algae-filelist.txt
cache/
ckpt.pt
contam-filelist.txt
filelist.txt
generated_prompts_algae1.txt_headed.fa
generated_prompts_algae2.txt_headed.fa
generated_prompts_algae3.txt_headed.fa
generated_prompts_archa1.txt_headed.fa
generated_prompts_archa2.txt_headed.fa
generated_prompts_archa3.txt_headed.fa
generated_prompts_bact1.txt_headed.fa
generated_prompts_bact2.txt_headed.fa
generated_prompts_bact3.txt_headed.fa
generated_prompts_fungi1.txt_headed.fa
generated_prompts_fungi2.txt_headed.fa
generated_prompts_fungi3.txt_headed.fa
generated_prompts_virus1.txt_headed.fa
generated_prompts_virus2.txt_headed.fa
generated_prompts_virus3.txt_headed.fa
infer_TI-inc-algaGPT.py
la4sr_sp2.sif
la4sr_sp2.sif.md5
llm-metrics-two-files.py
meta.pkl
model.py
out-algaGPT/
__pycache__/
__pycache__/model.cpython-312.pyc
README.txt
results-archive/
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_bact3.txt_headed_misclassified.txt
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_virus3.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_fungi2.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_archa2.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_bact3.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_bact2.txt_headed_report.txt
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_fungi3.txt_headed_algal.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_bact1.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_archa3.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_fungi3.txt_headed_report.txt
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_virus3.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_virus2.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_virus3.txt_headed_algal.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_bact1.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_bact1.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_fungi2.txt_headed_class_distribution.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_archa2.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_archa1.txt_headed_misclassified.txt
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_bact2.txt_headed_algal.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_virus1.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_virus1.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_virus1.txt_headed_class_distribution.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_archa1.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_bact3.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_fungi3.txt_headed_misclassified.txt
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_virus2.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_fungi1.txt_headed_class_distribution.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_virus1.txt_headed_algal.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_fungi3.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_archa2.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_archa1.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_fungi3.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_bact3.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_virus3.txt_headed_class_distribution.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_fungi1.txt_headed_misclassified.txt
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_virus3.txt_headed_report.txt
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_archa2.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_archa3.txt_headed_class_distribution.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_archa1.txt_headed_class_distribution.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_virus2.txt_headed_misclassified.txt
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_bact1.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_archa2.txt_headed_algal.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_fungi1.txt_headed_algal.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_virus2.txt_headed_class_distribution.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_fungi2.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_virus1.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_archa3.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_virus1.txt_headed_report.txt
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_bact3.txt_headed_algal.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_archa1.txt_headed_algal.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_virus2.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_fungi2.txt_headed_algal.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_bact1.txt_headed_algal.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_fungi3.txt_headed_class_distribution.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_archa2.txt_headed_class_distribution.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_bact2.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_bact3.txt_headed_class_distribution.png
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_virus3.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_fungi3.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_virus2.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_archa1.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_fungi2.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_virus2.txt_headed_algal.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_fungi1.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_archa3.txt_headed_report.txt
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_archa2.txt_headed_report.txt
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_archa3.txt_headed_algal.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_archa2.txt_headed_misclassified.txt
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_virus1.txt_headed_misclassified.txt
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_fungi1.txt_headed_report.txt
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_bact1.txt_headed_report.txt
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_fungi2.txt_headed_misclassified.txt
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_virus2.txt_headed_report.txt
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_archa1.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_bact2.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_bact2.txt_headed_misclassified.txt
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_archa2.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_fungi2.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_bact2.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_virus3.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_bact2.txt_headed_class_distribution.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_fungi2.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_archa3.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_archa1.txt_headed_report.txt
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_virus2.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_bact1.txt_headed_class_distribution.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_bact1.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_virus3.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_virus1.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_bact1.txt_headed_misclassified.txt
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_fungi1.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_fungi3.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_archa3.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_fungi1.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_bact3.txt_headed_report.txt
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_bact3.txt_headed_bacterial_tagged.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_fungi1.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_fungi1.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_bact2.txt_headed_metrics_by_class.png
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_archa3.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_virus1.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_archa3.txt_headed_misclassified.txt
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_bact2.txt_headed_algal_tagged.tsv
results-archive/generated_prompts_algae1.txt_headed_vs_generated_prompts_archa1.txt_headed_confusion_matrix.png
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_virus3.txt_headed_misclassified.txt
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_fungi3.txt_headed_bacterial.tsv
results-archive/generated_prompts_algae2.txt_headed_vs_generated_prompts_fungi2.txt_headed_report.txt
results-archive/generated_prompts_algae3.txt_headed_vs_generated_prompts_bact3.txt_headed_confusion_matrix.png
run_la4sr_loop.sbatch
run_la4sr_TI-inc-algaGPT.sh
slurm-10718799.out
tar: slurm-10718799.out: file changed as we read it
slurm-logs/
slurm-logs/arrayJob_10718778_2.err
slurm-logs/arrayJob_10718764_10.err
slurm-logs/arrayJob_10718778_8.err
slurm-logs/arrayJob_10718778_7.err
slurm-logs/arrayJob_10718764_9.out
slurm-logs/arrayJob_10718778_11.out
slurm-logs/arrayJob_10718764_4.err
slurm-logs/arrayJob_10718778_9.err
slurm-logs/arrayJob_10718764_10.out
slurm-logs/arrayJob_10718778_6.err
slurm-logs/arrayJob_10718778_1.err
slurm-logs/arrayJob_10718764_11.out
slurm-logs/arrayJob_10718778_12.out
slurm-logs/arrayJob_10718778_9.out
slurm-logs/arrayJob_10718764_11.err
slurm-logs/arrayJob_10718778_10.out
slurm-logs/arrayJob_10718764_9.err
slurm-logs/arrayJob_10718764_2.out
slurm-logs/arrayJob_10718778_2.out
slurm-logs/arrayJob_10718778_5.out
slurm-logs/arrayJob_10718764_12.out
slurm-logs/arrayJob_10718764_1.err
slurm-logs/arrayJob_10718764_8.err
slurm-logs/arrayJob_10718764_3.err
slurm-logs/arrayJob_10718778_1.out
slurm-logs/arrayJob_10718764_2.err
slurm-logs/arrayJob_10718778_10.err
slurm-logs/arrayJob_10718778_3.err
slurm-logs/arrayJob_10718778_5.err
slurm-logs/arrayJob_10718778_8.out
slurm-logs/arrayJob_10718778_4.out
slurm-logs/arrayJob_10718764_7.err
slurm-logs/arrayJob_10718778_3.out
slurm-logs/arrayJob_10718778_12.err
slurm-logs/arrayJob_10718764_3.out
slurm-logs/arrayJob_10718764_6.out
slurm-logs/arrayJob_10718764_5.err
slurm-logs/arrayJob_10718778_7.out
slurm-logs/arrayJob_10718764_7.out
slurm-logs/arrayJob_10718764_4.out
slurm-logs/arrayJob_10718764_6.err
slurm-logs/arrayJob_10718778_4.err
slurm-logs/arrayJob_10718764_5.out
slurm-logs/arrayJob_10718778_6.out
slurm-logs/arrayJob_10718764_1.out
slurm-logs/arrayJob_10718764_8.out
slurm-logs/arrayJob_10718764_12.err
slurm-logs/arrayJob_10718778_11.err
targz.sh