Delete wandb

wandb/debug-internal.log

@@ -1,6 +0,0 @@
-{"time":"2026-03-05T08:01:52.530712755Z","level":"INFO","msg":"stream: starting","core version":"0.25.0"}
-{"time":"2026-03-05T08:01:52.874673716Z","level":"INFO","msg":"stream: created new stream","id":"rg61703v"}
-{"time":"2026-03-05T08:01:52.874791666Z","level":"INFO","msg":"handler: started","stream_id":"rg61703v"}
-{"time":"2026-03-05T08:01:52.874924036Z","level":"INFO","msg":"stream: started","id":"rg61703v"}
-{"time":"2026-03-05T08:01:52.874933836Z","level":"INFO","msg":"writer: started","stream_id":"rg61703v"}
-{"time":"2026-03-05T08:01:52.874941716Z","level":"INFO","msg":"sender: started","stream_id":"rg61703v"}

wandb/debug.log

@@ -1,19 +0,0 @@
-2026-03-05 08:01:52,245 INFO    MainThread:3958978 [wandb_setup.py:_flush():81] Current SDK version is 0.25.0
-2026-03-05 08:01:52,245 INFO    MainThread:3958978 [wandb_setup.py:_flush():81] Configure stats pid to 3958978
-2026-03-05 08:01:52,245 INFO    MainThread:3958978 [wandb_setup.py:_flush():81] Loading settings from environment variables
-2026-03-05 08:01:52,245 INFO    MainThread:3958978 [wandb_init.py:setup_run_log_directory():717] Logging user logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_080152-rg61703v/logs/debug.log
-2026-03-05 08:01:52,245 INFO    MainThread:3958978 [wandb_init.py:setup_run_log_directory():718] Logging internal logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_080152-rg61703v/logs/debug-internal.log
-2026-03-05 08:01:52,245 INFO    MainThread:3958978 [wandb_init.py:init():844] calling init triggers
-2026-03-05 08:01:52,245 INFO    MainThread:3958978 [wandb_init.py:init():849] wandb.init called with sweep_config: {}
-config: {'_wandb': {}}
-2026-03-05 08:01:52,245 INFO    MainThread:3958978 [wandb_init.py:init():892] starting backend
-2026-03-05 08:01:52,518 INFO    MainThread:3958978 [wandb_init.py:init():895] sending inform_init request
-2026-03-05 08:01:52,526 INFO    MainThread:3958978 [wandb_init.py:init():903] backend started and connected
-2026-03-05 08:01:52,528 INFO    MainThread:3958978 [wandb_init.py:init():973] updated telemetry
-2026-03-05 08:01:52,535 INFO    MainThread:3958978 [wandb_init.py:init():997] communicating run to backend with 90.0 second timeout
-2026-03-05 08:01:54,342 INFO    MainThread:3958978 [wandb_init.py:init():1042] starting run threads in backend
-2026-03-05 08:01:54,439 INFO    MainThread:3958978 [wandb_run.py:_console_start():2524] atexit reg
-2026-03-05 08:01:54,440 INFO    MainThread:3958978 [wandb_run.py:_redirect():2373] redirect: wrap_raw
-2026-03-05 08:01:54,440 INFO    MainThread:3958978 [wandb_run.py:_redirect():2442] Wrapping output streams.
-2026-03-05 08:01:54,440 INFO    MainThread:3958978 [wandb_run.py:_redirect():2465] Redirects installed.
-2026-03-05 08:01:54,446 INFO    MainThread:3958978 [wandb_init.py:init():1082] run started, returning control to user process

wandb/run-20260305_040122-aq8j72f1/files/config.yaml

@@ -1,141 +0,0 @@
-_wandb:
-    value:
-        cli_version: 0.25.0
-        e:
-            f0ugcbwht0bzsznis5d33rdup7dudruj:
-                args:
-                    - --model_name_or_path
-                    - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000
-                    - --tokenizer_path
-                    - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json
-                    - --trust_remote_code
-                    - "True"
-                    - --data_path
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split
-                    - --kmer
-                    - "-1"
-                    - --run_name
-                    - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_seed42
-                    - --model_max_length
-                    - "100"
-                    - --per_device_train_batch_size
-                    - "128"
-                    - --per_device_eval_batch_size
-                    - "128"
-                    - --gradient_accumulation_steps
-                    - "1"
-                    - --learning_rate
-                    - "3e-5"
-                    - --num_train_epochs
-                    - "4"
-                    - --fp16
-                    - --save_steps
-                    - "200"
-                    - --output_dir
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers
-                    - --evaluation_strategy
-                    - steps
-                    - --eval_steps
-                    - "200"
-                    - --warmup_steps
-                    - "30"
-                    - --logging_steps
-                    - "100000"
-                    - --log_level
-                    - info
-                    - --seed
-                    - "42"
-                    - --find_unused_parameters
-                    - "False"
-                    - --project_name
-                    - genomic_bench_tune_hg38_1024
-                cpu_count: 128
-                cpu_count_logical: 255
-                cudaVersion: "12.2"
-                disk:
-                    /:
-                        total: "1876350566400"
-                        used: "546900058112"
-                email: mtapiapacheco@ucsd.edu
-                executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python
-                git:
-                    commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6
-                    remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks
-                gpu: NVIDIA A100 80GB PCIe
-                gpu_count: 8
-                gpu_nvidia:
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044
-                host: sn4622116170
-                memory:
-                    total: "4316310355968"
-                os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35
-                program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py
-                python: CPython 3.10.19
-                root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data
-                startedAt: "2026-03-05T04:01:22.935924Z"
-                writerId: f0ugcbwht0bzsznis5d33rdup7dudruj
-        m: []
-        python_version: 3.10.19
-        t:
-            "1":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "2":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "4": 3.10.19
-            "5": 0.25.0
-            "6": 5.3.0
-            "12": 0.25.0
-            "13": linux-x86_64

wandb/run-20260305_040122-aq8j72f1/files/output.log

@@ -1,37 +0,0 @@
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434

wandb/run-20260305_040122-aq8j72f1/files/requirements.txt

@@ -1,90 +0,0 @@
-hf-xet==1.3.2
-mpmath==1.3.0
-httpx==0.28.1
-markdown-it-py==4.0.0
-attrs==25.4.0
-pydantic_core==2.41.5
-cffi==2.0.0
-wheel==0.46.3
-tzdata==2025.3
-mdurl==0.1.2
-dill==0.4.0
-GitPython==3.1.46
-idna==3.11
-pycparser==2.23
-triton==3.1.0
-numpy==2.0.1
-numpy==2.2.6
-python-dateutil==2.9.0.post0
-gitdb==4.0.12
-rich==14.3.3
-PyYAML==6.0.3
-pytz==2026.1.post1
-packaging==25.0
-transformers==5.3.0
-networkx==3.4.2
-platformdirs==4.9.2
-ittapi==1.2.1
-yarl==1.23.0
-aiohttp==3.13.3
-typer==0.24.1
-mkl_fft==1.3.11
-psutil==7.2.2
-scipy==1.15.3
-httpcore==1.0.9
-Jinja2==3.1.6
-pip==26.0.1
-six==1.17.0
-frozenlist==1.8.0
-filelock==3.20.3
-annotated-doc==0.0.4
-multiprocess==0.70.18
-threadpoolctl==3.6.0
-typing_extensions==4.15.0
-pydantic==2.12.5
-async-timeout==5.0.1
-Pygments==2.19.2
-mkl_random==1.2.8
-certifi==2026.2.25
-exceptiongroup==1.3.1
-charset-normalizer==3.4.4
-wandb==0.25.0
-PySocks==1.7.1
-pandas==2.3.3
-smmap==5.0.2
-pyarrow==23.0.1
-safetensors==0.7.0
-tokenizers==0.22.2
-requests==2.32.5
-fsspec==2026.2.0
-aiosignal==1.4.0
-multidict==6.7.1
-typing-inspection==0.4.2
-accelerate==1.13.0
-torch==2.5.1
-brotlicffi==1.2.0.0
-gmpy2==2.2.2
-datasets==4.6.1
-anyio==4.12.1
-annotated-types==0.7.0
-tqdm==4.67.3
-mkl-service==2.4.0
-sentry-sdk==2.54.0
-torchvision==0.20.1
-shellingham==1.5.4
-torchaudio==2.5.1
-sympy==1.13.1
-h11==0.16.0
-pillow==12.1.1
-protobuf==6.33.5
-click==8.3.1
-MarkupSafe==3.0.2
-urllib3==2.6.3
-propcache==0.4.1
-regex==2026.2.28
-xxhash==3.6.0
-setuptools==80.10.2
-scikit-learn==1.7.2
-huggingface_hub==1.5.0
-joblib==1.5.3
-aiohappyeyeballs==2.6.1

wandb/run-20260305_040122-aq8j72f1/files/wandb-metadata.json

@@ -1,134 +0,0 @@
-{
-  "os":  "Linux-5.15.0-72-generic-x86_64-with-glibc2.35",
-  "python":  "CPython 3.10.19",
-  "startedAt":  "2026-03-05T04:01:22.935924Z",
-  "args":  [
-    "--model_name_or_path",
-    "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000",
-    "--tokenizer_path",
-    "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json",
-    "--trust_remote_code",
-    "True",
-    "--data_path",
-    "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers/split",
-    "--kmer",
-    "-1",
-    "--run_name",
-    "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_seed42",
-    "--model_max_length",
-    "100",
-    "--per_device_train_batch_size",
-    "128",
-    "--per_device_eval_batch_size",
-    "128",
-    "--gradient_accumulation_steps",
-    "1",
-    "--learning_rate",
-    "3e-5",
-    "--num_train_epochs",
-    "4",
-    "--fp16",
-    "--save_steps",
-    "200",
-    "--output_dir",
-    "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers",
-    "--evaluation_strategy",
-    "steps",
-    "--eval_steps",
-    "200",
-    "--warmup_steps",
-    "30",
-    "--logging_steps",
-    "100000",
-    "--log_level",
-    "info",
-    "--seed",
-    "42",
-    "--find_unused_parameters",
-    "False",
-    "--project_name",
-    "genomic_bench_tune_hg38_1024"
-  ],
-  "program":  "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py",
-  "git":  {
-    "remote":  "https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks",
-    "commit":  "5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6"
-  },
-  "email":  "mtapiapacheco@ucsd.edu",
-  "root":  "/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data",
-  "host":  "sn4622116170",
-  "executable":  "/home/n5huang/miniconda3/envs/nt_ft/bin/python",
-  "cpu_count":  128,
-  "cpu_count_logical":  255,
-  "gpu":  "NVIDIA A100 80GB PCIe",
-  "gpu_count":  8,
-  "disk":  {
-    "/":  {
-      "total":  "1876350566400",
-      "used":  "546900058112"
-    }
-  },
-  "memory":  {
-    "total":  "4316310355968"
-  },
-  "gpu_nvidia":  [
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-054a4d72-8520-5e4a-5cd3-7519a0966809"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-a18369da-b15a-c8af-72f1-7f6272e479af"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044"
-    }
-  ],
-  "cudaVersion":  "12.2",
-  "writerId":  "f0ugcbwht0bzsznis5d33rdup7dudruj"
-}

wandb/run-20260305_040122-aq8j72f1/files/wandb-summary.json

@@ -1 +0,0 @@
-{"_wandb":{"runtime":4},"_runtime":4}

wandb/run-20260305_040122-aq8j72f1/logs/debug-core.log

@@ -1,14 +0,0 @@
-{"time":"2026-03-05T04:01:22.988073404Z","level":"INFO","msg":"main: starting server","port-filename":"/tmp/tmpl7xhmno5/port-829742.txt","pid":829742,"log-level":0,"disable-analytics":false,"shutdown-on-parent-exit":false,"enable-dcgm-profiling":false}
-{"time":"2026-03-05T04:01:22.988972073Z","level":"INFO","msg":"server: will exit if parent process dies","ppid":829742}
-{"time":"2026-03-05T04:01:22.988944303Z","level":"INFO","msg":"server: accepting connections","addr":{"Name":"/tmp/wandb-829742-834959-3745343916/socket","Net":"unix"}}
-{"time":"2026-03-05T04:01:23.162413037Z","level":"INFO","msg":"connection: ManageConnectionData: new connection created","id":"1(@)"}
-{"time":"2026-03-05T04:01:23.170841351Z","level":"INFO","msg":"handleInformInit: received","streamId":"aq8j72f1","id":"1(@)"}
-{"time":"2026-03-05T04:01:23.508426463Z","level":"INFO","msg":"handleInformInit: stream started","streamId":"aq8j72f1","id":"1(@)"}
-{"time":"2026-03-05T04:01:28.255645799Z","level":"INFO","msg":"handleInformTeardown: server teardown initiated","id":"1(@)"}
-{"time":"2026-03-05T04:01:28.255921908Z","level":"INFO","msg":"server is shutting down"}
-{"time":"2026-03-05T04:01:28.255921138Z","level":"INFO","msg":"connection: closing","id":"1(@)"}
-{"time":"2026-03-05T04:01:28.256076588Z","level":"INFO","msg":"server: listener closed","addr":{"Name":"/tmp/wandb-829742-834959-3745343916/socket","Net":"unix"}}
-{"time":"2026-03-05T04:01:28.256116448Z","level":"INFO","msg":"connection: closed successfully","id":"1(@)"}
-{"time":"2026-03-05T04:01:28.899587734Z","level":"INFO","msg":"handleInformTeardown: server shutdown complete","id":"1(@)"}
-{"time":"2026-03-05T04:01:28.899628344Z","level":"INFO","msg":"connection: ManageConnectionData: connection closed","id":"1(@)"}
-{"time":"2026-03-05T04:01:28.899643424Z","level":"INFO","msg":"server is closed"}

wandb/run-20260305_040122-aq8j72f1/logs/debug-internal.log

@@ -1,11 +0,0 @@
-{"time":"2026-03-05T04:01:23.17099682Z","level":"INFO","msg":"stream: starting","core version":"0.25.0"}
-{"time":"2026-03-05T04:01:23.508165593Z","level":"INFO","msg":"stream: created new stream","id":"aq8j72f1"}
-{"time":"2026-03-05T04:01:23.508281043Z","level":"INFO","msg":"handler: started","stream_id":"aq8j72f1"}
-{"time":"2026-03-05T04:01:23.508409073Z","level":"INFO","msg":"stream: started","id":"aq8j72f1"}
-{"time":"2026-03-05T04:01:23.508438633Z","level":"INFO","msg":"sender: started","stream_id":"aq8j72f1"}
-{"time":"2026-03-05T04:01:23.508435253Z","level":"INFO","msg":"writer: started","stream_id":"aq8j72f1"}
-{"time":"2026-03-05T04:01:28.255910928Z","level":"INFO","msg":"stream: closing","id":"aq8j72f1"}
-{"time":"2026-03-05T04:01:28.748741506Z","level":"INFO","msg":"fileTransfer: Close: file transfer manager closed"}
-{"time":"2026-03-05T04:01:28.895497467Z","level":"INFO","msg":"handler: closed","stream_id":"aq8j72f1"}
-{"time":"2026-03-05T04:01:28.895665537Z","level":"INFO","msg":"sender: closed","stream_id":"aq8j72f1"}
-{"time":"2026-03-05T04:01:28.895680377Z","level":"INFO","msg":"stream: closed","id":"aq8j72f1"}

wandb/run-20260305_040122-aq8j72f1/logs/debug.log

@@ -1,21 +0,0 @@
-2026-03-05 04:01:22,938 INFO    MainThread:829742 [wandb_setup.py:_flush():81] Current SDK version is 0.25.0
-2026-03-05 04:01:22,938 INFO    MainThread:829742 [wandb_setup.py:_flush():81] Configure stats pid to 829742
-2026-03-05 04:01:22,938 INFO    MainThread:829742 [wandb_setup.py:_flush():81] Loading settings from environment variables
-2026-03-05 04:01:22,939 INFO    MainThread:829742 [wandb_init.py:setup_run_log_directory():717] Logging user logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_040122-aq8j72f1/logs/debug.log
-2026-03-05 04:01:22,939 INFO    MainThread:829742 [wandb_init.py:setup_run_log_directory():718] Logging internal logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_040122-aq8j72f1/logs/debug-internal.log
-2026-03-05 04:01:22,939 INFO    MainThread:829742 [wandb_init.py:init():844] calling init triggers
-2026-03-05 04:01:22,939 INFO    MainThread:829742 [wandb_init.py:init():849] wandb.init called with sweep_config: {}
-config: {'_wandb': {}}
-2026-03-05 04:01:22,939 INFO    MainThread:829742 [wandb_init.py:init():892] starting backend
-2026-03-05 04:01:23,163 INFO    MainThread:829742 [wandb_init.py:init():895] sending inform_init request
-2026-03-05 04:01:23,169 INFO    MainThread:829742 [wandb_init.py:init():903] backend started and connected
-2026-03-05 04:01:23,172 INFO    MainThread:829742 [wandb_init.py:init():973] updated telemetry
-2026-03-05 04:01:23,179 INFO    MainThread:829742 [wandb_init.py:init():997] communicating run to backend with 90.0 second timeout
-2026-03-05 04:01:24,005 INFO    MainThread:829742 [wandb_init.py:init():1042] starting run threads in backend
-2026-03-05 04:01:24,141 INFO    MainThread:829742 [wandb_run.py:_console_start():2524] atexit reg
-2026-03-05 04:01:24,141 INFO    MainThread:829742 [wandb_run.py:_redirect():2373] redirect: wrap_raw
-2026-03-05 04:01:24,141 INFO    MainThread:829742 [wandb_run.py:_redirect():2442] Wrapping output streams.
-2026-03-05 04:01:24,142 INFO    MainThread:829742 [wandb_run.py:_redirect():2465] Redirects installed.
-2026-03-05 04:01:24,148 INFO    MainThread:829742 [wandb_init.py:init():1082] run started, returning control to user process
-2026-03-05 04:01:28,247 INFO    wandb-AsyncioManager-main:829742 [service_client.py:_forward_responses():134] Reached EOF.
-2026-03-05 04:01:28,247 INFO    wandb-AsyncioManager-main:829742 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles.

wandb/run-20260305_040136-qpc17ycl/files/config.yaml

@@ -1,141 +0,0 @@
-_wandb:
-    value:
-        cli_version: 0.25.0
-        e:
-            t1x05ahrojkswcdknlxxvq1epngyd9kc:
-                args:
-                    - --model_name_or_path
-                    - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000
-                    - --tokenizer_path
-                    - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json
-                    - --trust_remote_code
-                    - "True"
-                    - --data_path
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split
-                    - --kmer
-                    - "-1"
-                    - --run_name
-                    - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_types_seed42
-                    - --model_max_length
-                    - "100"
-                    - --per_device_train_batch_size
-                    - "128"
-                    - --per_device_eval_batch_size
-                    - "128"
-                    - --gradient_accumulation_steps
-                    - "1"
-                    - --learning_rate
-                    - "3e-5"
-                    - --num_train_epochs
-                    - "4"
-                    - --fp16
-                    - --save_steps
-                    - "200"
-                    - --output_dir
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types
-                    - --evaluation_strategy
-                    - steps
-                    - --eval_steps
-                    - "200"
-                    - --warmup_steps
-                    - "30"
-                    - --logging_steps
-                    - "100000"
-                    - --log_level
-                    - info
-                    - --seed
-                    - "42"
-                    - --find_unused_parameters
-                    - "False"
-                    - --project_name
-                    - genomic_bench_tune_hg38_1024
-                cpu_count: 128
-                cpu_count_logical: 255
-                cudaVersion: "12.2"
-                disk:
-                    /:
-                        total: "1876350566400"
-                        used: "546902056960"
-                email: mtapiapacheco@ucsd.edu
-                executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python
-                git:
-                    commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6
-                    remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks
-                gpu: NVIDIA A100 80GB PCIe
-                gpu_count: 8
-                gpu_nvidia:
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044
-                host: sn4622116170
-                memory:
-                    total: "4316310355968"
-                os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35
-                program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py
-                python: CPython 3.10.19
-                root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data
-                startedAt: "2026-03-05T04:01:36.144515Z"
-                writerId: t1x05ahrojkswcdknlxxvq1epngyd9kc
-        m: []
-        python_version: 3.10.19
-        t:
-            "1":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "2":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "4": 3.10.19
-            "5": 0.25.0
-            "6": 5.3.0
-            "12": 0.25.0
-            "13": linux-x86_64

wandb/run-20260305_040136-qpc17ycl/files/output.log

@@ -1,37 +0,0 @@
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434

wandb/run-20260305_040136-qpc17ycl/files/requirements.txt

@@ -1,90 +0,0 @@
-hf-xet==1.3.2
-mpmath==1.3.0
-httpx==0.28.1
-markdown-it-py==4.0.0
-attrs==25.4.0
-pydantic_core==2.41.5
-cffi==2.0.0
-wheel==0.46.3
-tzdata==2025.3
-mdurl==0.1.2
-dill==0.4.0
-GitPython==3.1.46
-idna==3.11
-pycparser==2.23
-triton==3.1.0
-numpy==2.0.1
-numpy==2.2.6
-python-dateutil==2.9.0.post0
-gitdb==4.0.12
-rich==14.3.3
-PyYAML==6.0.3
-pytz==2026.1.post1
-packaging==25.0
-transformers==5.3.0
-networkx==3.4.2
-platformdirs==4.9.2
-ittapi==1.2.1
-yarl==1.23.0
-aiohttp==3.13.3
-typer==0.24.1
-mkl_fft==1.3.11
-psutil==7.2.2
-scipy==1.15.3
-httpcore==1.0.9
-Jinja2==3.1.6
-pip==26.0.1
-six==1.17.0
-frozenlist==1.8.0
-filelock==3.20.3
-annotated-doc==0.0.4
-multiprocess==0.70.18
-threadpoolctl==3.6.0
-typing_extensions==4.15.0
-pydantic==2.12.5
-async-timeout==5.0.1
-Pygments==2.19.2
-mkl_random==1.2.8
-certifi==2026.2.25
-exceptiongroup==1.3.1
-charset-normalizer==3.4.4
-wandb==0.25.0
-PySocks==1.7.1
-pandas==2.3.3
-smmap==5.0.2
-pyarrow==23.0.1
-safetensors==0.7.0
-tokenizers==0.22.2
-requests==2.32.5
-fsspec==2026.2.0
-aiosignal==1.4.0
-multidict==6.7.1
-typing-inspection==0.4.2
-accelerate==1.13.0
-torch==2.5.1
-brotlicffi==1.2.0.0
-gmpy2==2.2.2
-datasets==4.6.1
-anyio==4.12.1
-annotated-types==0.7.0
-tqdm==4.67.3
-mkl-service==2.4.0
-sentry-sdk==2.54.0
-torchvision==0.20.1
-shellingham==1.5.4
-torchaudio==2.5.1
-sympy==1.13.1
-h11==0.16.0
-pillow==12.1.1
-protobuf==6.33.5
-click==8.3.1
-MarkupSafe==3.0.2
-urllib3==2.6.3
-propcache==0.4.1
-regex==2026.2.28
-xxhash==3.6.0
-setuptools==80.10.2
-scikit-learn==1.7.2
-huggingface_hub==1.5.0
-joblib==1.5.3
-aiohappyeyeballs==2.6.1

