Mercurial > repos > bgruening > create_tool_recommendation_model
changeset 2:50753817983a draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/recommendation_training/tools/tool_recommendation_model commit c635df659fe1835679438589ded43136b0e515c6"
| author | bgruening |
|---|---|
| date | Sat, 09 May 2020 09:38:04 +0000 |
| parents | 275e98795e99 |
| children | 98bc44d17561 |
| files | create_tool_recommendation_model.xml extract_workflow_connections.py main.py optimise_hyperparameters.py predict_tool_usage.py prepare_data.py test-data/test_tool_usage test-data/test_workflows utils.py |
| diffstat | 9 files changed, 1881 insertions(+), 9657 deletions(-) [+] |
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--- a/create_tool_recommendation_model.xml Wed Sep 25 06:42:18 2019 -0400 +++ b/create_tool_recommendation_model.xml Sat May 09 09:38:04 2020 +0000 @@ -1,12 +1,12 @@ -<tool id="create_tool_recommendation_model" name="Create a model to recommend tools" version="0.0.1"> +<tool id="create_tool_recommendation_model" name="Create a model to recommend tools" version="0.0.2"> <description>using deep learning</description> <requirements> <requirement type="package" version="3.6">python</requirement> - <requirement type="package" version="1.14.0">tensorflow</requirement> - <requirement type="package" version="2.2.4">keras</requirement> - <requirement type="package" version="0.20.1">scikit-learn</requirement> + <requirement type="package" version="1.13.1">tensorflow</requirement> + <requirement type="package" version="2.3.0">keras</requirement> + <requirement type="package" version="0.21.3">scikit-learn</requirement> <requirement type="package" version="2.9.0">h5py</requirement> - <requirement type="package" version="1.0">csvkit</requirement> + <requirement type="package" version="1.0.4">csvkit</requirement> <requirement type="package" version="0.1.2">hyperopt</requirement> </requirements> <version_command>echo "@VERSION@"</version_command> @@ -21,7 +21,6 @@ --optimize_n_epochs '$training_parameters.optimize_n_epochs' --max_evals '$training_parameters.max_evals' --test_share '$training_parameters.test_share' - --validation_share '$training_parameters.validation_share' --batch_size '$nn_parameters.batch_size' --units '$nn_parameters.units' --embedding_size '$nn_parameters.embedding_size' @@ -29,8 +28,6 @@ --spatial_dropout '$nn_parameters.spatial_dropout' --recurrent_dropout '$nn_parameters.recurrent_dropout' --learning_rate '$nn_parameters.learning_rate' - --activation_recurrent '$nn_parameters.activation_recurrent' - --activation_output '$nn_parameters.activation_output' --output_model '$outfile_model' ]]> </command> @@ -38,26 +35,36 @@ <param name="input_tabular_workflows" type="data" format="tabular" label="Dataset containing workflows" help="Please provide Galaxy workflows as a tabular file."/> <param name="input_tabular_tool_usage" type="data" format="tabular" label="Dataset containing usage frequencies of tools" help="Please provide tools usage frequencies as a tabular file."/> <section name="data_parameters" title="Data parameters" expanded="False"> + <param name="input_cutoff_date" type="text" value="2017-12-01" label="Cutoff date" help="Provide a date (in the past) in yyyy-mm-dd format. The earliest date from which usage of tools will be extracted. For example, 2017-12-01 specifies that the usage of tools from this date until the data extraction date is extracted. The usage of tools before this date is not considered."/> + <param name="input_maximum_path_length" type="integer" value="25" label="Maximum number of tools in a tool sequence" help="Provide an integer between 1 and 25. A workflow is divided into unique paths and this number specifies the maximum number of tools a path can have. Paths longer than this number are ignored and are not included in the deep learning training."/> + </section> <section name="training_parameters" title="Training parameters" expanded="False"> - <param name="max_evals" type="integer" value="2" label="Maximum number of evaluations of different configurations of parameters" help="Provide an integer. Different combinations of parameters are sampled and optimized to find the best one. This number specifies the number of different configurations sampled and tested."/> - <param name="optimize_n_epochs" type="integer" value="2" label="Number of training iterations to optimize the neural network parameters" help="Provide an integer. This number specifies the number of training iterations done for each sampled configuration while optimising the parameters."/> - <param name="n_epochs" type="integer" value="2" label="Number of training iterations" help="Provide an integer. This specifies the number of deep learning training iterations done after finding the best/optimised configuration of neural network parameters."/> + <param name="max_evals" type="integer" value="20" label="Maximum number of evaluations of different configurations of parameters" help="Provide an integer. Different combinations of parameters are sampled and optimized to find the best one. This number specifies the number of different configurations sampled and tested."/> + + <param name="optimize_n_epochs" type="integer" value="5" label="Number of training iterations to optimize the neural network parameters" help="Provide an integer. This number specifies the number of training iterations done for each sampled configuration while optimising the parameters."/> + + <param name="n_epochs" type="integer" value="10" label="Number of training iterations" help="Provide an integer. This specifies the number of deep learning training iterations done after finding the best/optimised configuration of neural network parameters."/> + <param name="test_share" type="float" value="0.2" label="Share of the test data" help="Provide a real number between 0.0 and 1.0. This set of data is used to look through the prediction accuracy on unseen data after neural network training on an optimised configuration of parameters. It should be set to 0.0 while training for a model to be deployed to production. The minimum value can be 0.0 and maximum value should not be more than 0.5."/> - <param name="validation_share" type="float" value="0.2" label="Share of the validation data" help="Provide a real number between 0.0 and 1.0. This set of data is used to validate each step of learning while optimising the configurations of parameters. The minimum value can be 0.0 and maximum value should not be more than 0.5."/> + </section> <section name="nn_parameters" title="Neural network parameters" expanded="False"> - <param name="batch_size" type="text" value="30,500" label="Training batch size" help="Provide a comma-separated range to sample the batch size from. The training of the neural network is done using batch learning in this work. The training data is divided into equal batches and for each epoch (a training iteration), all the batches of data are trained one after another. An example: 10,500." /> - <param name="units" type="text" value="30,500" label="Number of hidden recurrent units" help="Provide a comma-separated range to sample the number of hidden recurrent units. A higher value provide stronger neural network model (may lead to overfitting in case of smaller data) and smaller value leads to weaker model (may lead to underfitting in case of larger data). An example: 30,500."/> - <param name="embedding_size" type="text" value="30,500" label="Embedding vector size" help="Provide a comma-separated range to sample the embedding size for tools. A fixed-size vector is learned for each tool. This number specifies the fixed-size. An example: 30,500."/> + <param name="batch_size" type="text" value="32,256" label="Training batch size" help="Provide a comma-separated range to sample the batch size from. The training of the neural network is done using batch learning in this work. The training data is divided into equal batches and for each epoch (a training iteration), all the batches of data are trained one after another. An example: 32,256." /> + + <param name="units" type="text" value="32,512" label="Number of hidden recurrent units" help="Provide a comma-separated range to sample the number of hidden recurrent units. A higher value provide stronger neural network model (may lead to overfitting in case of smaller data) and smaller value leads to weaker model (may lead to underfitting in case of larger data). An example: 32,512."/> + + <param name="embedding_size" type="text" value="32,512" label="Embedding vector size" help="Provide a comma-separated range to sample the embedding size for tools. A fixed-size vector is learned for each tool. This number specifies the fixed-size. An example: 32,512."/> + <param name="dropout" type="text" value="0.0,0.5" label="Dropout between neural network layers" help="Provide a comma-separated range to sample the amount of dropout to be used after neural netwrok layers. The minimum value should be 0.0 and the maximum value should be 1.0. Dropout is used to prevent or minimize overfitting after each neural network layer. An example: 0.0,0.5"/> + <param name="spatial_dropout" type="text" value="0.0,0.5" label="Dropout for the embedding layer" help="Provide a comma-separated range to sample the amount of dropout to be used after embedding layer. The minimum value should be 0.0 and the maximum value should be 1.0. Dropout is used to prevent or minimize overfitting in the embedding layer. An example: 0.0,0.5"/> + <param name="recurrent_dropout" type="text" value="0.0,0.5" label="Dropout for recurrent layers" help="Provide a comma-separated range to sample the amount of dropout to be used for the recurrent layers. The minimum value should be 0.0 and the maximum value should be 1.0. Dropout is used to prevent or minimize overfitting in the recurrent layers. An example: 0.0,0.5"/> + <param name="learning_rate" type="text" value="0.0001,0.1" label="Learning rate" help="Provide a range of positive real numbers to sample the learning rate. Learning rate defines the speed of neural network learning. A higher value will ensure fast learning and smaller value will ensure slower learning. An example: 0.0001,0.1"/> - <param name="activation_recurrent" type="text" value="elu" label="Name of the activation function for recurrent layers" help="It is a mathematical function that transforms the input of recurrent layers to the following neural network layer."/> - <param name="activation_output" type="text" value="sigmoid" label="Name of the activation function for output layer" help="It is a mathematical function that transforms the input of the last dense layer to the output of the neural network."/> </section> </inputs> <outputs> @@ -66,13 +73,71 @@ <tests> <test> <param name="input_tabular_workflows" value="test_workflows" ftype="tabular"/> + <param name="input_tabular_tool_usage" value="test_tool_usage" ftype="tabular"/> + <param name="max_evals" value="1"/> + <param name="batch_size" value="1,2"/> + <param name="optimize_n_epochs" value="1"/> + <param name="n_epochs" value="1"/> + <param name="test_share" value="0.2"/> + <output name="outfile_model"> + <assert_contents> + <has_h5_keys keys="best_parameters,class_weights,compatible_tools,data_dictionary,model_config,weight_0,weight_1,weight_2,weight_3,weight_4,weight_5,weight_6,weight_7,weight_8"/> + </assert_contents> + </output> + </test> + <test> + <param name="input_tabular_workflows" value="test_workflows" ftype="tabular"/> <param name="input_tabular_tool_usage" value="test_tool_usage" ftype="tabular"/> + <param name="max_evals" value="1"/> + <param name="batch_size" value="1,2"/> + <param name="optimize_n_epochs" value="1"/> + <param name="n_epochs" value="1"/> <output name="outfile_model"> <assert_contents> <has_h5_keys keys="best_parameters,class_weights,compatible_tools,data_dictionary,model_config,weight_0,weight_1,weight_2,weight_3,weight_4,weight_5,weight_6,weight_7,weight_8"/> </assert_contents> </output> </test> + <test expect_failure="true"> + <param name="input_tabular_workflows" value="test_workflows" ftype="tabular"/> + <param name="input_tabular_tool_usage" value="test_tool_usage" ftype="tabular"/> + <param name="test_share" value="0.0"/> + </test> + <test expect_failure="true"> + <param name="input_tabular_workflows" value="test_workflows" ftype="tabular"/> + <param name="input_tabular_tool_usage" value="test_tool_usage" ftype="tabular"/> + <param name="batch_size" value="1"/> + </test> + <test expect_failure="true"> + <param name="input_tabular_workflows" value="test_workflows" ftype="tabular"/> + <param name="input_tabular_tool_usage" value="test_tool_usage" ftype="tabular"/> + <param name="units" value="1"/> + </test> + <test expect_failure="true"> + <param name="input_tabular_workflows" value="test_workflows" ftype="tabular"/> + <param name="input_tabular_tool_usage" value="test_tool_usage" ftype="tabular"/> + <param name="embedding_size" value="1"/> + </test> + <test expect_failure="true"> + <param name="input_tabular_workflows" value="test_workflows" ftype="tabular"/> + <param name="input_tabular_tool_usage" value="test_tool_usage" ftype="tabular"/> + <param name="dropout" value="0.1"/> + </test> + <test expect_failure="true"> + <param name="input_tabular_workflows" value="test_workflows" ftype="tabular"/> + <param name="input_tabular_tool_usage" value="test_tool_usage" ftype="tabular"/> + <param name="spatial_dropout" value="0.1"/> + </test> + <test expect_failure="true"> + <param name="input_tabular_workflows" value="test_workflows" ftype="tabular"/> + <param name="input_tabular_tool_usage" value="test_tool_usage" ftype="tabular"/> + <param name="recurrent_dropout" value="0.1"/> + </test> + <test expect_failure="true"> + <param name="input_tabular_workflows" value="test_workflows" ftype="tabular"/> + <param name="input_tabular_tool_usage" value="test_tool_usage" ftype="tabular"/> + <param name="learning_rate" value="0.0001"/> + </test> </tests> <help> <![CDATA[ @@ -90,14 +155,14 @@ 1. The first file ("dataset containing workflows") contains tool connections for workflows in a tabular format. The workflows are arranged as pairs of tool connections. Each row is a pair of tool connections in a workflow as shown below: - ========== =================== ========= ================= ============= ========== ============ ============== - **wf_id** **wf_updated** **in_id** **in_tool** **in_tool_v** **out_id** **out_tool** **out_tool_v** - ---------- ------------------- --------- ----------------- ------------- ---------- ------------ -------------- - 3 2013-02-07 16:48:00 7 Remove beginning1 1.0.0 5 Grep1 1.0.1 - ========== =================== ========= ================= ============= ========== ============ ============== + ========== ================ ========== ============= ============= =========== ============= ============== ============== =========== ============= + **wf_id** **wf_updated** **in_id** **in_tool** **in_tool_v** **out_id** **out_tool** **out_tool_v** **published** **deleted** **has_error** + ---------- ---------------- ---------- ------------- ------------- ----------- ------------- -------------- -------------- ----------- ------------- + 3 2013-02-07 7 Cut1 1.0.0 5 Grep1 1.0.1 f t f + ========== ================ ========== ============= ============= =========== ============= ============== ============== =========== ============= -The first column (wf_id) is the workflow id, second (wf_updated) is the last updated date timestamp, third (in_id) is the id of the tool which is the input to the tool connection, fourth (in_tool) is the name of the input tool, fifth (in_tool_v) is the version of the input tool, sixth (out_id) is the id of the output tool in the tool connection, seventh (out_tool) is the name of the output tool and the last one (out_tool_v) is the version of the output tool. The tools connections (rows) for each workflow are used to recreate the workflow (directed acyclic graph) and unique tool sequences for each workflow are extracted. These tool sequences are then used to learn higher-order dependencies using a recurrent neural network to recommend tools. - +The first column (wf_id) is the workflow id, second (wf_updated) is the last updated date timestamp, third (in_id) is the id of the tool which is the input to the tool connection, fourth (in_tool) is the name of the input tool, fifth (in_tool_v) is the version of the input tool, sixth (out_id) is the id of the output tool in the tool connection, seventh (out_tool) is the name of the output tool and the last one (out_tool_v) is the version of the output tool. The tools connections (rows) for each workflow are used to recreate the workflow (directed acyclic graph) and unique tool sequences for each workflow are extracted. These tool sequences are then used to learn higher-order dependencies using a recurrent neural network to recommend tools. The last 3 columns give more information about workflows if they are published, non-deleted and has any errors. Collectively, they are useful to determine if the workflows are of good quality. + 2. The second file ("dataset containing usage frequencies of tools") is also a tabular file containing the usage frequencies of tools for a period of time. It has 3 columns: ============================================================================================ ========== === @@ -124,7 +189,6 @@ - "optimize_n_epochs": This number specifies how many iterations would the neural network executes to evaluate each sampled configuration. - "n_epochs": Once the best configuration of hyperparameters has been found, the neural network takes this configuration and runs for "n_epochs" number of times minimising the error to produce a model at the end. - "test_share": It specifies the size of the test set. For example, if it is 0.5, then the test set is half of the entire data available. It should not be set to more than 0.5. This set is used for evaluating the precision on an unseen set. - - "validation_share": It specifies the size of the validation set. For example, if it is 0.5, then the validation set is half of the entire data available. It should not be set to more than 0.5. This set is used for computing error while training on the best configuration. 3. Neural network parameters: - "batch_size": The training of the neural network is done using batch learning in this work. The training data is divided into equal batches and for each epoch (a training iteration), all batches of data are trained one after another. A higher or lower value can unsettle the training. Therefore, this parameter should be optimised. @@ -134,17 +198,15 @@ - "spatial_dropout": Similar to dropout, this is used to reduce overfitting in the embedding layer. This parameter should be optimised as well. - "recurrent_dropout": Similar to dropout and spatial dropout, this is used to reduce overfitting in the recurrent layers (hidden). This parameter should be optimised as well. - "learning_rate": The learning rate specifies the speed of learning. A higher value ensures fast learning (the optimiser may diverge) and a lower value causes slow learning (may not reach the optimum). This parameter should be optimised as well. - - "activation_recurrent": Activations are mathematical functions to transform input into output. This takes the name of an activation function from the list of Keras activations (https://keras.io/activations/) for recurrent layers. - - "activation_output": This takes the activation for transforming the input of the last layer to the output of the neural network. It is also taken from Keras activations (https://keras.io/activations/). ----- + **Output file** The output file (model) is an HDF5 file (http://docs.h5py.org/en/latest/high/file.html) containing multiple attributes like a dictionary of tools, neural network configuration and weights for each layer, weights of all tools and so on. After the tool has finished executing, it can be downloaded and placed at "/galaxy/database/" inside a Galaxy instance codebase. To see the recommended tools (enable the UI integrations) in Galaxy, the following changes should be made to "galaxy.yml" file: - Enable and then set the property "enable_tool_recommendation" to "true". - - Enable and then set the property "model_path" to "database/<<model_file_name>>". ]]> </help> @@ -153,8 +215,8 @@ @ARTICLE{anuprulez_galaxytools, Author = {Anup Kumar and Björn Grüning}, keywords = {bioinformatics, recommendation system, deep learning}, - title = {{Tool recommendation system for Galaxy workflows}}, - url = {https://github.com/anuprulez/galaxytools} + title = {{Tool recommendation system for Galaxy}}, + url = {https://github.com/bgruening/galaxytools} } </citation> </citations>
--- a/extract_workflow_connections.py Wed Sep 25 06:42:18 2019 -0400 +++ b/extract_workflow_connections.py Sat May 09 09:38:04 2020 +0000 @@ -11,11 +11,17 @@ class ExtractWorkflowConnections: - @classmethod def __init__(self): """ Init method. """ - @classmethod + def collect_standard_connections(self, row): + published = row[8] + deleted = row[9] + has_errors = row[10] + if published == "t" and deleted == "f" and has_errors == "f": + return True + return False + def read_tabular_file(self, raw_file_path): """ Read tabular file and extract workflow connections @@ -25,7 +31,8 @@ workflow_paths_dup = "" workflow_parents = dict() workflow_paths = list() - unique_paths = list() + unique_paths = dict() + standard_connections = dict() with open(raw_file_path, 'rt') as workflow_connections_file: workflow_connections = csv.reader(workflow_connections_file, delimiter='\t') for index, row in enumerate(workflow_connections): @@ -35,7 +42,15 @@ if wf_id not in workflows: workflows[wf_id] = list() if out_tool and in_tool and out_tool != in_tool: - workflows[wf_id].append((in_tool, out_tool)) + workflows[wf_id].append((out_tool, in_tool)) + qc = self.collect_standard_connections(row) + if qc: + i_t = utils.format_tool_id(in_tool) + o_t = utils.format_tool_id(out_tool) + if i_t not in standard_connections: + standard_connections[i_t] = list() + if o_t not in standard_connections[i_t]: + standard_connections[i_t].append(o_t) print("Processing workflows...") wf_ctr = 0 for wf_id in workflows: @@ -54,7 +69,6 @@ if len(paths) > 0: flow_paths.extend(paths) workflow_paths.extend(flow_paths) - print("Workflows processed: %d" % wf_ctr) # remove slashes from the tool ids @@ -75,9 +89,8 @@ print("Finding compatible next tools...") compatible_next_tools = self.set_compatible_next_tools(no_dup_paths) - return unique_paths, compatible_next_tools + return unique_paths, compatible_next_tools, standard_connections - @classmethod def set_compatible_next_tools(self, workflow_paths): """ Find next tools for each tool @@ -97,7 +110,6 @@ next_tools[tool] = ",".join(list(set(next_tools[tool].split(",")))) return next_tools - @classmethod def read_workflow(self, wf_id, workflow_rows): """ Read all connections for a workflow @@ -112,7 +124,6 @@ tool_parents[out_tool].append(in_tool) return tool_parents - @classmethod def get_roots_leaves(self, graph): roots = list() leaves = list() @@ -125,7 +136,6 @@ leaves = list(set(children).difference(set(all_parents))) return roots, leaves - @classmethod def find_tool_paths_workflow(self, graph, start, end, path=[]): path = path + [end] if start == end:
--- a/main.py Wed Sep 25 06:42:18 2019 -0400 +++ b/main.py Sat May 09 09:38:04 2020 +0000 @@ -8,6 +8,8 @@ import time # machine learning library +import tensorflow as tf +from keras import backend as K import keras.callbacks as callbacks import extract_workflow_connections @@ -18,78 +20,101 @@ class PredictTool: - @classmethod - def __init__(self): + def __init__(self, num_cpus): """ Init method. """ + # set the number of cpus + cpu_config = tf.ConfigProto( + device_count={"CPU": num_cpus}, + intra_op_parallelism_threads=num_cpus, + inter_op_parallelism_threads=num_cpus, + allow_soft_placement=True + ) + K.set_session(tf.Session(config=cpu_config)) - @classmethod - def find_train_best_network(self, network_config, reverse_dictionary, train_data, train_labels, test_data, test_labels, n_epochs, class_weights, usage_pred, compatible_next_tools): + def find_train_best_network(self, network_config, reverse_dictionary, train_data, train_labels, test_data, test_labels, n_epochs, class_weights, usage_pred, standard_connections, l_tool_freq, l_tool_tr_samples): """ Define recurrent neural network and train sequential data """ + # get tools with lowest representation + lowest_tool_ids = utils.get_lowest_tools(l_tool_freq) + print("Start hyperparameter optimisation...") hyper_opt = optimise_hyperparameters.HyperparameterOptimisation() - best_params = hyper_opt.train_model(network_config, reverse_dictionary, train_data, train_labels, test_data, test_labels, class_weights) - - # retrieve the model and train on complete dataset without validation set - model, best_params = utils.set_recurrent_network(best_params, reverse_dictionary, class_weights) + best_params, best_model = hyper_opt.train_model(network_config, reverse_dictionary, train_data, train_labels, test_data, test_labels, l_tool_tr_samples, class_weights) # define callbacks - predict_callback_test = PredictCallback(test_data, test_labels, reverse_dictionary, n_epochs, compatible_next_tools, usage_pred) - # tensor_board = callbacks.TensorBoard(log_dir=log_directory, histogram_freq=0, write_graph=True, write_images=True) - callbacks_list = [predict_callback_test] + early_stopping = callbacks.EarlyStopping(monitor='loss', mode='min', verbose=1, min_delta=1e-1, restore_best_weights=True) + predict_callback_test = PredictCallback(test_data, test_labels, reverse_dictionary, n_epochs, usage_pred, standard_connections, lowest_tool_ids) + + callbacks_list = [predict_callback_test, early_stopping] + + batch_size = int(best_params["batch_size"]) print("Start training on the best model...") - model_fit = model.fit( - train_data, - train_labels, - batch_size=int(best_params["batch_size"]), + train_performance = dict() + trained_model = best_model.fit_generator( + utils.balanced_sample_generator( + train_data, + train_labels, + batch_size, + l_tool_tr_samples + ), + steps_per_epoch=len(train_data) // batch_size, epochs=n_epochs, + callbacks=callbacks_list, + validation_data=(test_data, test_labels), verbose=2, - callbacks=callbacks_list, - shuffle="batch", - validation_data=(test_data, test_labels) + shuffle=True ) - - train_performance = { - "train_loss": np.array(model_fit.history["loss"]), - "model": model, - "best_parameters": best_params - } - - # if there is test data, add more information - if len(test_data) > 0: - train_performance["validation_loss"] = np.array(model_fit.history["val_loss"]) - train_performance["precision"] = predict_callback_test.precision - train_performance["usage_weights"] = predict_callback_test.usage_weights + train_performance["validation_loss"] = np.array(trained_model.history["val_loss"]) + train_performance["precision"] = predict_callback_test.precision + train_performance["usage_weights"] = predict_callback_test.usage_weights + train_performance["published_precision"] = predict_callback_test.published_precision + train_performance["lowest_pub_precision"] = predict_callback_test.lowest_pub_precision + train_performance["lowest_norm_precision"] = predict_callback_test.lowest_norm_precision + train_performance["train_loss"] = np.array(trained_model.history["loss"]) + train_performance["model"] = best_model + train_performance["best_parameters"] = best_params return train_performance class PredictCallback(callbacks.Callback): - def __init__(self, test_data, test_labels, reverse_data_dictionary, n_epochs, next_compatible_tools, usg_scores): + def __init__(self, test_data, test_labels, reverse_data_dictionary, n_epochs, usg_scores, standard_connections, lowest_tool_ids): self.test_data = test_data self.test_labels = test_labels self.reverse_data_dictionary = reverse_data_dictionary self.precision = list() self.usage_weights = list() + self.published_precision = list() self.n_epochs = n_epochs - self.next_compatible_tools = next_compatible_tools self.pred_usage_scores = usg_scores + self.standard_connections = standard_connections + self.lowest_tool_ids = lowest_tool_ids + self.lowest_pub_precision = list() + self.lowest_norm_precision = list() def on_epoch_end(self, epoch, logs={}): """ Compute absolute and compatible precision for test data """ if len(self.test_data) > 0: - precision, usage_weights = utils.verify_model(self.model, self.test_data, self.test_labels, self.reverse_data_dictionary, self.next_compatible_tools, self.pred_usage_scores) + usage_weights, precision, precision_pub, low_pub_prec, low_norm_prec, low_num = utils.verify_model(self.model, self.test_data, self.test_labels, self.reverse_data_dictionary, self.pred_usage_scores, self.standard_connections, self.lowest_tool_ids) self.precision.append(precision) self.usage_weights.append(usage_weights) - print("Epoch %d precision: %s" % (epoch + 1, precision)) + self.published_precision.append(precision_pub) + self.lowest_pub_precision.append(low_pub_prec) + self.lowest_norm_precision.append(low_norm_prec) print("Epoch %d usage weights: %s" % (epoch + 1, usage_weights)) + print("Epoch %d normal precision: %s" % (epoch + 1, precision)) + print("Epoch %d published precision: %s" % (epoch + 1, precision_pub)) + print("Epoch %d lowest published precision: %s" % (epoch + 1, low_pub_prec)) + print("Epoch %d lowest normal precision: %s" % (epoch + 1, low_norm_prec)) + print("Epoch %d number of test samples with lowest tool ids: %s" % (epoch + 1, low_num)) if __name__ == "__main__": start_time = time.time() + arg_parser = argparse.ArgumentParser() arg_parser.add_argument("-wf", "--workflow_file", required=True, help="workflows tabular file") arg_parser.add_argument("-tu", "--tool_usage_file", required=True, help="tool usage file") @@ -101,7 +126,6 @@ arg_parser.add_argument("-oe", "--optimize_n_epochs", required=True, help="number of iterations to run to find best model parameters") arg_parser.add_argument("-me", "--max_evals", required=True, help="maximum number of configuration evaluations") arg_parser.add_argument("-ts", "--test_share", required=True, help="share of data to be used for testing") - arg_parser.add_argument("-vs", "--validation_share", required=True, help="share of data to be used for validation") # neural network parameters arg_parser.add_argument("-bs", "--batch_size", required=True, help="size of the tranining batch i.e. the number of samples per batch") arg_parser.add_argument("-ut", "--units", required=True, help="number of hidden recurrent units") @@ -110,8 +134,7 @@ arg_parser.add_argument("-sd", "--spatial_dropout", required=True, help="1d dropout used for embedding layer") arg_parser.add_argument("-rd", "--recurrent_dropout", required=True, help="dropout for the recurrent layers") arg_parser.add_argument("-lr", "--learning_rate", required=True, help="learning rate") - arg_parser.add_argument("-ar", "--activation_recurrent", required=True, help="activation function for recurrent layers") - arg_parser.add_argument("-ao", "--activation_output", required=True, help="activation function for output layers") + # get argument values args = vars(arg_parser.parse_args()) tool_usage_path = args["tool_usage_file"] @@ -123,7 +146,6 @@ optimize_n_epochs = int(args["optimize_n_epochs"]) max_evals = int(args["max_evals"]) test_share = float(args["test_share"]) - validation_share = float(args["validation_share"]) batch_size = args["batch_size"] units = args["units"] embedding_size = args["embedding_size"] @@ -131,8 +153,7 @@ spatial_dropout = args["spatial_dropout"] recurrent_dropout = args["recurrent_dropout"] learning_rate = args["learning_rate"] - activation_recurrent = args["activation_recurrent"] - activation_output = args["activation_output"] + num_cpus = 16 config = { 'cutoff_date': cutoff_date, @@ -141,35 +162,28 @@ 'optimize_n_epochs': optimize_n_epochs, 'max_evals': max_evals, 'test_share': test_share, - 'validation_share': validation_share, 'batch_size': batch_size, 'units': units, 'embedding_size': embedding_size, 'dropout': dropout, 'spatial_dropout': spatial_dropout, 'recurrent_dropout': recurrent_dropout, - 'learning_rate': learning_rate, - 'activation_recurrent': activation_recurrent, - 'activation_output': activation_output + 'learning_rate': learning_rate } # Extract and process workflows connections = extract_workflow_connections.ExtractWorkflowConnections() - workflow_paths, compatible_next_tools = connections.read_tabular_file(workflows_path) + workflow_paths, compatible_next_tools, standard_connections = connections.read_tabular_file(workflows_path) # Process the paths from workflows print("Dividing data...") data = prepare_data.PrepareData(maximum_path_length, test_share) - train_data, train_labels, test_data, test_labels, data_dictionary, reverse_dictionary, class_weights, usage_pred = data.get_data_labels_matrices(workflow_paths, tool_usage_path, cutoff_date, compatible_next_tools) + train_data, train_labels, test_data, test_labels, data_dictionary, reverse_dictionary, class_weights, usage_pred, l_tool_freq, l_tool_tr_samples = data.get_data_labels_matrices(workflow_paths, tool_usage_path, cutoff_date, compatible_next_tools, standard_connections) # find the best model and start training - predict_tool = PredictTool() + predict_tool = PredictTool(num_cpus) # start training with weighted classes print("Training with weighted classes and samples ...") - results_weighted = predict_tool.find_train_best_network(config, reverse_dictionary, train_data, train_labels, test_data, test_labels, n_epochs, class_weights, usage_pred, compatible_next_tools) - print() - print("Best parameters \n") - print(results_weighted["best_parameters"]) - print() - utils.save_model(results_weighted, data_dictionary, compatible_next_tools, trained_model_path, class_weights) + results_weighted = predict_tool.find_train_best_network(config, reverse_dictionary, train_data, train_labels, test_data, test_labels, n_epochs, class_weights, usage_pred, standard_connections, l_tool_freq, l_tool_tr_samples) + utils.save_model(results_weighted, data_dictionary, compatible_next_tools, trained_model_path, class_weights, standard_connections) end_time = time.time() print() print("Program finished in %s seconds" % str(end_time - start_time))
