Mamingjie543
commented
1 year ago Very luckily, I solved this problem with the help of a kind person!!! Here is the help email from the well-wisher： Hi, It looks like you are using GTDB-Tk package R207_v1 with GTDB-Tk 2.1.1, That is why the path to gtdbtk_package_backbone.refpkg cannot be found. v2.1.0+ is not compatible with GTDB-Tk package R207_v1. It is necessary to upgrade to GTDB-Tk package R207_v2.
Cheers, Pierre
pchaumeil
==> Processed 62252/62292 sequences (100%) |██████████████▉| [569.91sequence/s, ETA 00:00] [2022-11-30 15:09:29] INFO: Completed 62,292 sequences in 1.61 minutes (38,645.61 sequences/minute). [2022-11-30 15:09:29] INFO: Masked bacterial alignment from 41,084 to 5,036 AAs. [2022-11-30 15:09:29] INFO: 0 bacterial user genomes have amino acids in <10.0% of columns in filtered MSA. [2022-11-30 15:09:29] INFO: Creating concatenated alignment for 62,292 bacterial GTDB and user genomes. [2022-11-30 15:09:52] INFO: Creating concatenated alignment for 1 bacterial user genomes. [2022-11-30 15:09:53] INFO: Done. [2022-11-30 15:09:54] TASK: Placing 1 bacterial genomes into backbone reference tree with pplacer using 10 CPUs (be patient). [2022-11-30 15:09:54] INFO: pplacer version: v1.1.alpha19-0-g807f6f3
==> . ==> Step 1 of 9: Starting pplacer.Uncaught exception: Sys_error("/data/home/mamj/db/gtdbtk/release207/split/backbone/pplacer/gtdbtk_package_backbone.refpkg: No such file or directory") Fatal error: exception Sys_error("/data/home/mamj/db/gtdbtk/release207/split/backbone/pplacer/gtdbtk_package_backbone.refpkg: No such file or directory")
==> Running pplacer v1.1.alpha19-0-g807f6f3 analysis on ./tax/align/gtdbtk.bac120.user_msa.fasta.gz....Process Process-55: Traceback (most recent call last): File "/data/home/mamj/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap self.run() File "/data/home/mamj/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/multiprocessing/process.py", line 108, in run self._target(*self._args, **self._kwargs) File "/data/home/mamj/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/site-packages/gtdbtk/external/pplacer.py", line 124, in _worker raise PplacerException('An error was encountered while ' gtdbtk.exceptions.PplacerException: An error was encountered while running pplacer, check the log file: ./tax/classify/intermediate_results/pplacer/pplacer.backbone.bac120.out
[2022-11-30 15:09:55] 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 "/data/home/mamj/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/site-packages/gtdbtk/main.py", line 98, in main gt_parser.parse_options(args) File "/data/home/mamj/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/site-packages/gtdbtk/main.py", line 834, in parse_options self.classify(options) File "/data/home/mamj/miniconda3/envs/gtdbtk-2.1.1/lib/python3.8/site-packages/gtdbtk/main.py", line 458, in classify classify.run(genomes=genomes, File "/data/home/mamj/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 "/data/home/mamj/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 "/data/home/mamj/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.