wandb/run-20260305_040136-qpc17ycl/files/wandb-metadata.json

@@ -1,134 +0,0 @@
-{
-  "os":  "Linux-5.15.0-72-generic-x86_64-with-glibc2.35",
-  "python":  "CPython 3.10.19",
-  "startedAt":  "2026-03-05T04:01:36.144515Z",
-  "args":  [
-    "--model_name_or_path",
-    "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000",
-    "--tokenizer_path",
-    "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json",
-    "--trust_remote_code",
-    "True",
-    "--data_path",
-    "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/enhancers_types/split",
-    "--kmer",
-    "-1",
-    "--run_name",
-    "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_enhancers_types_seed42",
-    "--model_max_length",
-    "100",
-    "--per_device_train_batch_size",
-    "128",
-    "--per_device_eval_batch_size",
-    "128",
-    "--gradient_accumulation_steps",
-    "1",
-    "--learning_rate",
-    "3e-5",
-    "--num_train_epochs",
-    "4",
-    "--fp16",
-    "--save_steps",
-    "200",
-    "--output_dir",
-    "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/enhancers_types",
-    "--evaluation_strategy",
-    "steps",
-    "--eval_steps",
-    "200",
-    "--warmup_steps",
-    "30",
-    "--logging_steps",
-    "100000",
-    "--log_level",
-    "info",
-    "--seed",
-    "42",
-    "--find_unused_parameters",
-    "False",
-    "--project_name",
-    "genomic_bench_tune_hg38_1024"
-  ],
-  "program":  "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py",
-  "git":  {
-    "remote":  "https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks",
-    "commit":  "5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6"
-  },
-  "email":  "mtapiapacheco@ucsd.edu",
-  "root":  "/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data",
-  "host":  "sn4622116170",
-  "executable":  "/home/n5huang/miniconda3/envs/nt_ft/bin/python",
-  "cpu_count":  128,
-  "cpu_count_logical":  255,
-  "gpu":  "NVIDIA A100 80GB PCIe",
-  "gpu_count":  8,
-  "disk":  {
-    "/":  {
-      "total":  "1876350566400",
-      "used":  "546902056960"
-    }
-  },
-  "memory":  {
-    "total":  "4316310355968"
-  },
-  "gpu_nvidia":  [
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-054a4d72-8520-5e4a-5cd3-7519a0966809"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-a18369da-b15a-c8af-72f1-7f6272e479af"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044"
-    }
-  ],
-  "cudaVersion":  "12.2",
-  "writerId":  "t1x05ahrojkswcdknlxxvq1epngyd9kc"
-}

wandb/run-20260305_040136-qpc17ycl/files/wandb-summary.json

@@ -1 +0,0 @@
-{"_wandb":{"runtime":4},"_runtime":4}

wandb/run-20260305_040136-qpc17ycl/logs/debug-core.log

@@ -1,14 +0,0 @@
-{"time":"2026-03-05T04:01:36.192499335Z","level":"INFO","msg":"main: starting server","port-filename":"/tmp/tmp2msnx2fh/port-839387.txt","pid":839387,"log-level":0,"disable-analytics":false,"shutdown-on-parent-exit":false,"enable-dcgm-profiling":false}
-{"time":"2026-03-05T04:01:36.193636514Z","level":"INFO","msg":"server: will exit if parent process dies","ppid":839387}
-{"time":"2026-03-05T04:01:36.193597344Z","level":"INFO","msg":"server: accepting connections","addr":{"Name":"/tmp/wandb-839387-843169-1818533415/socket","Net":"unix"}}
-{"time":"2026-03-05T04:01:36.373045063Z","level":"INFO","msg":"connection: ManageConnectionData: new connection created","id":"1(@)"}
-{"time":"2026-03-05T04:01:36.381815407Z","level":"INFO","msg":"handleInformInit: received","streamId":"qpc17ycl","id":"1(@)"}
-{"time":"2026-03-05T04:01:36.605075416Z","level":"INFO","msg":"handleInformInit: stream started","streamId":"qpc17ycl","id":"1(@)"}
-{"time":"2026-03-05T04:01:41.428807282Z","level":"INFO","msg":"handleInformTeardown: server teardown initiated","id":"1(@)"}
-{"time":"2026-03-05T04:01:41.428890622Z","level":"INFO","msg":"connection: closing","id":"1(@)"}
-{"time":"2026-03-05T04:01:41.428935822Z","level":"INFO","msg":"server is shutting down"}
-{"time":"2026-03-05T04:01:41.428963162Z","level":"INFO","msg":"connection: closed successfully","id":"1(@)"}
-{"time":"2026-03-05T04:01:41.429207262Z","level":"INFO","msg":"server: listener closed","addr":{"Name":"/tmp/wandb-839387-843169-1818533415/socket","Net":"unix"}}
-{"time":"2026-03-05T04:01:42.189558787Z","level":"INFO","msg":"handleInformTeardown: server shutdown complete","id":"1(@)"}
-{"time":"2026-03-05T04:01:42.189609677Z","level":"INFO","msg":"connection: ManageConnectionData: connection closed","id":"1(@)"}
-{"time":"2026-03-05T04:01:42.189631697Z","level":"INFO","msg":"server is closed"}

wandb/run-20260305_040136-qpc17ycl/logs/debug-internal.log

@@ -1,11 +0,0 @@
-{"time":"2026-03-05T04:01:36.381990357Z","level":"INFO","msg":"stream: starting","core version":"0.25.0"}
-{"time":"2026-03-05T04:01:36.604810616Z","level":"INFO","msg":"stream: created new stream","id":"qpc17ycl"}
-{"time":"2026-03-05T04:01:36.604929986Z","level":"INFO","msg":"handler: started","stream_id":"qpc17ycl"}
-{"time":"2026-03-05T04:01:36.605021236Z","level":"INFO","msg":"stream: started","id":"qpc17ycl"}
-{"time":"2026-03-05T04:01:36.605060696Z","level":"INFO","msg":"writer: started","stream_id":"qpc17ycl"}
-{"time":"2026-03-05T04:01:36.605078496Z","level":"INFO","msg":"sender: started","stream_id":"qpc17ycl"}
-{"time":"2026-03-05T04:01:41.428903472Z","level":"INFO","msg":"stream: closing","id":"qpc17ycl"}
-{"time":"2026-03-05T04:01:41.972459774Z","level":"INFO","msg":"fileTransfer: Close: file transfer manager closed"}
-{"time":"2026-03-05T04:01:42.186106269Z","level":"INFO","msg":"handler: closed","stream_id":"qpc17ycl"}
-{"time":"2026-03-05T04:01:42.186301579Z","level":"INFO","msg":"sender: closed","stream_id":"qpc17ycl"}
-{"time":"2026-03-05T04:01:42.186324099Z","level":"INFO","msg":"stream: closed","id":"qpc17ycl"}

wandb/run-20260305_040136-qpc17ycl/logs/debug.log

@@ -1,21 +0,0 @@
-2026-03-05 04:01:36,147 INFO    MainThread:839387 [wandb_setup.py:_flush():81] Current SDK version is 0.25.0
-2026-03-05 04:01:36,147 INFO    MainThread:839387 [wandb_setup.py:_flush():81] Configure stats pid to 839387
-2026-03-05 04:01:36,148 INFO    MainThread:839387 [wandb_setup.py:_flush():81] Loading settings from environment variables
-2026-03-05 04:01:36,148 INFO    MainThread:839387 [wandb_init.py:setup_run_log_directory():717] Logging user logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_040136-qpc17ycl/logs/debug.log
-2026-03-05 04:01:36,148 INFO    MainThread:839387 [wandb_init.py:setup_run_log_directory():718] Logging internal logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_040136-qpc17ycl/logs/debug-internal.log
-2026-03-05 04:01:36,148 INFO    MainThread:839387 [wandb_init.py:init():844] calling init triggers
-2026-03-05 04:01:36,148 INFO    MainThread:839387 [wandb_init.py:init():849] wandb.init called with sweep_config: {}
-config: {'_wandb': {}}
-2026-03-05 04:01:36,148 INFO    MainThread:839387 [wandb_init.py:init():892] starting backend
-2026-03-05 04:01:36,373 INFO    MainThread:839387 [wandb_init.py:init():895] sending inform_init request
-2026-03-05 04:01:36,379 INFO    MainThread:839387 [wandb_init.py:init():903] backend started and connected
-2026-03-05 04:01:36,382 INFO    MainThread:839387 [wandb_init.py:init():973] updated telemetry
-2026-03-05 04:01:36,389 INFO    MainThread:839387 [wandb_init.py:init():997] communicating run to backend with 90.0 second timeout
-2026-03-05 04:01:37,287 INFO    MainThread:839387 [wandb_init.py:init():1042] starting run threads in backend
-2026-03-05 04:01:37,438 INFO    MainThread:839387 [wandb_run.py:_console_start():2524] atexit reg
-2026-03-05 04:01:37,439 INFO    MainThread:839387 [wandb_run.py:_redirect():2373] redirect: wrap_raw
-2026-03-05 04:01:37,439 INFO    MainThread:839387 [wandb_run.py:_redirect():2442] Wrapping output streams.
-2026-03-05 04:01:37,440 INFO    MainThread:839387 [wandb_run.py:_redirect():2465] Redirects installed.
-2026-03-05 04:01:37,445 INFO    MainThread:839387 [wandb_init.py:init():1082] run started, returning control to user process
-2026-03-05 04:01:41,428 INFO    wandb-AsyncioManager-main:839387 [service_client.py:_forward_responses():134] Reached EOF.
-2026-03-05 04:01:41,429 INFO    wandb-AsyncioManager-main:839387 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles.

