_low_tree( File "/home/metaGEM/workflow/envs/metagem/lib/python3.8/site-packages/gtdbtk/classify.py", line 824, in _place_in_low_tree low_classify_tree = self.place_genomes(submsa_file_path, File "/home/metaGEM/workflow/envs/metagem/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 "/home/metaGEM/workflow/envs/metagem/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.

Process Process-68: ^C Process Process-67: