My memory is about 150 GB, but I still get this error.
[2026-03-05 13:47:06] INFO: GTDB-Tk v2.3.2
[2026-03-05 13:47:06] INFO: gtdbtk classify --genome_dir 1 --align_dir ../04GTDB_res214/1 --out_dir ../04GTDB_res214/1 -x fa --cpus 6 --skip_ani_screen
[2026-03-05 13:47:06] INFO: Using GTDB-Tk reference data version r214: /mnt/hgfs/1.runed_database/renhe/meta/gtdb-tk_database/release214
[2026-03-05 13:47:09] TASK: Placing 72 bacterial genomes into backbone reference tree with pplacer using 6 CPUs (be patient).
[2026-03-05 13:47:09] INFO: pplacer version: v1.1.alpha19-0-g807f6f3
[2026-03-05 13:52:15] INFO: Calculating RED values based on reference tree.
[2026-03-05 13:52:16] INFO: 72 out of 72 have an class assignments. Those genomes will be reclassified.
[2026-03-05 13:52:16] TASK: Placing 31 bacterial genomes into class-level reference tree 4 (1/6) with pplacer using 6 CPUs (be patient).
[2026-03-05 14:03:53] INFO: Calculating RED values based on reference tree.
[2026-03-05 14:03:55] TASK: Traversing tree to determine classification method.
[2026-03-05 14:03:56] INFO: Completed 31 genomes in 0.49 seconds (62.77 genomes/second).
[2026-03-05 14:03:56] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2026-03-05 14:06:00] INFO: Completed 804 comparisons in 2.05 minutes (392.91 comparisons/minute).
[2026-03-05 14:06:03] INFO: 3 genome(s) have been classified using FastANI and pplacer.
[2026-03-05 14:06:03] TASK: Placing 11 bacterial genomes into class-level reference tree 7 (2/6) with pplacer using 6 CPUs (be patient).
[2026-03-05 14:14:22] INFO: Calculating RED values based on reference tree.
[2026-03-05 14:14:24] TASK: Traversing tree to determine classification method.
[2026-03-05 14:14:24] INFO: Completed 11 genomes in 0.01 seconds (1,755.54 genomes/second).
[2026-03-05 14:14:24] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2026-03-05 14:14:42] INFO: Completed 516 comparisons in 16.96 seconds (30.43 comparisons/second).
[2026-03-05 14:14:43] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2026-03-05 14:14:43] TASK: Placing 10 bacterial genomes into class-level reference tree 1 (3/6) with pplacer using 6 CPUs (be patient).
[2026-03-05 14:27:05] INFO: Calculating RED values based on reference tree.
[2026-03-05 14:27:08] TASK: Traversing tree to determine classification method.
[2026-03-05 14:27:08] INFO: Completed 10 genomes in 0.00 seconds (2,329.39 genomes/second).
[2026-03-05 14:27:08] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2026-03-05 14:28:05] INFO: Completed 372 comparisons in 56.50 seconds (6.58 comparisons/second).
[2026-03-05 14:28:07] INFO: 4 genome(s) have been classified using FastANI and pplacer.
[2026-03-05 14:28:07] TASK: Placing 9 bacterial genomes into class-level reference tree 8 (4/6) with pplacer using 6 CPUs (be patient).
[2026-03-05 14:32:38] INFO: Calculating RED values based on reference tree.
[2026-03-05 14:32:40] TASK: Traversing tree to determine classification method.
[2026-03-05 14:32:40] INFO: Completed 9 genomes in 0.00 seconds (6,928.92 genomes/second).
[2026-03-05 14:32:40] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2026-03-05 14:32:43] INFO: Completed 20 comparisons in 2.87 seconds (6.96 comparisons/second).
[2026-03-05 14:32:44] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2026-03-05 14:32:44] TASK: Placing 8 bacterial genomes into class-level reference tree 3 (5/6) with pplacer using 6 CPUs (be patient).
[2026-03-05 14:45:40] INFO: Calculating RED values based on reference tree.
[2026-03-05 14:45:43] TASK: Traversing tree to determine classification method.
[2026-03-05 14:45:43] INFO: Completed 8 genomes in 0.05 seconds (153.73 genomes/second).
[2026-03-05 14:45:44] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2026-03-05 14:48:48] INFO: Completed 1,204 comparisons in 3.05 minutes (394.61 comparisons/minute).
[2026-03-05 14:48:49] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2026-03-05 14:48:49] TASK: Placing 3 bacterial genomes into class-level reference tree 6 (6/6) with pplacer using 6 CPUs (be patient).
[2026-03-05 14:58:20] INFO: Calculating RED values based on reference tree.
[2026-03-05 14:58:23] TASK: Traversing tree to determine classification method.
[2026-03-05 14:58:23] INFO: Completed 3 genomes in 0.00 seconds (7,375.68 genomes/second).
[2026-03-05 14:58:23] TASK: Calculating average nucleotide identity using FastANI (v1.32).
[2026-03-05 14:58:25] INFO: Completed 6 comparisons in 1.44 seconds (4.18 comparisons/second).
[2026-03-05 14:58:26] INFO: 0 genome(s) have been classified using FastANI and pplacer.
[2026-03-05 14:58:26] ERROR: Uncontrolled exit resulting from an unexpected error.
================================================================================
EXCEPTION: OSError
MESSAGE: [Errno 95] Operation not supported: ‘classify/gtdbtk.bac120.summary.tsv’ → ‘../04GTDB_res214/1/gtdbtk.bac120.summary.tsv’
Traceback (most recent call last):
File “/home/l/miniconda3/envs/gtdbtk214/lib/python3.8/site-packages/gtdbtk/main.py”, line 102, in main
gt_parser.parse_options(args)
File “/home/l/miniconda3/envs/gtdbtk214/lib/python3.8/site-packages/gtdbtk/main.py”, line 1204, in parse_options
self.classify(options)
File “/home/l/miniconda3/envs/gtdbtk214/lib/python3.8/site-packages/gtdbtk/main.py”, line 587, in classify
reports = classify.run(genomes=genomes,
File “/home/l/miniconda3/envs/gtdbtk214/lib/python3.8/site-packages/gtdbtk/classify.py”, line 659, in run
symlink_f(PATH_BAC120_SUMMARY_OUT.format(prefix=prefix),
File “/home/l/miniconda3/envs/gtdbtk214/lib/python3.8/site-packages/gtdbtk/tools.py”, line 269, in symlink_f
os.symlink(src, dst)
OSError: [Errno 95] Operation not supported: ‘classify/gtdbtk.bac120.summary.tsv’ → ‘../04GTDB_res214/1/gtdbtk.bac120.summary.tsv’