--- a/optimise_hyperparameters.py Wed Sep 25 06:42:18 2019 -0400 +++ b/optimise_hyperparameters.py Sat May 09 09:38:04 2020 +0000 @@ -17,18 +17,13 @@ class HyperparameterOptimisation: - @classmethod def __init__(self): """ Init method. """ - @classmethod - def train_model(self, config, reverse_dictionary, train_data, train_labels, test_data, test_labels, class_weights): + def train_model(self, config, reverse_dictionary, train_data, train_labels, test_data, test_labels, l_tool_tr_samples, class_weights): """ Train a model and report accuracy """ - l_recurrent_activations = config["activation_recurrent"].split(",") - l_output_activations = config["activation_output"].split(",") - # convert items to integer l_batch_size = list(map(int, config["batch_size"].split(","))) l_embedding_size = list(map(int, config["embedding_size"].split(","))) @@ -41,20 +36,17 @@ l_recurrent_dropout = list(map(float, config["recurrent_dropout"].split(","))) optimize_n_epochs = int(config["optimize_n_epochs"]) - validation_split = float(config["validation_share"]) # get dimensions dimensions = len(reverse_dictionary) + 1 best_model_params = dict() - early_stopping = EarlyStopping(monitor='val_loss', mode='min', min_delta=1e-4, verbose=1, patience=1) + early_stopping = EarlyStopping(monitor='val_loss', mode='min', verbose=1, min_delta=1e-1, restore_best_weights=True) # specify the search space for finding the best combination of parameters using Bayesian optimisation params = { "embedding_size": hp.quniform("embedding_size", l_embedding_size[0], l_embedding_size[1], 1), "units": hp.quniform("units", l_units[0], l_units[1], 1), "batch_size": hp.quniform("batch_size", l_batch_size[0], l_batch_size[1], 1), - "activation_recurrent": hp.choice("activation_recurrent", l_recurrent_activations), - "activation_output": hp.choice("activation_output", l_output_activations), "learning_rate": hp.loguniform("learning_rate", np.log(l_learning_rate[0]), np.log(l_learning_rate[1])), "dropout": hp.uniform("dropout", l_dropout[0], l_dropout[1]), "spatial_dropout": hp.uniform("spatial_dropout", l_spatial_dropout[0], l_spatial_dropout[1]), @@ -65,35 +57,36 @@ model = Sequential() model.add(Embedding(dimensions, int(params["embedding_size"]), mask_zero=True)) model.add(SpatialDropout1D(params["spatial_dropout"])) - model.add(GRU(int(params["units"]), dropout=params["dropout"], recurrent_dropout=params["recurrent_dropout"], return_sequences=True, activation=params["activation_recurrent"])) + model.add(GRU(int(params["units"]), dropout=params["dropout"], recurrent_dropout=params["recurrent_dropout"], return_sequences=True, activation="elu")) + model.add(Dropout(params["dropout"])) + model.add(GRU(int(params["units"]), dropout=params["dropout"], recurrent_dropout=params["recurrent_dropout"], return_sequences=False, activation="elu")) model.add(Dropout(params["dropout"])) - model.add(GRU(int(params["units"]), dropout=params["dropout"], recurrent_dropout=params["recurrent_dropout"], return_sequences=False, activation=params["activation_recurrent"])) - model.add(Dropout(params["dropout"])) - model.add(Dense(dimensions, activation=params["activation_output"])) + model.add(Dense(2 * dimensions, activation="sigmoid")) optimizer_rms = RMSprop(lr=params["learning_rate"]) + batch_size = int(params["batch_size"]) model.compile(loss=utils.weighted_loss(class_weights), optimizer=optimizer_rms) - model_fit = model.fit( - train_data, - train_labels, - batch_size=int(params["batch_size"]), + print(model.summary()) + model_fit = model.fit_generator( + utils.balanced_sample_generator( + train_data, + train_labels, + batch_size, + l_tool_tr_samples + ), + steps_per_epoch=len(train_data) // batch_size, epochs=optimize_n_epochs, - shuffle="batch", + callbacks=[early_stopping], + validation_data=(test_data, test_labels), verbose=2, - validation_split=validation_split, - callbacks=[early_stopping] + shuffle=True ) - return {'loss': model_fit.history["val_loss"][-1], 'status': STATUS_OK} - # minimize the objective function using the set of parameters above4 + return {'loss': model_fit.history["val_loss"][-1], 'status': STATUS_OK, 'model': model} + # minimize the objective function using the set of parameters above trials = Trials() learned_params = fmin(create_model, params, trials=trials, algo=tpe.suggest, max_evals=int(config["max_evals"])) - print(learned_params) + best_model = trials.results[np.argmin([r['loss'] for r in trials.results])]['model'] # set the best params with respective values for item in learned_params: item_val = learned_params[item] - if item == 'activation_output': - best_model_params[item] = l_output_activations[item_val] - elif item == 'activation_recurrent': - best_model_params[item] = l_recurrent_activations[item_val] - else: - best_model_params[item] = item_val - return best_model_params + best_model_params[item] = item_val + return best_model_params, best_model
--- a/predict_tool_usage.py Wed Sep 25 06:42:18 2019 -0400 +++ b/predict_tool_usage.py Sat May 09 09:38:04 2020 +0000 @@ -21,11 +21,9 @@ class ToolPopularity: - @classmethod def __init__(self): """ Init method. """ - @classmethod def extract_tool_usage(self, tool_usage_file, cutoff_date, dictionary): """ Extract the tool usage over time for each tool @@ -63,7 +61,6 @@ tool_usage_dict[tool] = collections.OrderedDict(sorted(usage.items())) return tool_usage_dict - @classmethod def learn_tool_popularity(self, x_reshaped, y_reshaped): """ Fit a curve for the tool usage over time to predict future tool usage @@ -93,7 +90,6 @@ except Exception: return epsilon - @classmethod def get_pupularity_prediction(self, tools_usage): """ Get the popularity prediction for each tool
--- a/prepare_data.py Wed Sep 25 06:42:18 2019 -0400 +++ b/prepare_data.py Sat May 09 09:38:04 2020 +0000 @@ -10,19 +10,18 @@ import random import predict_tool_usage +import utils main_path = os.getcwd() class PrepareData: - @classmethod def __init__(self, max_seq_length, test_data_share): """ Init method. """ self.max_tool_sequence_len = max_seq_length self.test_share = test_data_share - @classmethod def process_workflow_paths(self, workflow_paths): """ Get all the tools and complete set of individual paths for each workflow @@ -40,7 +39,6 @@ tokens = np.reshape(tokens, [-1, ]) return tokens, raw_paths - @classmethod def create_new_dict(self, new_data_dict): """ Create new data dictionary @@ -48,7 +46,6 @@ reverse_dict = dict((v, k) for k, v in new_data_dict.items()) return new_data_dict, reverse_dict - @classmethod def assemble_dictionary(self, new_data_dict, old_data_dictionary={}): """ Create/update tools indices in the forward and backward dictionary @@ -56,7 +53,6 @@ new_data_dict, reverse_dict = self.create_new_dict(new_data_dict) return new_data_dict, reverse_dict - @classmethod def create_data_dictionary(self, words, old_data_dictionary={}): """ Create two dictionaries having tools names and their indexes @@ -68,7 +64,6 @@ dictionary, reverse_dictionary = self.assemble_dictionary(dictionary, old_data_dictionary) return dictionary, reverse_dictionary - @classmethod def decompose_paths(self, paths, dictionary): """ Decompose the paths to variable length sub-paths keeping the first tool fixed @@ -86,7 +81,6 @@ sub_paths_pos = list(set(sub_paths_pos)) return sub_paths_pos - @classmethod def prepare_paths_labels_dictionary(self, dictionary, reverse_dictionary, paths, compatible_next_tools): """ Create a dictionary of sequences with their labels for training and test paths @@ -116,8 +110,7 @@ paths_labels[item] = ",".join(list(set(paths_labels[item].split(",")))) return paths_labels - @classmethod - def pad_paths(self, paths_dictionary, num_classes): + def pad_test_paths(self, paths_dictionary, num_classes): """ Add