wandb/run-20260305_040149-wwzikjfe/files/config.yaml

@@ -1,141 +0,0 @@
-_wandb:
-    value:
-        cli_version: 0.25.0
-        e:
-            sglafjcvr8er2m8m2ct1kp5m6yzyiu0z:
-                args:
-                    - --model_name_or_path
-                    - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000
-                    - --tokenizer_path
-                    - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json
-                    - --trust_remote_code
-                    - "True"
-                    - --data_path
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split
-                    - --kmer
-                    - "-1"
-                    - --run_name
-                    - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_all_seed42
-                    - --model_max_length
-                    - "80"
-                    - --per_device_train_batch_size
-                    - "128"
-                    - --per_device_eval_batch_size
-                    - "128"
-                    - --gradient_accumulation_steps
-                    - "1"
-                    - --learning_rate
-                    - "3e-5"
-                    - --num_train_epochs
-                    - "2"
-                    - --fp16
-                    - --save_steps
-                    - "200"
-                    - --output_dir
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all
-                    - --evaluation_strategy
-                    - steps
-                    - --eval_steps
-                    - "200"
-                    - --warmup_steps
-                    - "30"
-                    - --logging_steps
-                    - "100000"
-                    - --log_level
-                    - info
-                    - --seed
-                    - "42"
-                    - --find_unused_parameters
-                    - "False"
-                    - --project_name
-                    - genomic_bench_tune_hg38_1024
-                cpu_count: 128
-                cpu_count_logical: 255
-                cudaVersion: "12.2"
-                disk:
-                    /:
-                        total: "1876350566400"
-                        used: "546902155264"
-                email: mtapiapacheco@ucsd.edu
-                executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python
-                git:
-                    commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6
-                    remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks
-                gpu: NVIDIA A100 80GB PCIe
-                gpu_count: 8
-                gpu_nvidia:
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044
-                host: sn4622116170
-                memory:
-                    total: "4316310355968"
-                os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35
-                program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py
-                python: CPython 3.10.19
-                root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data
-                startedAt: "2026-03-05T04:01:49.227236Z"
-                writerId: sglafjcvr8er2m8m2ct1kp5m6yzyiu0z
-        m: []
-        python_version: 3.10.19
-        t:
-            "1":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "2":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "4": 3.10.19
-            "5": 0.25.0
-            "6": 5.3.0
-            "12": 0.25.0
-            "13": linux-x86_64

wandb/run-20260305_040149-wwzikjfe/files/output.log

@@ -1,37 +0,0 @@
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434

wandb/run-20260305_040149-wwzikjfe/files/requirements.txt

@@ -1,90 +0,0 @@
-hf-xet==1.3.2
-mpmath==1.3.0
-httpx==0.28.1
-markdown-it-py==4.0.0
-attrs==25.4.0
-pydantic_core==2.41.5
-cffi==2.0.0
-wheel==0.46.3
-tzdata==2025.3
-mdurl==0.1.2
-dill==0.4.0
-GitPython==3.1.46
-idna==3.11
-pycparser==2.23
-triton==3.1.0
-numpy==2.0.1
-numpy==2.2.6
-python-dateutil==2.9.0.post0
-gitdb==4.0.12
-rich==14.3.3
-PyYAML==6.0.3
-pytz==2026.1.post1
-packaging==25.0
-transformers==5.3.0
-networkx==3.4.2
-platformdirs==4.9.2
-ittapi==1.2.1
-yarl==1.23.0
-aiohttp==3.13.3
-typer==0.24.1
-mkl_fft==1.3.11
-psutil==7.2.2
-scipy==1.15.3
-httpcore==1.0.9
-Jinja2==3.1.6
-pip==26.0.1
-six==1.17.0
-frozenlist==1.8.0
-filelock==3.20.3
-annotated-doc==0.0.4
-multiprocess==0.70.18
-threadpoolctl==3.6.0
-typing_extensions==4.15.0
-pydantic==2.12.5
-async-timeout==5.0.1
-Pygments==2.19.2
-mkl_random==1.2.8
-certifi==2026.2.25
-exceptiongroup==1.3.1
-charset-normalizer==3.4.4
-wandb==0.25.0
-PySocks==1.7.1
-pandas==2.3.3
-smmap==5.0.2
-pyarrow==23.0.1
-safetensors==0.7.0
-tokenizers==0.22.2
-requests==2.32.5
-fsspec==2026.2.0
-aiosignal==1.4.0
-multidict==6.7.1
-typing-inspection==0.4.2
-accelerate==1.13.0
-torch==2.5.1
-brotlicffi==1.2.0.0
-gmpy2==2.2.2
-datasets==4.6.1
-anyio==4.12.1
-annotated-types==0.7.0
-tqdm==4.67.3
-mkl-service==2.4.0
-sentry-sdk==2.54.0
-torchvision==0.20.1
-shellingham==1.5.4
-torchaudio==2.5.1
-sympy==1.13.1
-h11==0.16.0
-pillow==12.1.1
-protobuf==6.33.5
-click==8.3.1
-MarkupSafe==3.0.2
-urllib3==2.6.3
-propcache==0.4.1
-regex==2026.2.28
-xxhash==3.6.0
-setuptools==80.10.2
-scikit-learn==1.7.2
-huggingface_hub==1.5.0
-joblib==1.5.3
-aiohappyeyeballs==2.6.1

wandb/run-20260305_040149-wwzikjfe/files/wandb-metadata.json

@@ -1,134 +0,0 @@
-{
-  "os":  "Linux-5.15.0-72-generic-x86_64-with-glibc2.35",
-  "python":  "CPython 3.10.19",
-  "startedAt":  "2026-03-05T04:01:49.227236Z",
-  "args":  [
-    "--model_name_or_path",
-    "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000",
-    "--tokenizer_path",
-    "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json",
-    "--trust_remote_code",
-    "True",
-    "--data_path",
-    "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_all/split",
-    "--kmer",
-    "-1",
-    "--run_name",
-    "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_all_seed42",
-    "--model_max_length",
-    "80",
-    "--per_device_train_batch_size",
-    "128",
-    "--per_device_eval_batch_size",
-    "128",
-    "--gradient_accumulation_steps",
-    "1",
-    "--learning_rate",
-    "3e-5",
-    "--num_train_epochs",
-    "2",
-    "--fp16",
-    "--save_steps",
-    "200",
-    "--output_dir",
-    "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_all",
-    "--evaluation_strategy",
-    "steps",
-    "--eval_steps",
-    "200",
-    "--warmup_steps",
-    "30",
-    "--logging_steps",
-    "100000",
-    "--log_level",
-    "info",
-    "--seed",
-    "42",
-    "--find_unused_parameters",
-    "False",
-    "--project_name",
-    "genomic_bench_tune_hg38_1024"
-  ],
-  "program":  "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py",
-  "git":  {
-    "remote":  "https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks",
-    "commit":  "5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6"
-  },
-  "email":  "mtapiapacheco@ucsd.edu",
-  "root":  "/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data",
-  "host":  "sn4622116170",
-  "executable":  "/home/n5huang/miniconda3/envs/nt_ft/bin/python",
-  "cpu_count":  128,
-  "cpu_count_logical":  255,
-  "gpu":  "NVIDIA A100 80GB PCIe",
-  "gpu_count":  8,
-  "disk":  {
-    "/":  {
-      "total":  "1876350566400",
-      "used":  "546902155264"
-    }
-  },
-  "memory":  {
-    "total":  "4316310355968"
-  },
-  "gpu_nvidia":  [
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-054a4d72-8520-5e4a-5cd3-7519a0966809"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-a18369da-b15a-c8af-72f1-7f6272e479af"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044"
-    }
-  ],
-  "cudaVersion":  "12.2",
-  "writerId":  "sglafjcvr8er2m8m2ct1kp5m6yzyiu0z"
-}

wandb/run-20260305_040149-wwzikjfe/files/wandb-summary.json

@@ -1 +0,0 @@
-{"_runtime":3,"_wandb":{"runtime":3}}

wandb/run-20260305_040149-wwzikjfe/logs/debug-core.log

@@ -1,14 +0,0 @@
-{"time":"2026-03-05T04:01:49.277464466Z","level":"INFO","msg":"main: starting server","port-filename":"/tmp/tmpjecm12rs/port-847746.txt","pid":847746,"log-level":0,"disable-analytics":false,"shutdown-on-parent-exit":false,"enable-dcgm-profiling":false}
-{"time":"2026-03-05T04:01:49.278225636Z","level":"INFO","msg":"server: will exit if parent process dies","ppid":847746}
-{"time":"2026-03-05T04:01:49.278214366Z","level":"INFO","msg":"server: accepting connections","addr":{"Name":"/tmp/wandb-847746-850953-3006558163/socket","Net":"unix"}}
-{"time":"2026-03-05T04:01:49.457283694Z","level":"INFO","msg":"connection: ManageConnectionData: new connection created","id":"1(@)"}
-{"time":"2026-03-05T04:01:49.464871069Z","level":"INFO","msg":"handleInformInit: received","streamId":"wwzikjfe","id":"1(@)"}
-{"time":"2026-03-05T04:01:49.679048533Z","level":"INFO","msg":"handleInformInit: stream started","streamId":"wwzikjfe","id":"1(@)"}
-{"time":"2026-03-05T04:01:53.081990996Z","level":"INFO","msg":"handleInformTeardown: server teardown initiated","id":"1(@)"}
-{"time":"2026-03-05T04:01:53.082058986Z","level":"INFO","msg":"server is shutting down"}
-{"time":"2026-03-05T04:01:53.082055136Z","level":"INFO","msg":"connection: closing","id":"1(@)"}
-{"time":"2026-03-05T04:01:53.082137256Z","level":"INFO","msg":"connection: closed successfully","id":"1(@)"}
-{"time":"2026-03-05T04:01:53.082228726Z","level":"INFO","msg":"server: listener closed","addr":{"Name":"/tmp/wandb-847746-850953-3006558163/socket","Net":"unix"}}
-{"time":"2026-03-05T04:01:53.890893787Z","level":"INFO","msg":"handleInformTeardown: server shutdown complete","id":"1(@)"}
-{"time":"2026-03-05T04:01:53.890925467Z","level":"INFO","msg":"connection: ManageConnectionData: connection closed","id":"1(@)"}
-{"time":"2026-03-05T04:01:53.890938347Z","level":"INFO","msg":"server is closed"}

wandb/run-20260305_040149-wwzikjfe/logs/debug-internal.log

@@ -1,11 +0,0 @@
-{"time":"2026-03-05T04:01:49.464997619Z","level":"INFO","msg":"stream: starting","core version":"0.25.0"}
-{"time":"2026-03-05T04:01:49.678841853Z","level":"INFO","msg":"stream: created new stream","id":"wwzikjfe"}
-{"time":"2026-03-05T04:01:49.678956223Z","level":"INFO","msg":"handler: started","stream_id":"wwzikjfe"}
-{"time":"2026-03-05T04:01:49.679032943Z","level":"INFO","msg":"stream: started","id":"wwzikjfe"}
-{"time":"2026-03-05T04:01:49.679071013Z","level":"INFO","msg":"writer: started","stream_id":"wwzikjfe"}
-{"time":"2026-03-05T04:01:49.679076583Z","level":"INFO","msg":"sender: started","stream_id":"wwzikjfe"}
-{"time":"2026-03-05T04:01:53.082092886Z","level":"INFO","msg":"stream: closing","id":"wwzikjfe"}
-{"time":"2026-03-05T04:01:53.690660614Z","level":"INFO","msg":"fileTransfer: Close: file transfer manager closed"}
-{"time":"2026-03-05T04:01:53.846223788Z","level":"INFO","msg":"handler: closed","stream_id":"wwzikjfe"}
-{"time":"2026-03-05T04:01:53.846364988Z","level":"INFO","msg":"sender: closed","stream_id":"wwzikjfe"}
-{"time":"2026-03-05T04:01:53.846375638Z","level":"INFO","msg":"stream: closed","id":"wwzikjfe"}

