gistfile1.txt

(thalamus-venv)Administrators-MacBook-Pro:thalamus eddie$ run_ml
Starting run
Setting run id to 5
Loading files from S3
File ./Manifest_QC_Clinical_BW_012414.just_metabolon_samples.txt exists, skipping get from s3
File ./Manifest_QC_Clinical_BW_012414.txt exists, skipping get from s3
File ./counts_v2_genes_exons.gc.frozen_ref.txt exists, skipping get from s3
File ./counts_v2_genes_exons.gc.just_genes.frozen_ref.txt exists, skipping get from s3
File ./restricted_features_mx_lx_21Feb14.txt exists, skipping get from s3
File ./scaled_imp_mx_lx_formatted_21Feb14.txt exists, skipping get from s3
Doing run with transforms: male-wo-blood-volume
Read manifest Manifest_QC_Clinical_BW_012414.txt: found 293 samples and 288 keys
Removing 22 samples found in counts but not in manifest
Read tabular data source counts_v2_genes_exons.gc.just_genes.frozen_ref.txt: found 293 samples and 23228 features
#MachineLearningPipeline 0.01
#Date 2014-03-08 13:24:20.319602
counts_file	partition_state	feature_engineering	feature_selection	classifier	outer_n_reps	n_features	n_samples	n_train_samples	n_test_samples	name	k	feature_type	feature_counts
Adding 10 parameters to this run
Transforming: LowCountLog2
WARNING Duplicate feature ADC found in table, removing
Transforming: add-blood-volume
Transforming: GenderFilter
Traceback (most recent call last):
  File "/Users/eddie/Programming/projects/thalamus/thalamus-venv/bin/run_ml", line 9, in <module>
    load_entry_point('thalamus==0.0.1.0-local', 'console_scripts', 'run_ml')()
  File "/Users/eddie/Programming/projects/thalamus/thalamus/mlp/executive/stdlib_executor.py", line 69, in run_stdlib
    for jobspec, scores, results in run_ml_tasks(queue, num_tasks=None):
  File "/Users/eddie/Programming/projects/thalamus/thalamus/mlp/executive/ml_runner.py", line 247, in run_ml_tasks
    ml_tasks.run()
  File "/Users/eddie/Programming/projects/medula/code/medulla/medulla/process/parallel.py", line 627, in run
    self.results.append(self.wrapped_tasks_function(*task_args, **task_kwargs))
  File "/Users/eddie/Programming/projects/medula/code/medulla/medulla/process/parallel.py", line 581, in inner_wrapper
    result = target_func(*args, **kwargs)
  File "/Users/eddie/Programming/projects/thalamus/thalamus/mlp/trainml.py", line 63, in train_and_assess_classifier
    raise Exception("hi")
Exception: hi
(thalamus-venv)Administrators-MacBook-Pro:thalamus eddie$