padding to the tools sequences and create multi-hot encoded labels """ @@ -135,7 +128,35 @@ train_counter += 1 return data_mat, label_mat - @classmethod + def pad_paths(self, paths_dictionary, num_classes, standard_connections, reverse_dictionary): + """ + Add padding to the tools sequences and create multi-hot encoded labels + """ + size_data = len(paths_dictionary) + data_mat = np.zeros([size_data, self.max_tool_sequence_len]) + label_mat = np.zeros([size_data, 2 * (num_classes + 1)]) + pos_flag = 1.0 + train_counter = 0 + for train_seq, train_label in list(paths_dictionary.items()): + pub_connections = list() + positions = train_seq.split(",") + last_tool_id = positions[-1] + last_tool_name = reverse_dictionary[int(last_tool_id)] + start_pos = self.max_tool_sequence_len - len(positions) + for id_pos, pos in enumerate(positions): + data_mat[train_counter][start_pos + id_pos] = int(pos) + if last_tool_name in standard_connections: + pub_connections = standard_connections[last_tool_name] + for label_item in train_label.split(","): + label_pos = int(label_item) + label_row = label_mat[train_counter] + if reverse_dictionary[label_pos] in pub_connections: + label_row[label_pos] = pos_flag + else: + label_row[label_pos + num_classes + 1] = pos_flag + train_counter += 1 + return data_mat, label_mat + def split_test_train_data(self, multilabels_paths): """ Split into test and train data randomly for each run @@ -152,15 +173,6 @@ train_dict[path] = multilabels_paths[path] return train_dict, test_dict - @classmethod - def verify_overlap(self, train_paths, test_paths): - """ - Verify the overlapping of samples in train and test data - """ - intersection = list(set(train_paths).intersection(set(test_paths))) - print("Overlap in train and test: %d" % len(intersection)) - - @classmethod def get_predicted_usage(self, data_dictionary, predicted_usage): """ Get predicted usage for tools @@ -180,43 +192,53 @@ continue return usage - @classmethod def assign_class_weights(self, n_classes, predicted_usage): """ Compute class weights using usage """ class_weights = dict() class_weights[str(0)] = 0.0 - for key in range(1, n_classes): + for key in range(1, n_classes + 1): u_score = predicted_usage[key] if u_score < 1.0: u_score += 1.0 - class_weights[key] = np.log(u_score) + class_weights[key] = np.round(np.log(u_score), 6) return class_weights - @classmethod - def get_sample_weights(self, train_data, reverse_dictionary, paths_frequency): + def get_train_last_tool_freq(self, train_paths, reverse_dictionary): """ - Compute the frequency of paths in training data + Get the frequency of last tool of each tool sequence + to estimate the frequency of tool sequences """ - path_weights = np.zeros(len(train_data)) - for path_index, path in enumerate(train_data): - sample_pos = np.where(path > 0)[0] - sample_tool_pos = path[sample_pos[0]:] - path_name = ",".join([reverse_dictionary[int(tool_pos)] for tool_pos in sample_tool_pos]) - try: - path_weights[path_index] = int(paths_frequency[path_name]) - except Exception: - path_weights[path_index] = 1 - return path_weights + last_tool_freq = dict() + inv_freq = dict() + for path in train_paths: + last_tool = path.split(",")[-1] + if last_tool not in last_tool_freq: + last_tool_freq[last_tool] = 0 + last_tool_freq[last_tool] += 1 + max_freq = max(last_tool_freq.values()) + for t in last_tool_freq: + inv_freq[t] = int(np.round(max_freq / float(last_tool_freq[t]), 0)) + return last_tool_freq, inv_freq - @classmethod - def get_data_labels_matrices(self, workflow_paths, tool_usage_path, cutoff_date, compatible_next_tools, old_data_dictionary={}): + def get_toolid_samples(self, train_data, l_tool_freq): + l_tool_tr_samples = dict() + for tool_id in l_tool_freq: + for index, tr_sample in enumerate(train_data): + last_tool_id = str(int(tr_sample[-1])) + if last_tool_id == tool_id: + if last_tool_id not in l_tool_tr_samples: + l_tool_tr_samples[last_tool_id] = list() + l_tool_tr_samples[last_tool_id].append(index) + return l_tool_tr_samples + + def get_data_labels_matrices(self, workflow_paths, tool_usage_path, cutoff_date, compatible_next_tools, standard_connections, old_data_dictionary={}): """ Convert the training and test paths into corresponding numpy matrices """ processed_data, raw_paths = self.process_workflow_paths(workflow_paths) - dictionary, reverse_dictionary = self.create_data_dictionary(processed_data, old_data_dictionary) + dictionary, rev_dict = self.create_data_dictionary(processed_data, old_data_dictionary) num_classes = len(dictionary) print("Raw paths: %d" % len(raw_paths)) @@ -227,25 +249,32 @@ random.shuffle(all_unique_paths) print("Creating dictionaries...") - multilabels_paths = self.prepare_paths_labels_dictionary(dictionary, reverse_dictionary, all_unique_paths, compatible_next_tools) + multilabels_paths = self.prepare_paths_labels_dictionary(dictionary, rev_dict, all_unique_paths, compatible_next_tools) print("Complete data: %d" % len(multilabels_paths)) train_paths_dict, test_paths_dict = self.split_test_train_data(multilabels_paths) + # get sample frequency + l_tool_freq, inv_last_tool_freq = self.get_train_last_tool_freq(train_paths_dict, rev_dict) + print("Train data: %d" % len(train_paths_dict)) print("Test data: %d" % len(test_paths_dict)) - test_data, test_labels = self.pad_paths(test_paths_dict, num_classes) - train_data, train_labels = self.pad_paths(train_paths_dict, num_classes) + print("Padding train and test data...") + # pad training and test data with leading zeros + test_data, test_labels = self.pad_paths(test_paths_dict, num_classes, standard_connections, rev_dict) + train_data, train_labels = self.pad_paths(train_paths_dict, num_classes, standard_connections, rev_dict) + + l_tool_tr_samples = self.get_toolid_samples(train_data, l_tool_freq) # Predict tools usage print("Predicting tools' usage...") usage_pred = predict_tool_usage.ToolPopularity() usage = usage_pred.extract_tool_usage(tool_usage_path, cutoff_date, dictionary) tool_usage_prediction = usage_pred.get_pupularity_prediction(usage) - tool_predicted_usage = self.get_predicted_usage(dictionary, tool_usage_prediction) + t_pred_usage = self.get_predicted_usage(dictionary, tool_usage_prediction) # get class weights using the predicted usage for each tool - class_weights = self.assign_class_weights(train_labels.shape[1], tool_predicted_usage) + class_weights = self.assign_class_weights(num_classes, t_pred_usage) - return train_data, train_labels, test_data, test_labels, dictionary, reverse_dictionary, class_weights, tool_predicted_usage + return train_data, train_labels, test_data, test_labels, dictionary, rev_dict, class_weights, t_pred_usage, l_tool_freq, l_tool_tr_samples
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-29 2013-02-14 17:12:00 266 Show beginning1 1.0.0 259 Extract genomic DNA 1 2.2.2 -29 2013-02-14 17:12:00 265 trap 260 -29 2013-02-14 17:12:00 263 Show beginning1 1.0.0 261 Extract genomic DNA 1 2.2.2 -29 2013-02-14 17:12:00 264 meme_meme 1.0.0 263 Show beginning1 1.0.0 -31 2013-02-18 11:33:00 275 addValue 1.0.0 274 -31 2013-02-18 11:33:00 276 mergeCols1 1.0.1 275 addValue 1.0.0 -33 2013-02-16 18:11:00 284 gops_intersect_1 1.0.0 283 -33 2013-02-16 18:11:00 284 gops_intersect_1 1.0.0 285 -33 2013-02-16 18:11:00 287 barchart_gnuplot 1.0.0 286 Count1 1.0.0 -34 2013-02-18 11:26:00 289 cshl_awk_tool 1.0.0 288 -36 2013-02-18 11:32:00 292 cshl_awk_tool 1.0.0 293 -38 2013-02-18 15:28:00 298 barchart_gnuplot 297 Count1 -39 2013-02-18 15:29:00 302 Count1 301 gops_intersect_1 -39 2013-02-18 15:29:00 303 barchart_gnuplot 302 Count1 -41 2013-02-18 15:36:00 310 gops_intersect_1 1.0.0 309 -41 2013-02-18 15:36:00 312 Count1 1.0.0 310 gops_intersect_1 1.0.0 -41 2013-02-18 15:36:00 310 gops_intersect_1 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446 Count1 1.0.0 -81 2013-02-18 16:22:00 466 addValue 1.0.0 465 -81 2013-02-18 16:22:00 468 Cut1 1.0.1 467 mergeCols1 1.0.1 -81 2013-02-18 16:22:00 474 barchart_gnuplot 1.0.0 473 Count1 1.0.0 -82 2013-02-18 16:22:00 477 addValue 1.0.0 476 CONVERTER_interval_to_bedstrict_0 1.0.0 -82 2013-02-18 16:22:00 478 mergeCols1 1.0.1 477 addValue 1.0.0 -82 2013-02-18 16:22:00 483 gops_intersect_1 1.0.0 482 get_flanks1 1.0.0 -82 2013-02-18 16:22:00 483 gops_intersect_1 1.0.0 484 cshl_find_and_replace 1.0.0 -82 2013-02-18 16:22:00 485 CONVERTER_interval_to_bed_0 1.0.0 484 cshl_find_and_replace 1.0.0 -82 2013-02-18 16:22:00 488 