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Running prediction pipeline for INPUT_FILE=data/Arabidopsis_thaliana.TAIR10.dna.chromosome.4.fa.gz
python scripts/extract.py extract_fasta_file \
--species-id athaliana \
--fasta-file data/Arabidopsis_thaliana.TAIR10.dna.chromosome.4.fa.gz \
--chrom-map "4:4" \
--tokenizer-path kuleshov-group/PlantCAD2-Large-l48-d1536 \
--output results/pipeline/sequences.zarr
2025-09-12 19:23:13,559 - INFO - Parsed chromosome mapping: {'4': '4'}
2025-09-12 19:23:20,075 - INFO - Loading tokenizer from kuleshov-group/PlantCAD2-Large-l48-d1536
2025-09-12 19:23:20,545 - INFO - Vectorizing token map: {'c': 4, 'C': 4, 'g': 5, 'G': 5, 'a': 3, 'A': 3, 't': 6, 'T': 6, 'm': 2, 'M': 2, 'r': 2, 'R': 2, 'w': 2, 'W': 2, 's': 2, 'S': 2, 'y': 2, 'Y': 2, 'k': 2, 'K': 2, 'v': 2, 'V': 2, 'h': 2, 'H': 2, 'd': 2, 'D': 2, 'b': 2, 'B': 2, 'x': 2, 'X': 2, 'n': 2, 'N': 2}
2025-09-12 19:23:20,545 - INFO - [species=athaliana] Processing FASTA file: data/Arabidopsis_thaliana.TAIR10.dna.chromosome.4.fa.gz
2025-09-12 19:23:20,843 - INFO - [species=athaliana] Added 4 (from 4), length: 18585056
2025-09-12 19:23:20,844 - INFO - [species=athaliana] Found 1 total chromosomes
2025-09-12 19:23:20,844 - INFO - [species=athaliana] Processing chromosome: 4
2025-09-12 19:23:22,437 - INFO - [species=athaliana] Creating dataset...
2025-09-12 19:23:22,464 - INFO - [species=athaliana] Tokenizing forward strand: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ...
2025-09-12 19:23:24,030 - INFO - [species=athaliana] Token ID frequencies: {3: 5940546, 6: 5914038, 4: 3371349, 5: 3356091, 2: 3032}
2025-09-12 19:23:24,047 - INFO - [species=athaliana] Tokenizing reverse strand: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ...
2025-09-12 19:23:25,612 - INFO - [species=athaliana] Token ID frequencies: {6: 5940546, 3: 5914038, 5: 3371349, 4: 3356091, 2: 3032}
2025-09-12 19:23:25,707 - INFO - [species=athaliana] Saving 4 dataset to results/pipeline/sequences.zarr
2025-09-12 19:23:27,729 - INFO - [species=athaliana] Saved 1 chromosome sequences to results/pipeline/sequences.zarr
2025-09-12 19:23:27,897 - INFO - Final data tree:
<xarray.DataTree>
Group: /
└── Group: /athaliana
└── Group: /athaliana/4
Dimensions: (strand: 2, sequence: 18585056)
Coordinates:
* sequence (sequence) int64 149MB 0 1 2 ... 18585054 18585055
* strand (strand) <U8 64B 'positive' 'negative'
Data variables:
sequence_masks (strand, sequence) bool 37MB ...
sequence_input_ids (strand, sequence) int64 297MB ...
sequence_tokens (strand, sequence) |S1 37MB ...
Attributes:
species_id: athaliana
chromosome_id: 4
2025-09-12 19:23:27,898 - INFO - Done
python scripts/predict.py create_predictions \
--input results/pipeline/sequences.zarr \
--output-dir results/pipeline/predictions.zarr \
--model-path kuleshov-group/PlantCAD2-Large-l48-d1536 \
--model-checkpoint plantcad/GeneCAD-l8-d768-PC2-Large \
--species-id athaliana \
--chromosome-id 4 \
--batch-size 32 \
--dtype bfloat16
2025-09-12 19:23:35,239 - INFO - Loading model from plantcad/GeneCAD-l8-d768-PC2-Large
2025-09-12 19:23:35,240 - INFO - Local path for classifier plantcad/GeneCAD-l8-d768-PC2-Large not found; attempting Hugging Face download ...