wandb/run-20260305_040149-wwzikjfe/logs/debug.log

@@ -1,21 +0,0 @@
-2026-03-05 04:01:49,231 INFO    MainThread:847746 [wandb_setup.py:_flush():81] Current SDK version is 0.25.0
-2026-03-05 04:01:49,231 INFO    MainThread:847746 [wandb_setup.py:_flush():81] Configure stats pid to 847746
-2026-03-05 04:01:49,231 INFO    MainThread:847746 [wandb_setup.py:_flush():81] Loading settings from environment variables
-2026-03-05 04:01:49,231 INFO    MainThread:847746 [wandb_init.py:setup_run_log_directory():717] Logging user logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_040149-wwzikjfe/logs/debug.log
-2026-03-05 04:01:49,231 INFO    MainThread:847746 [wandb_init.py:setup_run_log_directory():718] Logging internal logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_040149-wwzikjfe/logs/debug-internal.log
-2026-03-05 04:01:49,232 INFO    MainThread:847746 [wandb_init.py:init():844] calling init triggers
-2026-03-05 04:01:49,232 INFO    MainThread:847746 [wandb_init.py:init():849] wandb.init called with sweep_config: {}
-config: {'_wandb': {}}
-2026-03-05 04:01:49,232 INFO    MainThread:847746 [wandb_init.py:init():892] starting backend
-2026-03-05 04:01:49,457 INFO    MainThread:847746 [wandb_init.py:init():895] sending inform_init request
-2026-03-05 04:01:49,462 INFO    MainThread:847746 [wandb_init.py:init():903] backend started and connected
-2026-03-05 04:01:49,463 INFO    MainThread:847746 [wandb_init.py:init():973] updated telemetry
-2026-03-05 04:01:49,469 INFO    MainThread:847746 [wandb_init.py:init():997] communicating run to backend with 90.0 second timeout
-2026-03-05 04:01:49,921 INFO    MainThread:847746 [wandb_init.py:init():1042] starting run threads in backend
-2026-03-05 04:01:50,012 INFO    MainThread:847746 [wandb_run.py:_console_start():2524] atexit reg
-2026-03-05 04:01:50,012 INFO    MainThread:847746 [wandb_run.py:_redirect():2373] redirect: wrap_raw
-2026-03-05 04:01:50,012 INFO    MainThread:847746 [wandb_run.py:_redirect():2442] Wrapping output streams.
-2026-03-05 04:01:50,012 INFO    MainThread:847746 [wandb_run.py:_redirect():2465] Redirects installed.
-2026-03-05 04:01:50,016 INFO    MainThread:847746 [wandb_init.py:init():1082] run started, returning control to user process
-2026-03-05 04:01:53,080 INFO    wandb-AsyncioManager-main:847746 [service_client.py:_forward_responses():134] Reached EOF.
-2026-03-05 04:01:53,080 INFO    wandb-AsyncioManager-main:847746 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles.

wandb/run-20260305_040201-sq11rclj/files/config.yaml

@@ -1,141 +0,0 @@
-_wandb:
-    value:
-        cli_version: 0.25.0
-        e:
-            vfpu61gd7bux48d6r9tpwknkwvqgw5gv:
-                args:
-                    - --model_name_or_path
-                    - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000
-                    - --tokenizer_path
-                    - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json
-                    - --trust_remote_code
-                    - "True"
-                    - --data_path
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_no_tata/split
-                    - --kmer
-                    - "-1"
-                    - --run_name
-                    - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_no_tata_seed42
-                    - --model_max_length
-                    - "80"
-                    - --per_device_train_batch_size
-                    - "128"
-                    - --per_device_eval_batch_size
-                    - "128"
-                    - --gradient_accumulation_steps
-                    - "1"
-                    - --learning_rate
-                    - "3e-5"
-                    - --num_train_epochs
-                    - "2"
-                    - --fp16
-                    - --save_steps
-                    - "200"
-                    - --output_dir
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata
-                    - --evaluation_strategy
-                    - steps
-                    - --eval_steps
-                    - "200"
-                    - --warmup_steps
-                    - "30"
-                    - --logging_steps
-                    - "100000"
-                    - --log_level
-                    - info
-                    - --seed
-                    - "42"
-                    - --find_unused_parameters
-                    - "False"
-                    - --project_name
-                    - genomic_bench_tune_hg38_1024
-                cpu_count: 128
-                cpu_count_logical: 255
-                cudaVersion: "12.2"
-                disk:
-                    /:
-                        total: "1876350566400"
-                        used: "546902290432"
-                email: mtapiapacheco@ucsd.edu
-                executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python
-                git:
-                    commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6
-                    remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks
-                gpu: NVIDIA A100 80GB PCIe
-                gpu_count: 8
-                gpu_nvidia:
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044
-                host: sn4622116170
-                memory:
-                    total: "4316310355968"
-                os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35
-                program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py
-                python: CPython 3.10.19
-                root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data
-                startedAt: "2026-03-05T04:02:01.072664Z"
-                writerId: vfpu61gd7bux48d6r9tpwknkwvqgw5gv
-        m: []
-        python_version: 3.10.19
-        t:
-            "1":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "2":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "4": 3.10.19
-            "5": 0.25.0
-            "6": 5.3.0
-            "12": 0.25.0
-            "13": linux-x86_64

wandb/run-20260305_040201-sq11rclj/files/output.log

@@ -1,37 +0,0 @@
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434

wandb/run-20260305_040201-sq11rclj/files/requirements.txt

@@ -1,90 +0,0 @@
-hf-xet==1.3.2
-mpmath==1.3.0
-httpx==0.28.1
-markdown-it-py==4.0.0
-attrs==25.4.0
-pydantic_core==2.41.5
-cffi==2.0.0
-wheel==0.46.3
-tzdata==2025.3
-mdurl==0.1.2
-dill==0.4.0
-GitPython==3.1.46
-idna==3.11
-pycparser==2.23
-triton==3.1.0
-numpy==2.0.1
-numpy==2.2.6
-python-dateutil==2.9.0.post0
-gitdb==4.0.12
-rich==14.3.3
-PyYAML==6.0.3
-pytz==2026.1.post1
-packaging==25.0
-transformers==5.3.0
-networkx==3.4.2
-platformdirs==4.9.2
-ittapi==1.2.1
-yarl==1.23.0
-aiohttp==3.13.3
-typer==0.24.1
-mkl_fft==1.3.11
-psutil==7.2.2
-scipy==1.15.3
-httpcore==1.0.9
-Jinja2==3.1.6
-pip==26.0.1
-six==1.17.0
-frozenlist==1.8.0
-filelock==3.20.3
-annotated-doc==0.0.4
-multiprocess==0.70.18
-threadpoolctl==3.6.0
-typing_extensions==4.15.0
-pydantic==2.12.5
-async-timeout==5.0.1
-Pygments==2.19.2
-mkl_random==1.2.8
-certifi==2026.2.25
-exceptiongroup==1.3.1
-charset-normalizer==3.4.4
-wandb==0.25.0
-PySocks==1.7.1
-pandas==2.3.3
-smmap==5.0.2
-pyarrow==23.0.1
-safetensors==0.7.0
-tokenizers==0.22.2
-requests==2.32.5
-fsspec==2026.2.0
-aiosignal==1.4.0
-multidict==6.7.1
-typing-inspection==0.4.2
-accelerate==1.13.0
-torch==2.5.1
-brotlicffi==1.2.0.0
-gmpy2==2.2.2
-datasets==4.6.1
-anyio==4.12.1
-annotated-types==0.7.0
-tqdm==4.67.3
-mkl-service==2.4.0
-sentry-sdk==2.54.0
-torchvision==0.20.1
-shellingham==1.5.4
-torchaudio==2.5.1
-sympy==1.13.1
-h11==0.16.0
-pillow==12.1.1
-protobuf==6.33.5
-click==8.3.1
-MarkupSafe==3.0.2
-urllib3==2.6.3
-propcache==0.4.1
-regex==2026.2.28
-xxhash==3.6.0
-setuptools==80.10.2
-scikit-learn==1.7.2
-huggingface_hub==1.5.0
-joblib==1.5.3
-aiohappyeyeballs==2.6.1

wandb/run-20260305_040201-sq11rclj/files/wandb-metadata.json

@@ -1,134 +0,0 @@
-{
-  "os":  "Linux-5.15.0-72-generic-x86_64-with-glibc2.35",
-  "python":  "CPython 3.10.19",
-  "startedAt":  "2026-03-05T04:02:01.072664Z",
-  "args":  [
-    "--model_name_or_path",
-    "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000",
-    "--tokenizer_path",
-    "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json",
-    "--trust_remote_code",
-    "True",
-    "--data_path",
-    "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_no_tata/split",
-    "--kmer",
-    "-1",
-    "--run_name",
-    "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_no_tata_seed42",
-    "--model_max_length",
-    "80",
-    "--per_device_train_batch_size",
-    "128",
-    "--per_device_eval_batch_size",
-    "128",
-    "--gradient_accumulation_steps",
-    "1",
-    "--learning_rate",
-    "3e-5",
-    "--num_train_epochs",
-    "2",
-    "--fp16",
-    "--save_steps",
-    "200",
-    "--output_dir",
-    "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_no_tata",
-    "--evaluation_strategy",
-    "steps",
-    "--eval_steps",
-    "200",
-    "--warmup_steps",
-    "30",
-    "--logging_steps",
-    "100000",
-    "--log_level",
-    "info",
-    "--seed",
-    "42",
-    "--find_unused_parameters",
-    "False",
-    "--project_name",
-    "genomic_bench_tune_hg38_1024"
-  ],
-  "program":  "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py",
-  "git":  {
-    "remote":  "https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks",
-    "commit":  "5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6"
-  },
-  "email":  "mtapiapacheco@ucsd.edu",
-  "root":  "/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data",
-  "host":  "sn4622116170",
-  "executable":  "/home/n5huang/miniconda3/envs/nt_ft/bin/python",
-  "cpu_count":  128,
-  "cpu_count_logical":  255,
-  "gpu":  "NVIDIA A100 80GB PCIe",
-  "gpu_count":  8,
-  "disk":  {
-    "/":  {
-      "total":  "1876350566400",
-      "used":  "546902290432"
-    }
-  },
-  "memory":  {
-    "total":  "4316310355968"
-  },
-  "gpu_nvidia":  [
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-054a4d72-8520-5e4a-5cd3-7519a0966809"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-a18369da-b15a-c8af-72f1-7f6272e479af"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044"
-    }
-  ],
-  "cudaVersion":  "12.2",
-  "writerId":  "vfpu61gd7bux48d6r9tpwknkwvqgw5gv"
-}