barchart_gnuplot 1.0.0 487 Count1 1.0.0 -83 2013-02-18 19:10:00 492 Count1 1.0.0 490 gops_intersect_1 1.0.0 -86 2013-02-19 12:08:00 505 gops_intersect_1 1.0.0 504 -86 2013-02-19 12:08:00 505 gops_intersect_1 1.0.0 506 -86 2013-02-19 12:08:00 508 barchart_gnuplot 1.0.0 507 Count1 1.0.0 -95 2013-02-20 10:03:00 672 gops_intersect_1 1.0.0 671 -95 2013-02-20 10:03:00 672 gops_intersect_1 1.0.0 673 -97 2013-02-20 10:11:00 701 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 1.4.1 700 -97 2013-02-20 10:11:00 701 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 1.4.1 702 -97 2013-02-20 10:11:00 708 gops_intersect_1 1.0.0 703 cshl_awk_tool 1.0.0 -97 2013-02-20 10:11:00 711 Extract genomic DNA 1 2.2.2 704 gops_subtract_1 1.0.0 -97 2013-02-20 10:11:00 708 gops_intersect_1 1.0.0 705 cshl_awk_tool 1.0.0 -97 2013-02-20 10:11:00 706 get_flanks1 1.0.0 707 -97 2013-02-20 10:11:00 711 Extract genomic DNA 1 2.2.2 710 -97 2013-02-20 10:11:00 714 tab2fasta 1.1.0 713 Show beginning1 1.0.0 -97 2013-02-20 10:11:00 715 meme_meme 1.0.0 714 tab2fasta 1.1.0 -97 2013-02-20 10:11:00 717 Show beginning1 1.0.0 716 fasta2tab 1.1.0 -97 2013-02-20 10:11:00 718 tab2fasta 1.1.0 717 Show beginning1 1.0.0 -97 2013-02-20 10:11:00 721 barchart_gnuplot 1.0.0 720 Count1 1.0.0 -98 2013-02-20 10:44:00 726 mergeCols1 1.0.1 725 addValue 1.0.0 -100 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beginning1 890 fasta2tab -109 2013-02-20 15:49:00 892 tab2fasta 891 Show beginning1 -109 2013-02-20 15:49:00 893 meme_meme 892 tab2fasta -110 2013-02-20 15:54:00 897 cshl_awk_tool 1.0.0 895 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 1.4.1 -110 2013-02-20 15:54:00 901 gops_subtract_1 1.0.0 900 -110 2013-02-20 15:54:00 901 gops_subtract_1 1.0.0 902 get_flanks1 1.0.0 -110 2013-02-20 15:54:00 902 get_flanks1 1.0.0 903 -110 2013-02-20 15:54:00 905 Extract genomic DNA 1 2.2.2 904 gops_intersect_1 1.0.0 -110 2013-02-20 15:54:00 911 Count1 1.0.0 904 gops_intersect_1 1.0.0 -110 2013-02-20 15:54:00 907 fasta2tab 1.1.0 905 Extract genomic DNA 1 2.2.2 -110 2013-02-20 15:54:00 905 Extract genomic DNA 1 2.2.2 906 -110 2013-02-20 15:54:00 909 tab2fasta 1.1.0 908 Show beginning1 1.0.0 -110 2013-02-20 15:54:00 910 meme_meme 1.0.0 909 tab2fasta 1.1.0 -110 2013-02-20 15:54:00 912 barchart_gnuplot 1.0.0 911 Count1 1.0.0 -110 2013-02-20 15:54:00 914 barchart_gnuplot 1.0.0 913 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15:52:00 971 gops_subtract_1 967 -113 2013-02-20 15:52:00 968 gops_intersect_1 969 get_flanks1 -113 2013-02-20 15:52:00 971 gops_subtract_1 969 get_flanks1 -113 2013-02-20 15:52:00 969 get_flanks1 970 -113 2013-02-20 15:52:00 979 fasta2tab 977 Extract genomic DNA 1 -114 2013-02-20 15:58:00 985 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 984 -114 2013-02-20 15:58:00 987 cshl_awk_tool 985 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 -114 2013-02-20 15:58:00 985 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 986 -114 2013-02-20 15:58:00 991 gops_intersect_1 990 -114 2013-02-20 15:58:00 995 gops_subtract_1 990 -114 2013-02-20 15:58:00 998 Extract genomic DNA 1 991 gops_intersect_1 -114 2013-02-20 15:58:00 991 gops_intersect_1 992 get_flanks1 -114 2013-02-20 15:58:00 995 gops_subtract_1 992 get_flanks1 -114 2013-02-20 15:58:00 997 barchart_gnuplot 996 Count1 -114 2013-02-20 15:58:00 1000 fasta2tab 998 Extract genomic DNA 1 -114 2013-02-20 15:58:00 998 Extract genomic DNA 1 999 -114 2013-02-20 15:58:00 1001 Show beginning1 1000 fasta2tab -114 2013-02-20 15:58:00 1002 tab2fasta 1001 Show beginning1 -115 2013-02-20 16:00:00 1006 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 1.4.1 1005 -115 2013-02-20 16:00:00 1006 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 1.4.1 1007 -115 2013-02-20 16:00:00 1009 gops_subtract_1 1.0.0 1008 cshl_awk_tool 1.0.0 -115 2013-02-20 16:00:00 1027 Count1 1.0.0 1009 gops_subtract_1 1.0.0 -115 2013-02-20 16:00:00 1009 gops_subtract_1 1.0.0 1010 cshl_awk_tool 1.0.0 -115 2013-02-20 16:00:00 1011 get_flanks1 1.0.0 1012 -115 2013-02-20 16:00:00 1025 Count1 1.0.0 1013 gops_intersect_1 1.0.0 -115 2013-02-20 16:00:00 1021 fasta2tab 1.1.0 1014 Extract genomic DNA 1 2.2.2 -115 2013-02-20 16:00:00 1017 fasta2tab 1.1.0 1016 Extract genomic DNA 1 2.2.2 -115 2013-02-20 16:00:00 1019 tab2fasta 1.1.0 1018 Show beginning1 1.0.0 -115 2013-02-20 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Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11464 cat1 1.0.0 11483 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11464 cat1 1.0.0 11484 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11464 cat1 1.0.0 11485 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11464 cat1 1.0.0 11486 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11464 cat1 1.0.0 11487 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11363 cat1 1.0.0 11488 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11343 heatmapper 1.3 11491 Filter1 1.1.0 -577 2013-10-21 10:42:00 11369 heatmapper 1.3 11492 Filter1 1.1.0 -577 2013-10-21 10:42:00 11341 heatmapper 1.3 11493 Filter1 1.1.0 -577 2013-10-21 10:42:00 11379 heatmapper 1.3 11494 Filter1 1.1.0 -577 2013-10-21 10:42:00 11368 heatmapper 1.3 11495 Filter1 1.1.0 -577 2013-10-21 10:42:00 11381 heatmapper 1.3 11496 Filter1 1.1.0 -577 2013-10-21 10:42:00 11378 heatmapper 1.3 11497 Filter1 1.1.0 -577 2013-10-21 10:42:00 11375 heatmapper 1.3 11498 Filter1 1.1.0 -577 2013-10-21 10:42:00 11479 Cut1 1.0.2 11502 cat1 1.0.0 -577 2013-10-21 10:42:00 11511 Remove beginning1 1.0.0 11504 heatmapper 1.3 -577 2013-10-21 10:42:00 11480 Remove beginning1 1.0.0 11506 heatmapper 1.3 -577 2013-10-21 10:42:00 11395 Remove beginning1 1.0.0 11508 heatmapper 1.3 -577 2013-10-21 10:42:00 11414 Remove beginning1 1.0.0 11510 heatmapper 1.3 -577 2013-10-21 10:42:00 11291 Remove_ending 1.0.0 11511 Remove beginning1 1.0.0 -577 2013-10-21 10:42:00 11531 Remove_ending 1.0.0 11512 Remove beginning1 1.0.0 -577 2013-10-21 10:42:00 11251 Remove_ending 1.0.0 11514 Remove beginning1 1.0.0 -577 2013-10-21 10:42:00 11265 heatmapper 1.3 11515 Filter1 1.1.0 -577 2013-10-21 10:42:00 11266 heatmapper 1.3 11516 Filter1 1.1.0 -577 2013-10-21 10:42:00 11261 heatmapper 1.3 11517 Filter1 1.1.0 -577 2013-10-21 10:42:00 11262 heatmapper 1.3 11518 Filter1 1.1.0 -577 2013-10-21 10:42:00 11263 heatmapper 1.3 11519 Filter1 1.1.0 -577 2013-10-21 10:42:00 11264 heatmapper 1.3 11520 Filter1 1.1.0 -577 2013-10-21 10:42:00 11257 heatmapper 1.3 11521 Filter1 1.1.0 -577 2013-10-21 10:42:00 11258 heatmapper 1.3 11522 Filter1 1.1.0 -577 2013-10-21 10:42:00 11510 heatmapper 1.3 11524 Filter1 1.1.0 -577 2013-10-21 10:42:00 11523 cat1 1.0.0 11526 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11475 cat1 1.0.0 11527 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11523 cat1 1.0.0 11528 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11363 cat1 1.0.0 11529 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11523 cat1 1.0.0 11530 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11523 cat1 1.0.0 11532 Remove_ending 1.0.0 -577 2013-10-21 10:42:00 11257 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11258 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11259 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11261 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11262 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11263 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11264 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11265 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11266 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11290 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11293 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11294 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11300 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11301 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11302 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11306 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11337 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11341 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11342 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11343 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11349 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11368 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11369 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11374 