2025-09-12 19:23:41,534 - INFO - Downloaded classifier to /root/.cache/huggingface/hub/models--plantcad--GeneCAD-l8-d768-PC2-Large/snapshots/0c0f7b4cdd7b381f794d5816ec40bc539e4f7a8b/model.ckpt
A new version of the following files was downloaded from https://huggingface.co/kuleshov-group/PlantCAD2-Large-l48-d1536:
- configuration_caduceus.py
. Make sure to double-check they do not contain any added malicious code. To avoid downloading new versions of the code file, you can pin a revision.
A new version of the following files was downloaded from https://huggingface.co/kuleshov-group/PlantCAD2-Large-l48-d1536:
- modeling_rcps.py
. Make sure to double-check they do not contain any added malicious code. To avoid downloading new versions of the code file, you can pin a revision.
A new version of the following files was downloaded from https://huggingface.co/kuleshov-group/PlantCAD2-Large-l48-d1536:
- modeling_caduceus.py
- modeling_rcps.py
. Make sure to double-check they do not contain any added malicious code. To avoid downloading new versions of the code file, you can pin a revision.
2025-09-12 19:23:56,628 - INFO - Loading tokenizer from kuleshov-group/PlantCAD2-Large-l48-d1536
2025-09-12 19:23:56,682 - INFO - Opening input sequence datatree from results/pipeline/sequences.zarr
2025-09-12 19:23:56,852 - INFO - Input sequences:
<xarray.DataTree>
Group: /
└── Group: /athaliana
└── Group: /athaliana/4
Dimensions: (strand: 2, sequence: 18585056)
Coordinates:
* sequence (sequence) int64 149MB 0 1 2 ... 18585054 18585055
* strand (strand) <U8 64B 'positive' 'negative'
Data variables:
sequence_masks (strand, sequence) bool 37MB ...
sequence_input_ids (strand, sequence) int64 297MB ...
sequence_tokens (strand, sequence) |S1 37MB ...
Attributes:
species_id: athaliana
chromosome_id: 4
2025-09-12 19:23:56,853 - INFO - Selecting data for species 'athaliana' and chromosome '4'
2025-09-12 19:23:56,853 - INFO - Loaded dataset with dimensions: {'strand': 2, 'sequence': 18585056}
2025-09-12 19:23:56,853 - INFO - Running predictions for athaliana/4
2025-09-12 19:23:56,853 - INFO - Generating predictions with args.batch_size=32, args.window_size=8192, args.stride=4096 (rank=0, world_size=1)
2025-09-12 19:23:56,853 - INFO - Using pad_value=2 (UNK token) for sequence padding
2025-09-12 19:23:56,853 - INFO - Processing strand: positive
2025-09-12 19:23:58,165 - INFO - Processing 4537 windows in 141 batches of size 32
2025-09-12 19:23:58,165 - INFO - Processing batch 1 of 141 [rank=0, world_size=1]
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2025-09-12 19:51:34,991 - INFO - Loading completed predictions from results/pipeline/predictions.zarr/predictions.0.zarr (rank=0, world_size=1)
2025-09-12 19:51:35,260 - INFO - Complete predictions dataset:
<xarray.DataTree>
Group: /
├── Group: /negative
│ Dimensions: (sequence: 18585056, token: 17, feature: 5)
│ Coordinates:
│ * feature (feature) <U15 300B 'intergenic' ... 'three_prime_utr'
│ * token (token) <U17 1kB 'intergenic' ... 'U-three_prime_utr'
│ * sequence (sequence) int64 149MB 18447840 18447841 ... 130527
│ Data variables:
│ token_logits (sequence, token) float32 1GB ...
│ feature_predictions (sequence) int64 149MB ...
│ token_predictions (sequence) int64 149MB ...
│ feature_logits (sequence, feature) float32 372MB ...
│ Attributes:
│ strand: negative
│ species_id: athaliana
│ chromosome_id: 4
│ model_checkpoint: plantcad/GeneCAD-l8-d768-PC2-Large
│ model_path: kuleshov-group/PlantCAD2-Large-l48-d1536
└── Group: /positive
Dimensions: (sequence: 18585056, token: 17, feature: 5)
Coordinates:
* feature (feature) <U15 300B 'intergenic' ... 'three_prime_utr'
* token (token) <U17 1kB 'intergenic' ... 'U-three_prime_utr'
* sequence (sequence) int64 149MB 0 1 2 ... 18585054 18585055
Data variables:
token_logits (sequence, token) float32 1GB ...
feature_predictions (sequence) int64 149MB ...
feature_logits (sequence, feature) float32 372MB ...
token_predictions (sequence) int64 149MB ...