wandb/run-20260305_040201-sq11rclj/files/wandb-summary.json

@@ -1 +0,0 @@
-{"_wandb":{"runtime":3},"_runtime":3}

wandb/run-20260305_040201-sq11rclj/logs/debug-core.log

@@ -1,28 +0,0 @@
-{"time":"2026-03-05T04:02:01.035830101Z","level":"INFO","msg":"main: starting server","port-filename":"/tmp/tmpb8f5c4aq/port-854595.txt","pid":854595,"log-level":0,"disable-analytics":false,"shutdown-on-parent-exit":false,"enable-dcgm-profiling":false}
-{"time":"2026-03-05T04:02:01.036796181Z","level":"INFO","msg":"server: will exit if parent process dies","ppid":854595}
-{"time":"2026-03-05T04:02:01.036772781Z","level":"INFO","msg":"server: accepting connections","addr":{"Name":"/tmp/wandb-854595-858323-2593424575/socket","Net":"unix"}}
-{"time":"2026-03-05T04:02:01.114848368Z","level":"INFO","msg":"main: starting server","port-filename":"/tmp/tmp8j5_wew9/port-854603.txt","pid":854603,"log-level":0,"disable-analytics":false,"shutdown-on-parent-exit":false,"enable-dcgm-profiling":false}
-{"time":"2026-03-05T04:02:01.115824327Z","level":"INFO","msg":"server: will exit if parent process dies","ppid":854603}
-{"time":"2026-03-05T04:02:01.115791417Z","level":"INFO","msg":"server: accepting connections","addr":{"Name":"/tmp/wandb-854603-858338-249176528/socket","Net":"unix"}}
-{"time":"2026-03-05T04:02:01.21482506Z","level":"INFO","msg":"connection: ManageConnectionData: new connection created","id":"1(@)"}
-{"time":"2026-03-05T04:02:01.224395583Z","level":"INFO","msg":"handleInformInit: received","streamId":"xn5hs8vr","id":"1(@)"}
-{"time":"2026-03-05T04:02:01.294047516Z","level":"INFO","msg":"connection: ManageConnectionData: new connection created","id":"1(@)"}
-{"time":"2026-03-05T04:02:01.299690942Z","level":"INFO","msg":"handleInformInit: received","streamId":"sq11rclj","id":"1(@)"}
-{"time":"2026-03-05T04:02:01.452767968Z","level":"INFO","msg":"handleInformInit: stream started","streamId":"xn5hs8vr","id":"1(@)"}
-{"time":"2026-03-05T04:02:01.50988476Z","level":"INFO","msg":"handleInformInit: stream started","streamId":"sq11rclj","id":"1(@)"}
-{"time":"2026-03-05T04:02:02.720389447Z","level":"INFO","msg":"handleInformTeardown: server teardown initiated","id":"1(@)"}
-{"time":"2026-03-05T04:02:02.720442477Z","level":"INFO","msg":"connection: closing","id":"1(@)"}
-{"time":"2026-03-05T04:02:02.720455457Z","level":"INFO","msg":"server is shutting down"}
-{"time":"2026-03-05T04:02:02.720511017Z","level":"INFO","msg":"connection: closed successfully","id":"1(@)"}
-{"time":"2026-03-05T04:02:02.720610627Z","level":"INFO","msg":"server: listener closed","addr":{"Name":"/tmp/wandb-854595-858323-2593424575/socket","Net":"unix"}}
-{"time":"2026-03-05T04:02:04.034386065Z","level":"INFO","msg":"handleInformTeardown: server shutdown complete","id":"1(@)"}
-{"time":"2026-03-05T04:02:04.034420224Z","level":"INFO","msg":"connection: ManageConnectionData: connection closed","id":"1(@)"}
-{"time":"2026-03-05T04:02:04.034442724Z","level":"INFO","msg":"server is closed"}
-{"time":"2026-03-05T04:02:05.624640563Z","level":"INFO","msg":"handleInformTeardown: server teardown initiated","id":"1(@)"}
-{"time":"2026-03-05T04:02:05.624749983Z","level":"INFO","msg":"connection: closing","id":"1(@)"}
-{"time":"2026-03-05T04:02:05.624766873Z","level":"INFO","msg":"server is shutting down"}
-{"time":"2026-03-05T04:02:05.624853623Z","level":"INFO","msg":"connection: closed successfully","id":"1(@)"}
-{"time":"2026-03-05T04:02:05.625023253Z","level":"INFO","msg":"server: listener closed","addr":{"Name":"/tmp/wandb-854603-858338-249176528/socket","Net":"unix"}}
-{"time":"2026-03-05T04:02:06.4983357Z","level":"INFO","msg":"handleInformTeardown: server shutdown complete","id":"1(@)"}
-{"time":"2026-03-05T04:02:06.49838058Z","level":"INFO","msg":"connection: ManageConnectionData: connection closed","id":"1(@)"}
-{"time":"2026-03-05T04:02:06.49840084Z","level":"INFO","msg":"server is closed"}

wandb/run-20260305_040201-sq11rclj/logs/debug-internal.log

@@ -1,11 +0,0 @@
-{"time":"2026-03-05T04:02:01.299807052Z","level":"INFO","msg":"stream: starting","core version":"0.25.0"}
-{"time":"2026-03-05T04:02:01.50967075Z","level":"INFO","msg":"stream: created new stream","id":"sq11rclj"}
-{"time":"2026-03-05T04:02:01.5097839Z","level":"INFO","msg":"handler: started","stream_id":"sq11rclj"}
-{"time":"2026-03-05T04:02:01.50987232Z","level":"INFO","msg":"stream: started","id":"sq11rclj"}
-{"time":"2026-03-05T04:02:01.50991242Z","level":"INFO","msg":"sender: started","stream_id":"sq11rclj"}
-{"time":"2026-03-05T04:02:01.50991703Z","level":"INFO","msg":"writer: started","stream_id":"sq11rclj"}
-{"time":"2026-03-05T04:02:05.624785803Z","level":"INFO","msg":"stream: closing","id":"sq11rclj"}
-{"time":"2026-03-05T04:02:06.164423986Z","level":"INFO","msg":"fileTransfer: Close: file transfer manager closed"}
-{"time":"2026-03-05T04:02:06.494789352Z","level":"INFO","msg":"handler: closed","stream_id":"sq11rclj"}
-{"time":"2026-03-05T04:02:06.494948882Z","level":"INFO","msg":"sender: closed","stream_id":"sq11rclj"}
-{"time":"2026-03-05T04:02:06.494963802Z","level":"INFO","msg":"stream: closed","id":"sq11rclj"}

wandb/run-20260305_040201-sq11rclj/logs/debug.log

@@ -1,21 +0,0 @@
-2026-03-05 04:02:01,075 INFO    MainThread:854603 [wandb_setup.py:_flush():81] Current SDK version is 0.25.0
-2026-03-05 04:02:01,075 INFO    MainThread:854603 [wandb_setup.py:_flush():81] Configure stats pid to 854603
-2026-03-05 04:02:01,075 INFO    MainThread:854603 [wandb_setup.py:_flush():81] Loading settings from environment variables
-2026-03-05 04:02:01,075 INFO    MainThread:854603 [wandb_init.py:setup_run_log_directory():717] Logging user logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_040201-sq11rclj/logs/debug.log
-2026-03-05 04:02:01,075 INFO    MainThread:854603 [wandb_init.py:setup_run_log_directory():718] Logging internal logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_040201-sq11rclj/logs/debug-internal.log
-2026-03-05 04:02:01,075 INFO    MainThread:854603 [wandb_init.py:init():844] calling init triggers
-2026-03-05 04:02:01,075 INFO    MainThread:854603 [wandb_init.py:init():849] wandb.init called with sweep_config: {}
-config: {'_wandb': {}}
-2026-03-05 04:02:01,075 INFO    MainThread:854603 [wandb_init.py:init():892] starting backend
-2026-03-05 04:02:01,294 INFO    MainThread:854603 [wandb_init.py:init():895] sending inform_init request
-2026-03-05 04:02:01,298 INFO    MainThread:854603 [wandb_init.py:init():903] backend started and connected
-2026-03-05 04:02:01,299 INFO    MainThread:854603 [wandb_init.py:init():973] updated telemetry
-2026-03-05 04:02:01,304 INFO    MainThread:854603 [wandb_init.py:init():997] communicating run to backend with 90.0 second timeout
-2026-03-05 04:02:02,439 INFO    MainThread:854603 [wandb_init.py:init():1042] starting run threads in backend
-2026-03-05 04:02:02,587 INFO    MainThread:854603 [wandb_run.py:_console_start():2524] atexit reg
-2026-03-05 04:02:02,587 INFO    MainThread:854603 [wandb_run.py:_redirect():2373] redirect: wrap_raw
-2026-03-05 04:02:02,587 INFO    MainThread:854603 [wandb_run.py:_redirect():2442] Wrapping output streams.
-2026-03-05 04:02:02,587 INFO    MainThread:854603 [wandb_run.py:_redirect():2465] Redirects installed.
-2026-03-05 04:02:02,591 INFO    MainThread:854603 [wandb_init.py:init():1082] run started, returning control to user process
-2026-03-05 04:02:05,624 INFO    wandb-AsyncioManager-main:854603 [service_client.py:_forward_responses():134] Reached EOF.
-2026-03-05 04:02:05,625 INFO    wandb-AsyncioManager-main:854603 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles.