Attributes:
strand: positive
species_id: athaliana
chromosome_id: 4
model_checkpoint: plantcad/GeneCAD-l8-d768-PC2-Large
model_path: kuleshov-group/PlantCAD2-Large-l48-d1536
2025-09-12 19:51:35,260 - INFO - Done
python scripts/predict.py detect_intervals \
--input-dir results/pipeline/predictions.zarr \
--output results/pipeline/intervals.zarr \
--decoding-methods "direct,viterbi" \
--remove-incomplete-features yes
2025-09-12 19:51:42,074 - INFO - Detecting intervals from rank files in results/pipeline/predictions.zarr and saving to results/pipeline/intervals.zarr
2025-09-12 19:51:42,074 - INFO - Found 1 rank prediction files: ['results/pipeline/predictions.zarr/predictions.0.zarr']
2025-09-12 19:51:42,074 - INFO - Processing strand: positive
2025-09-12 19:51:42,354 - INFO - Concatenating 1 rank datasets for 'positive' strand along the sequence dimension.
2025-09-12 19:51:44,042 - INFO - Processing strand: negative
2025-09-12 19:51:44,302 - INFO - Concatenating 1 rank datasets for 'negative' strand along the sequence dimension.
2025-09-12 19:51:46,196 - INFO - Concatenating 2 datasets along the strand dimension.
2025-09-12 19:51:46,534 - INFO - Concatenated sequence predictions dataset:
<xarray.Dataset> Size: 1GB
Dimensions: (strand: 2, sequence: 18585056, feature: 5, token: 17)
Coordinates:
* strand (strand) object 16B 'positive' 'negative'
* feature (feature) <U15 300B 'intergenic' ... 'three_prime_utr'
* token (token) <U17 1kB 'intergenic' ... 'U-three_prime_utr'
* sequence (sequence) int64 149MB 0 1 2 ... 18585054 18585055
Data variables:
feature_predictions (strand, sequence) int64 297MB 0 0 0 0 0 ... 0 0 0 0 0
feature_logits (strand, sequence, feature) float32 743MB 4.312 ... ...
Attributes:
species_id: athaliana
chromosome_id: 4
model_checkpoint: plantcad/GeneCAD-l8-d768-PC2-Large
model_path: kuleshov-group/PlantCAD2-Large-l48-d1536
2025-09-12 19:51:46,537 - INFO - Detecting intervals
2025-09-12 19:51:46,537 - INFO - Inferring regions from predicted labels
2025-09-12 19:51:46,537 - INFO - Running decoding methods: ['direct', 'viterbi']
2025-09-12 19:51:46,538 - INFO - Running direct decoding for 'positive' strand
2025-09-12 19:51:48,173 - INFO - Running viterbi decoding for 'positive' strand
2025-09-12 19:51:48,313 - INFO - Running viterbi decoding (alpha=None)
2025-09-12 19:51:58,857 - INFO - Running direct decoding for 'negative' strand
2025-09-12 19:52:00,470 - INFO - Running viterbi decoding for 'negative' strand
2025-09-12 19:52:00,766 - INFO - Running viterbi decoding (alpha=None)
2025-09-12 19:52:09,327 - INFO - Region intervals detected:
entity_index start stop strand decoding entity_name
interval
0 1 13518 13518 positive direct transcript
1 1 13523 16074 positive direct transcript
2 1 16076 16077 positive direct transcript
3 1 16084 16084 positive direct transcript
4 1 17747 17747 positive direct transcript
... ... ... ... ... ... ...
231189 6 18557202 18557537 negative viterbi three_prime_utr
231190 6 18559793 18559924 negative viterbi three_prime_utr
231191 6 18560871 18561204 negative viterbi three_prime_utr
231192 6 18571381 18571680 negative viterbi three_prime_utr
231193 6 18580811 18581083 negative viterbi three_prime_utr
[231194 rows x 6 columns]
2025-09-12 19:52:09,327 - INFO - Region interval info:
2025-09-12 19:52:09,351 - INFO - Merging sequence and interval predictions
2025-09-12 19:52:09,355 - INFO - Final results:
<xarray.DataTree>
Group: /
├── Group: /sequences
│ Dimensions: (strand: 2, sequence: 18585056, feature: 5, token: 17)
│ Coordinates:
│ * strand (strand) object 16B 'positive' 'negative'
│ * feature (feature) <U15 300B 'intergenic' ... 'three_prime_utr'
│ * token (token) <U17 1kB 'intergenic' ... 'U-three_prime_utr'
│ * sequence (sequence) int64 149MB 0 1 2 ... 18585054 18585055
│ Data variables:
│ feature_predictions (strand, sequence) int64 297MB 0 0 0 0 0 ... 0 0 0 0 0
│ feature_logits (strand, sequence, feature) float32 743MB 4.312 ... ...
│ Attributes:
│ species_id: athaliana
│ chromosome_id: 4
│ model_checkpoint: plantcad/GeneCAD-l8-d768-PC2-Large
│ model_path: kuleshov-group/PlantCAD2-Large-l48-d1536
└── Group: /intervals
Dimensions: (interval: 231194)
Coordinates:
* interval (interval) int64 2MB 0 1 2 3 4 ... 231190 231191 231192 231193
Data variables:
entity_index (interval) int64 2MB 1 1 1 1 1 1 1 1 1 1 ... 6 6 6 6 6 6 6 6 6
start (interval) int64 2MB 13518 13523 16076 ... 18571381 18580811
stop (interval) int64 2MB 13518 16074 16077 ... 18571680 18581083
strand (interval) object 2MB 'positive' 'positive' ... 'negative'
decoding (interval) object 2MB 'direct' 'direct' ... 'viterbi'
entity_name (interval) object 2MB 'transcript' ... 'three_prime_utr'
Attributes:
interval_entity_names: ['transcript', 'exon', 'intron', 'five_prime_utr'...
species_id: athaliana
chromosome_id: 4
model_checkpoint: plantcad/GeneCAD-l8-d768-PC2-Large
model_path: kuleshov-group/PlantCAD2-Large-l48-d1536
2025-09-12 19:52:09,355 - INFO - Saving results to output path results/pipeline/intervals.zarr
2025-09-12 19:52:10,198 - INFO - Done
<class 'pandas.core.frame.DataFrame'>
RangeIndex: 231194 entries, 0 to 231193
Data columns (total 6 columns):
# Column Non-Null Count Dtype
--- ------ -------------- -----
0 entity_index 231194 non-null int64
1 start 231194 non-null int64
2 stop 231194 non-null int64
3 strand 231194 non-null object
4 decoding 231194 non-null object
5 entity_name 231194 non-null object
dtypes: int64(3), object(3)
memory usage: 10.6+ MB
python scripts/predict.py export_gff \
--input results/pipeline/intervals.zarr \
--output results/pipeline/predictions__raw.gff \
--decoding-method viterbi \
--min-transcript-length 3 \
--strip-introns yes
2025-09-12 19:52:16,606 - INFO - Loading predictions from results/pipeline/intervals.zarr
2025-09-12 19:52:16,763 - INFO - Loaded intervals for chromosome: 4
2025-09-12 19:52:16,763 - INFO - Converting interval predictions to DataFrame
2025-09-12 19:52:16,902 - INFO - Filtered intervals to 71017 rows using decoding method: viterbi
2025-09-12 19:52:16,902 - INFO - Grouping intervals by transcript
2025-09-12 19:52:16,906 - INFO - Filtered out 0 transcripts below minimum length of 3bp
2025-09-12 19:52:16,906 - INFO - Retained 3777 transcripts
100%|██████████| 3777/3777 [00:15<00:00, 244.52it/s]
2025-09-12 19:52:32,360 - INFO - Grouped intervals into 3777 transcripts/genes.