wandb/run-20260305_040214-vyqcoynz/files/config.yaml

@@ -1,141 +0,0 @@
-_wandb:
-    value:
-        cli_version: 0.25.0
-        e:
-            ffxm8q6qp1l1piwxz1h1pyrnbob5nzwb:
-                args:
-                    - --model_name_or_path
-                    - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000
-                    - --tokenizer_path
-                    - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json
-                    - --trust_remote_code
-                    - "True"
-                    - --data_path
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_tata/split
-                    - --kmer
-                    - "-1"
-                    - --run_name
-                    - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_tata_seed42
-                    - --model_max_length
-                    - "80"
-                    - --per_device_train_batch_size
-                    - "128"
-                    - --per_device_eval_batch_size
-                    - "128"
-                    - --gradient_accumulation_steps
-                    - "1"
-                    - --learning_rate
-                    - "3e-5"
-                    - --num_train_epochs
-                    - "2"
-                    - --fp16
-                    - --save_steps
-                    - "200"
-                    - --output_dir
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata
-                    - --evaluation_strategy
-                    - steps
-                    - --eval_steps
-                    - "200"
-                    - --warmup_steps
-                    - "30"
-                    - --logging_steps
-                    - "100000"
-                    - --log_level
-                    - info
-                    - --seed
-                    - "42"
-                    - --find_unused_parameters
-                    - "False"
-                    - --project_name
-                    - genomic_bench_tune_hg38_1024
-                cpu_count: 128
-                cpu_count_logical: 255
-                cudaVersion: "12.2"
-                disk:
-                    /:
-                        total: "1876350566400"
-                        used: "546902446080"
-                email: mtapiapacheco@ucsd.edu
-                executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python
-                git:
-                    commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6
-                    remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks
-                gpu: NVIDIA A100 80GB PCIe
-                gpu_count: 8
-                gpu_nvidia:
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044
-                host: sn4622116170
-                memory:
-                    total: "4316310355968"
-                os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35
-                program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py
-                python: CPython 3.10.19
-                root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data
-                startedAt: "2026-03-05T04:02:14.197174Z"
-                writerId: ffxm8q6qp1l1piwxz1h1pyrnbob5nzwb
-        m: []
-        python_version: 3.10.19
-        t:
-            "1":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "2":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "4": 3.10.19
-            "5": 0.25.0
-            "6": 5.3.0
-            "12": 0.25.0
-            "13": linux-x86_64

wandb/run-20260305_040214-vyqcoynz/files/output.log

@@ -1,37 +0,0 @@
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434

wandb/run-20260305_040214-vyqcoynz/files/requirements.txt

@@ -1,90 +0,0 @@
-hf-xet==1.3.2
-mpmath==1.3.0
-httpx==0.28.1
-markdown-it-py==4.0.0
-attrs==25.4.0
-pydantic_core==2.41.5
-cffi==2.0.0
-wheel==0.46.3
-tzdata==2025.3
-mdurl==0.1.2
-dill==0.4.0
-GitPython==3.1.46
-idna==3.11
-pycparser==2.23
-triton==3.1.0
-numpy==2.0.1
-numpy==2.2.6
-python-dateutil==2.9.0.post0
-gitdb==4.0.12
-rich==14.3.3
-PyYAML==6.0.3
-pytz==2026.1.post1
-packaging==25.0
-transformers==5.3.0
-networkx==3.4.2
-platformdirs==4.9.2
-ittapi==1.2.1
-yarl==1.23.0
-aiohttp==3.13.3
-typer==0.24.1
-mkl_fft==1.3.11
-psutil==7.2.2
-scipy==1.15.3
-httpcore==1.0.9
-Jinja2==3.1.6
-pip==26.0.1
-six==1.17.0
-frozenlist==1.8.0
-filelock==3.20.3
-annotated-doc==0.0.4
-multiprocess==0.70.18
-threadpoolctl==3.6.0
-typing_extensions==4.15.0
-pydantic==2.12.5
-async-timeout==5.0.1
-Pygments==2.19.2
-mkl_random==1.2.8
-certifi==2026.2.25
-exceptiongroup==1.3.1
-charset-normalizer==3.4.4
-wandb==0.25.0
-PySocks==1.7.1
-pandas==2.3.3
-smmap==5.0.2
-pyarrow==23.0.1
-safetensors==0.7.0
-tokenizers==0.22.2
-requests==2.32.5
-fsspec==2026.2.0
-aiosignal==1.4.0
-multidict==6.7.1
-typing-inspection==0.4.2
-accelerate==1.13.0
-torch==2.5.1
-brotlicffi==1.2.0.0
-gmpy2==2.2.2
-datasets==4.6.1
-anyio==4.12.1
-annotated-types==0.7.0
-tqdm==4.67.3
-mkl-service==2.4.0
-sentry-sdk==2.54.0
-torchvision==0.20.1
-shellingham==1.5.4
-torchaudio==2.5.1
-sympy==1.13.1
-h11==0.16.0
-pillow==12.1.1
-protobuf==6.33.5
-click==8.3.1
-MarkupSafe==3.0.2
-urllib3==2.6.3
-propcache==0.4.1
-regex==2026.2.28
-xxhash==3.6.0
-setuptools==80.10.2
-scikit-learn==1.7.2
-huggingface_hub==1.5.0
-joblib==1.5.3
-aiohappyeyeballs==2.6.1

wandb/run-20260305_040214-vyqcoynz/files/wandb-metadata.json

@@ -1,134 +0,0 @@
-{
-  "os":  "Linux-5.15.0-72-generic-x86_64-with-glibc2.35",
-  "python":  "CPython 3.10.19",
-  "startedAt":  "2026-03-05T04:02:14.197174Z",
-  "args":  [
-    "--model_name_or_path",
-    "/home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000",
-    "--tokenizer_path",
-    "/home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json",
-    "--trust_remote_code",
-    "True",
-    "--data_path",
-    "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/promoter_tata/split",
-    "--kmer",
-    "-1",
-    "--run_name",
-    "hg38_BPE_base__baseline_bpe_tokenizer_3e-5_promoter_tata_seed42",
-    "--model_max_length",
-    "80",
-    "--per_device_train_batch_size",
-    "128",
-    "--per_device_eval_batch_size",
-    "128",
-    "--gradient_accumulation_steps",
-    "1",
-    "--learning_rate",
-    "3e-5",
-    "--num_train_epochs",
-    "2",
-    "--fp16",
-    "--save_steps",
-    "200",
-    "--output_dir",
-    "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/promoter_tata",
-    "--evaluation_strategy",
-    "steps",
-    "--eval_steps",
-    "200",
-    "--warmup_steps",
-    "30",
-    "--logging_steps",
-    "100000",
-    "--log_level",
-    "info",
-    "--seed",
-    "42",
-    "--find_unused_parameters",
-    "False",
-    "--project_name",
-    "genomic_bench_tune_hg38_1024"
-  ],
-  "program":  "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py",
-  "git":  {
-    "remote":  "https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks",
-    "commit":  "5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6"
-  },
-  "email":  "mtapiapacheco@ucsd.edu",
-  "root":  "/data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data",
-  "host":  "sn4622116170",
-  "executable":  "/home/n5huang/miniconda3/envs/nt_ft/bin/python",
-  "cpu_count":  128,
-  "cpu_count_logical":  255,
-  "gpu":  "NVIDIA A100 80GB PCIe",
-  "gpu_count":  8,
-  "disk":  {
-    "/":  {
-      "total":  "1876350566400",
-      "used":  "546902446080"
-    }
-  },
-  "memory":  {
-    "total":  "4316310355968"
-  },
-  "gpu_nvidia":  [
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-054a4d72-8520-5e4a-5cd3-7519a0966809"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-a18369da-b15a-c8af-72f1-7f6272e479af"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0"
-    },
-    {
-      "name":  "NVIDIA A100 80GB PCIe",
-      "memoryTotal":  "85899345920",
-      "cudaCores":  6912,
-      "architecture":  "Ampere",
-      "uuid":  "GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044"
-    }
-  ],
-  "cudaVersion":  "12.2",
-  "writerId":  "ffxm8q6qp1l1piwxz1h1pyrnbob5nzwb"
-}

wandb/run-20260305_040214-vyqcoynz/files/wandb-summary.json

@@ -1 +0,0 @@
-{"_wandb":{"runtime":0},"_runtime":0}

wandb/run-20260305_040214-vyqcoynz/logs/debug-core.log

@@ -1,14 +0,0 @@
-{"time":"2026-03-05T04:02:14.241981112Z","level":"INFO","msg":"main: starting server","port-filename":"/tmp/tmpmdp3n0po/port-862282.txt","pid":862282,"log-level":0,"disable-analytics":false,"shutdown-on-parent-exit":false,"enable-dcgm-profiling":false}
-{"time":"2026-03-05T04:02:14.242785411Z","level":"INFO","msg":"server: will exit if parent process dies","ppid":862282}
-{"time":"2026-03-05T04:02:14.242761071Z","level":"INFO","msg":"server: accepting connections","addr":{"Name":"/tmp/wandb-862282-865966-116471094/socket","Net":"unix"}}
-{"time":"2026-03-05T04:02:14.417987463Z","level":"INFO","msg":"connection: ManageConnectionData: new connection created","id":"1(@)"}
-{"time":"2026-03-05T04:02:14.424510438Z","level":"INFO","msg":"handleInformInit: received","streamId":"vyqcoynz","id":"1(@)"}
-{"time":"2026-03-05T04:02:14.86330486Z","level":"INFO","msg":"handleInformInit: stream started","streamId":"vyqcoynz","id":"1(@)"}
-{"time":"2026-03-05T04:02:15.893947878Z","level":"INFO","msg":"handleInformTeardown: server teardown initiated","id":"1(@)"}
-{"time":"2026-03-05T04:02:15.894036258Z","level":"INFO","msg":"connection: closing","id":"1(@)"}
-{"time":"2026-03-05T04:02:15.894053418Z","level":"INFO","msg":"server is shutting down"}
-{"time":"2026-03-05T04:02:15.894138338Z","level":"INFO","msg":"connection: closed successfully","id":"1(@)"}
-{"time":"2026-03-05T04:02:15.894415387Z","level":"INFO","msg":"server: listener closed","addr":{"Name":"/tmp/wandb-862282-865966-116471094/socket","Net":"unix"}}
-{"time":"2026-03-05T04:02:16.738004163Z","level":"INFO","msg":"handleInformTeardown: server shutdown complete","id":"1(@)"}
-{"time":"2026-03-05T04:02:16.738038093Z","level":"INFO","msg":"connection: ManageConnectionData: connection closed","id":"1(@)"}
-{"time":"2026-03-05T04:02:16.738055533Z","level":"INFO","msg":"server is closed"}

wandb/run-20260305_040214-vyqcoynz/logs/debug-internal.log

@@ -1,11 +0,0 @@
-{"time":"2026-03-05T04:02:14.425487117Z","level":"INFO","msg":"stream: starting","core version":"0.25.0"}
-{"time":"2026-03-05T04:02:14.86305706Z","level":"INFO","msg":"stream: created new stream","id":"vyqcoynz"}
-{"time":"2026-03-05T04:02:14.86318508Z","level":"INFO","msg":"handler: started","stream_id":"vyqcoynz"}
-{"time":"2026-03-05T04:02:14.86329272Z","level":"INFO","msg":"stream: started","id":"vyqcoynz"}
-{"time":"2026-03-05T04:02:14.86330179Z","level":"INFO","msg":"sender: started","stream_id":"vyqcoynz"}
-{"time":"2026-03-05T04:02:14.86330073Z","level":"INFO","msg":"writer: started","stream_id":"vyqcoynz"}
-{"time":"2026-03-05T04:02:15.894061138Z","level":"INFO","msg":"stream: closing","id":"vyqcoynz"}
-{"time":"2026-03-05T04:02:16.546359143Z","level":"INFO","msg":"fileTransfer: Close: file transfer manager closed"}
-{"time":"2026-03-05T04:02:16.729581739Z","level":"INFO","msg":"handler: closed","stream_id":"vyqcoynz"}
-{"time":"2026-03-05T04:02:16.729693029Z","level":"INFO","msg":"sender: closed","stream_id":"vyqcoynz"}
-{"time":"2026-03-05T04:02:16.729710929Z","level":"INFO","msg":"stream: closed","id":"vyqcoynz"}

wandb/run-20260305_040214-vyqcoynz/logs/debug.log

@@ -1,21 +0,0 @@
-2026-03-05 04:02:14,200 INFO    MainThread:862282 [wandb_setup.py:_flush():81] Current SDK version is 0.25.0
-2026-03-05 04:02:14,200 INFO    MainThread:862282 [wandb_setup.py:_flush():81] Configure stats pid to 862282
-2026-03-05 04:02:14,200 INFO    MainThread:862282 [wandb_setup.py:_flush():81] Loading settings from environment variables
-2026-03-05 04:02:14,200 INFO    MainThread:862282 [wandb_init.py:setup_run_log_directory():717] Logging user logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_040214-vyqcoynz/logs/debug.log
-2026-03-05 04:02:14,200 INFO    MainThread:862282 [wandb_init.py:setup_run_log_directory():718] Logging internal logs to /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data/wandb/run-20260305_040214-vyqcoynz/logs/debug-internal.log
-2026-03-05 04:02:14,200 INFO    MainThread:862282 [wandb_init.py:init():844] calling init triggers
-2026-03-05 04:02:14,200 INFO    MainThread:862282 [wandb_init.py:init():849] wandb.init called with sweep_config: {}
-config: {'_wandb': {}}
-2026-03-05 04:02:14,200 INFO    MainThread:862282 [wandb_init.py:init():892] starting backend
-2026-03-05 04:02:14,418 INFO    MainThread:862282 [wandb_init.py:init():895] sending inform_init request
-2026-03-05 04:02:14,422 INFO    MainThread:862282 [wandb_init.py:init():903] backend started and connected
-2026-03-05 04:02:14,423 INFO    MainThread:862282 [wandb_init.py:init():973] updated telemetry
-2026-03-05 04:02:14,429 INFO    MainThread:862282 [wandb_init.py:init():997] communicating run to backend with 90.0 second timeout
-2026-03-05 04:02:15,264 INFO    MainThread:862282 [wandb_init.py:init():1042] starting run threads in backend
-2026-03-05 04:02:15,353 INFO    MainThread:862282 [wandb_run.py:_console_start():2524] atexit reg
-2026-03-05 04:02:15,353 INFO    MainThread:862282 [wandb_run.py:_redirect():2373] redirect: wrap_raw
-2026-03-05 04:02:15,353 INFO    MainThread:862282 [wandb_run.py:_redirect():2442] Wrapping output streams.
-2026-03-05 04:02:15,353 INFO    MainThread:862282 [wandb_run.py:_redirect():2465] Redirects installed.
-2026-03-05 04:02:15,356 INFO    MainThread:862282 [wandb_init.py:init():1082] run started, returning control to user process
-2026-03-05 04:02:15,894 INFO    wandb-AsyncioManager-main:862282 [service_client.py:_forward_responses():134] Reached EOF.
-2026-03-05 04:02:15,894 INFO    wandb-AsyncioManager-main:862282 [mailbox.py:close():155] Closing mailbox, abandoning 1 handles.

wandb/run-20260305_040223-yfxomrbt/files/config.yaml

@@ -1,141 +0,0 @@
-_wandb:
-    value:
-        cli_version: 0.25.0
-        e:
-            4wgvlh1jxxjwyr68cc0n54olcpzgaplm:
-                args:
-                    - --model_name_or_path
-                    - /home/n5huang/dna_token/pretrain/models/model_cpu_test_1/checkpoint-100000
-                    - --tokenizer_path
-                    - /home/n5huang/dna_token/tokenizer_evaluation/baseline_bpe/tokenizer.json
-                    - --trust_remote_code
-                    - "True"
-                    - --data_path
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/NT-benchmarks/nucleotide_transformer_downstream_tasks_revised/splice_sites_acceptors/split
-                    - --kmer
-                    - "-1"
-                    - --run_name
-                    - hg38_BPE_base__baseline_bpe_tokenizer_3e-5_splice_sites_acceptors_seed42
-                    - --model_max_length
-                    - "140"
-                    - --per_device_train_batch_size
-                    - "128"
-                    - --per_device_eval_batch_size
-                    - "128"
-                    - --gradient_accumulation_steps
-                    - "1"
-                    - --learning_rate
-                    - "3e-5"
-                    - --num_train_epochs
-                    - "4"
-                    - --fp16
-                    - --save_steps
-                    - "200"
-                    - --output_dir
-                    - /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/full_output_multi_tune_hg38_1024/base__baseline_bpe_tokenizer/splice_sites_acceptors
-                    - --evaluation_strategy
-                    - steps
-                    - --eval_steps
-                    - "200"
-                    - --warmup_steps
-                    - "30"
-                    - --logging_steps
-                    - "100000"
-                    - --log_level
-                    - info
-                    - --seed
-                    - "42"
-                    - --find_unused_parameters
-                    - "False"
-                    - --project_name
-                    - genomic_bench_tune_hg38_1024
-                cpu_count: 128
-                cpu_count_logical: 255
-                cudaVersion: "12.2"
-                disk:
-                    /:
-                        total: "1876350566400"
-                        used: "546902515712"
-                email: mtapiapacheco@ucsd.edu
-                executable: /home/n5huang/miniconda3/envs/nt_ft/bin/python
-                git:
-                    commit: 5dc8fdf47bc12e22d02cfdaea49a6cbeb2fdf4d6
-                    remote: https://huggingface.co/JessieZhou25/Finetune-GenomicBenchmarks
-                gpu: NVIDIA A100 80GB PCIe
-                gpu_count: 8
-                gpu_nvidia:
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-dc4eaee8-f907-9592-417e-e0dbe37f86a3
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-054a4d72-8520-5e4a-5cd3-7519a0966809
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-8d529af8-bcca-cbbc-fa00-78bf605d4eab
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-a18369da-b15a-c8af-72f1-7f6272e479af
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-fb2ffc63-6c8a-5e90-0466-bd865bdd8b10
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-b8dce99b-6337-0212-03f4-56e6e689fa2e
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-d097eb04-aaca-ea9a-2730-e29dca4737a0
-                    - architecture: Ampere
-                      cudaCores: 6912
-                      memoryTotal: "85899345920"
-                      name: NVIDIA A100 80GB PCIe
-                      uuid: GPU-889b7e9a-34bf-f9b3-1168-16a2b3798044
-                host: sn4622116170
-                memory:
-                    total: "4316310355968"
-                os: Linux-5.15.0-72-generic-x86_64-with-glibc2.35
-                program: /home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py
-                python: CPython 3.10.19
-                root: /data/n5huang/dna_token/Finetune-GenomicBenchmarks/ft_data
-                startedAt: "2026-03-05T04:02:23.923029Z"
-                writerId: 4wgvlh1jxxjwyr68cc0n54olcpzgaplm
-        m: []
-        python_version: 3.10.19
-        t:
-            "1":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "2":
-                - 1
-                - 5
-                - 11
-                - 41
-                - 49
-                - 51
-                - 53
-                - 71
-            "4": 3.10.19
-            "5": 0.25.0
-            "6": 5.3.0
-            "12": 0.25.0
-            "13": linux-x86_64

wandb/run-20260305_040223-yfxomrbt/files/output.log

@@ -1,37 +0,0 @@
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-WARNING:root:Perform single sequence classification...
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434
-Traceback (most recent call last):
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 455, in <module>
-    train()
-  File "/home/n5huang/dna_token/mario/Finetune-NucleotideTransformerBenchmarks/train.py", line 406, in train
-    model = transformers.AutoModelForSequenceClassification.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/models/auto/auto_factory.py", line 374, in from_pretrained
-    return model_class.from_pretrained(
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4137, in from_pretrained
-    loading_info, disk_offload_index = cls._load_pretrained_model(model, state_dict, checkpoint_files, load_config)
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 4252, in _load_pretrained_model
-    merged_state_dict.update(load_state_dict(ckpt_file))
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/modeling_utils.py", line 319, in load_state_dict
-    check_torch_load_is_safe()
-  File "/home/n5huang/miniconda3/envs/nt_ft/lib/python3.10/site-packages/transformers/utils/import_utils.py", line 1270, in check_torch_load_is_safe
-    raise ValueError(
-ValueError: Due to a serious vulnerability issue in `torch.load`, even with `weights_only=True`, we now require users to upgrade torch to at least v2.6 in order to use the function. This version restriction does not apply when loading files with safetensors.
-See the vulnerability report here https://nvd.nist.gov/vuln/detail/CVE-2025-32434

wandb/run-20260305_040223-yfxomrbt/files/requirements.txt

@@ -1,90 +0,0 @@
-hf-xet==1.3.2
-mpmath==1.3.0
-httpx==0.28.1
-markdown-it-py==4.0.0
-attrs==25.4.0
-pydantic_core==2.41.5
-cffi==2.0.0
-wheel==0.46.3
-tzdata==2025.3
-mdurl==0.1.2
-dill==0.4.0
-GitPython==3.1.46
-idna==3.11
-pycparser==2.23
-triton==3.1.0
-numpy==2.0.1
-numpy==2.2.6
-python-dateutil==2.9.0.post0
-gitdb==4.0.12
-rich==14.3.3
-PyYAML==6.0.3
-pytz==2026.1.post1
-packaging==25.0
-transformers==5.3.0
-networkx==3.4.2
-platformdirs==4.9.2
-ittapi==1.2.1
-yarl==1.23.0
-aiohttp==3.13.3
-typer==0.24.1
-mkl_fft==1.3.11
-psutil==7.2.2
-scipy==1.15.3
-httpcore==1.0.9
-Jinja2==3.1.6
-pip==26.0.1
-six==1.17.0
-frozenlist==1.8.0
-filelock==3.20.3
-annotated-doc==0.0.4
-multiprocess==0.70.18
-threadpoolctl==3.6.0
-typing_extensions==4.15.0
-pydantic==2.12.5
-async-timeout==5.0.1
-Pygments==2.19.2
-mkl_random==1.2.8
-certifi==2026.2.25
-exceptiongroup==1.3.1
-charset-normalizer==3.4.4
-wandb==0.25.0
-PySocks==1.7.1
-pandas==2.3.3
-smmap==5.0.2
-pyarrow==23.0.1
-safetensors==0.7.0
-tokenizers==0.22.2
-requests==2.32.5
-fsspec==2026.2.0
-aiosignal==1.4.0
-multidict==6.7.1
-typing-inspection==0.4.2
-accelerate==1.13.0
-torch==2.5.1
-brotlicffi==1.2.0.0
-gmpy2==2.2.2
-datasets==4.6.1
-anyio==4.12.1
-annotated-types==0.7.0
-tqdm==4.67.3
-mkl-service==2.4.0
-sentry-sdk==2.54.0
-torchvision==0.20.1
-shellingham==1.5.4
-torchaudio==2.5.1
-sympy==1.13.1
-h11==0.16.0
-pillow==12.1.1
-protobuf==6.33.5
-click==8.3.1
-MarkupSafe==3.0.2
-urllib3==2.6.3
-propcache==0.4.1
-regex==2026.2.28
-xxhash==3.6.0
-setuptools==80.10.2
-scikit-learn==1.7.2
-huggingface_hub==1.5.0
-joblib==1.5.3
-aiohappyeyeballs==2.6.1