2025-09-12 19:52:32,361 - INFO - Generating GFF3 output for 3777 genes on 4
2025-09-12 19:52:36,199 - INFO - Writing 36220 lines to results/pipeline/predictions__raw.gff
2025-09-12 19:52:36,212 - INFO - GFF export complete
python scripts/gff.py filter_to_min_feature_length \
--input results/pipeline/predictions__raw.gff \
--output results/pipeline/predictions__raw__feat_len_2.gff \
--feature-types "five_prime_UTR,three_prime_UTR,CDS" \
--min-length 2
2025-09-12 19:52:38,346 - INFO - Filtering results/pipeline/predictions__raw.gff to remove ['five_prime_UTR', 'three_prime_UTR', 'CDS'] features shorter than 2 bp
2025-09-12 19:52:38,346 - INFO - Loading GFF file results/pipeline/predictions__raw.gff
2025-09-12 19:52:38,448 - INFO - Loading complete: 36219 records found
2025-09-12 19:52:38,455 - INFO - Validated feature types: ['CDS', 'five_prime_UTR', 'three_prime_UTR'] (all valid)
2025-09-12 19:52:38,457 - INFO - Found 274 small features to remove
2025-09-12 19:53:07,549 - INFO - Boundary updates:
2025-09-12 19:53:07,549 - INFO - - Genes: 194/3777 (5.1%) had boundaries updated
2025-09-12 19:53:07,549 - INFO - - Transcripts: 194/3777 (5.1%) had boundaries updated
2025-09-12 19:53:07,549 - INFO - Writing GFF to results/pipeline/predictions__raw__feat_len_2.gff
2025-09-12 19:53:07,649 - INFO - Complete: 35945 records written
2025-09-12 19:53:07,649 - INFO - Filter complete: 274 features removed, 35945/36219 records retained
python scripts/gff.py filter_to_min_gene_length \
--input results/pipeline/predictions__raw__feat_len_2.gff \
--output results/pipeline/predictions__raw__feat_len_2__gene_len_30.gff \
--min-length 30
2025-09-12 19:53:08,334 - INFO - Filtering results/pipeline/predictions__raw__feat_len_2.gff to remove genes shorter than 30 bp
2025-09-12 19:53:08,334 - INFO - Loading GFF file results/pipeline/predictions__raw__feat_len_2.gff
2025-09-12 19:53:08,434 - INFO - Loading complete: 35945 records found
2025-09-12 19:53:08,444 - INFO - Found 3777 gene features to check for length
2025-09-12 19:53:08,445 - INFO - Found 0 genes shorter than 30 bp
2025-09-12 19:53:08,450 - INFO - Removing 0 genes directly (too short)
2025-09-12 19:53:08,450 - INFO - Removing 0 features indirectly (parent gene too short)
2025-09-12 19:53:08,450 - INFO - Total features removed: 0
2025-09-12 19:53:08,450 - INFO - Writing GFF to results/pipeline/predictions__raw__feat_len_2__gene_len_30.gff
2025-09-12 19:53:08,547 - INFO - Complete: 35945 records written
2025-09-12 19:53:08,547 - INFO - Filter complete: 35945/35945 records retained
python scripts/gff.py filter_to_valid_genes \
--input results/pipeline/predictions__raw__feat_len_2__gene_len_30.gff \
--output results/pipeline/predictions__raw__feat_len_2__gene_len_30__has_req_feats.gff \
--require-utrs yes
2025-09-12 19:53:09,220 - INFO - Filtering results/pipeline/predictions__raw__feat_len_2__gene_len_30.gff to keep only valid transcripts and genes
2025-09-12 19:53:09,220 - INFO - Requiring five_prime_UTR, CDS, and three_prime_UTR for valid transcripts
2025-09-12 19:53:09,220 - INFO - Loading GFF file results/pipeline/predictions__raw__feat_len_2__gene_len_30.gff
2025-09-12 19:53:09,321 - INFO - Loading complete: 35945 records found
2025-09-12 19:53:09,331 - INFO - Found 3777 mRNA features
2025-09-12 19:53:15,001 - INFO - Found 3591 valid mRNAs and 186 invalid mRNAs
2025-09-12 19:53:15,014 - INFO - Removed 186 invalid mRNAs, 472 child features, 658 total features
2025-09-12 19:53:15,016 - INFO - Found 3777 gene features
2025-09-12 19:53:15,019 - INFO - Found 186 genes with no valid transcripts
2025-09-12 19:53:15,030 - INFO - Removed 186 invalid genes, 0 child features, 186 total features
2025-09-12 19:53:15,030 - INFO - Writing GFF to results/pipeline/predictions__raw__feat_len_2__gene_len_30__has_req_feats.gff
2025-09-12 19:53:15,125 - INFO - Complete: 35101 records written
2025-09-12 19:53:15,125 - INFO - Filter complete: 35101/35945 records retained
cp results/pipeline/predictions__raw__feat_len_2__gene_len_30__has_req_feats.gff results/predictions.gff