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11375 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11376 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11377 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11378 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11379 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11381 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11409 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11435 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11444 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11445 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11447 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11448 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11459 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11503 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11505 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11506 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11507 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11508 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11510 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11533 heatmapper 1.3 11536 -577 2013-10-21 10:42:00 11275 cshl_word_list_grep 1.0.0 11537 -577 2013-10-21 10:42:00 11455 cshl_word_list_grep 1.0.0 11537 -577 2013-10-21 10:42:00 11457 cshl_word_list_grep 1.0.0 11537 -577 2013-10-21 10:42:00 11281 Filter1 1.1.0 11538 -577 2013-10-21 10:42:00 11283 Filter1 1.1.0 11538 -577 2013-10-21 10:42:00 11361 Filter1 1.1.0 11538 -577 2013-10-21 10:42:00 11426 Filter1 1.1.0 11538 -578 2013-10-21 10:57:00 11798 cat1 1.0.0 11540 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11798 cat1 1.0.0 11541 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11798 cat1 1.0.0 11542 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11798 cat1 1.0.0 11543 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11798 cat1 1.0.0 11544 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11798 cat1 1.0.0 11545 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11798 cat1 1.0.0 11546 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11798 cat1 1.0.0 11547 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11617 cat1 1.0.0 11549 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11617 cat1 1.0.0 11550 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11798 cat1 1.0.0 11551 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11659 cat1 1.0.0 11552 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11625 Remove beginning1 1.0.0 11554 heatmapper 1.3 -578 2013-10-21 10:57:00 11631 Remove beginning1 1.0.0 11556 heatmapper 1.3 -578 2013-10-21 10:57:00 11621 Remove beginning1 1.0.0 11557 heatmapper 1.3 -578 2013-10-21 10:57:00 11634 heatmapper 1.3 11565 Filter1 1.1.0 -578 2013-10-21 10:57:00 11635 heatmapper 1.3 11566 Filter1 1.1.0 -578 2013-10-21 10:57:00 11603 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11604 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11605 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11607 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11611 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11612 Filter1 1.1.0 11568 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11695 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11697 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11698 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11699 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11700 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11701 Filter1 1.1.0 11569 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11703 Filter1 1.1.0 11570 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11811 Filter1 1.1.0 11570 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11812 Filter1 1.1.0 11570 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11813 Filter1 1.1.0 11570 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11816 Filter1 1.1.0 11570 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11643 Filter1 1.1.0 11571 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11820 Filter1 1.1.0 11571 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11821 Filter1 1.1.0 11571 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11711 Remove_ending 1.0.0 11572 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11618 Paste1 1.0.0 11576 Paste1 1.0.0 -578 2013-10-21 10:57:00 11712 Remove_ending 1.0.0 11580 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11661 Remove_ending 1.0.0 11581 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11616 Paste1 1.0.0 11583 Cut1 1.0.2 -578 2013-10-21 10:57:00 11618 Paste1 1.0.0 11584 Cut1 1.0.2 -578 2013-10-21 10:57:00 11576 Paste1 1.0.0 11585 Paste1 1.0.0 -578 2013-10-21 10:57:00 11713 Remove beginning1 1.0.0 11586 heatmapper 1.3 -578 2013-10-21 10:57:00 11617 cat1 1.0.0 11587 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11716 Remove beginning1 1.0.0 11589 heatmapper 1.3 -578 2013-10-21 10:57:00 11724 Remove beginning1 1.0.0 11593 heatmapper 1.3 -578 2013-10-21 10:57:00 11720 Remove beginning1 1.0.0 11594 heatmapper 1.3 -578 2013-10-21 10:57:00 11628 Remove beginning1 1.0.0 11598 heatmapper 1.3 -578 2013-10-21 10:57:00 11617 cat1 1.0.0 11599 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11617 cat1 1.0.0 11600 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11735 Remove_ending 1.0.0 11601 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11602 heatmapper 1.3 11608 Filter1 1.1.0 -578 2013-10-21 10:57:00 11633 heatmapper 1.3 11609 Filter1 1.1.0 -578 2013-10-21 10:57:00 11616 Paste1 1.0.0 11618 Paste1 1.0.0 -578 2013-10-21 10:57:00 11652 Remove_ending 1.0.0 11619 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11822 Remove_ending 1.0.0 11620 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11650 Remove_ending 1.0.0 11625 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11714 Remove_ending 1.0.0 11628 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11690 Remove_ending 1.0.0 11629 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11660 Remove_ending 1.0.0 11630 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11656 Remove_ending 1.0.0 11631 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11655 Remove beginning1 1.0.0 11632 heatmapper 1.3 -578 2013-10-21 10:57:00 11693 Remove beginning1 1.0.0 11633 heatmapper 1.3 -578 2013-10-21 10:57:00 11762 Remove beginning1 1.0.0 11635 heatmapper 1.3 -578 2013-10-21 10:57:00 11705 heatmapper 1.3 11639 heatmapper 1.3 -578 2013-10-21 10:57:00 11801 heatmapper 1.3 11640 Filter1 1.1.0 -578 2013-10-21 10:57:00 11802 heatmapper 1.3 11641 Filter1 1.1.0 -578 2013-10-21 10:57:00 11803 heatmapper 1.3 11642 Filter1 1.1.0 -578 2013-10-21 10:57:00 11804 heatmapper 1.3 11643 Filter1 1.1.0 -578 2013-10-21 10:57:00 11809 Remove beginning1 1.0.0 11645 heatmapper 1.3 -578 2013-10-21 10:57:00 11799 heatmapper 1.3 11646 Filter1 1.1.0 -578 2013-10-21 10:57:00 11828 Remove_ending 1.0.0 11649 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11659 cat1 1.0.0 11652 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11750 Cut1 1.0.2 11657 Filter1 1.1.0 -578 2013-10-21 10:57:00 11785 Cut1 1.0.2 11659 cat1 1.0.0 -578 2013-10-21 10:57:00 11659 cat1 1.0.0 11661 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11734 Remove beginning1 1.0.0 11664 heatmapper 1.3 -578 2013-10-21 10:57:00 11709 Remove beginning1 1.0.0 11665 heatmapper 1.3 -578 2013-10-21 10:57:00 11581 Remove beginning1 1.0.0 11670 heatmapper 1.3 -578 2013-10-21 10:57:00 11672 heatmapper 1.3 11684 Filter1 1.1.0 -578 2013-10-21 10:57:00 11732 heatmapper 1.3 11686 Filter1 1.1.0 -578 2013-10-21 10:57:00 11743 heatmapper 1.3 11687 Filter1 1.1.0 -578 2013-10-21 10:57:00 11576 Paste1 1.0.0 11689 Cut1 1.0.2 -578 2013-10-21 10:57:00 11659 cat1 1.0.0 11692 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11773 Remove_ending 1.0.0 11693 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11592 heatmapper 1.3 11695 Filter1 1.1.0 -578 2013-10-21 10:57:00 11598 heatmapper 1.3 11701 Filter1 1.1.0 -578 2013-10-21 10:57:00 11556 heatmapper 1.3 11702 Filter1 1.1.0 -578 2013-10-21 10:57:00 11555 heatmapper 1.3 11703 Filter1 1.1.0 -578 2013-10-21 10:57:00 11779 Remove_ending 1.0.0 11704 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11777 Remove_ending 1.0.0 11706 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11550 Remove_ending 1.0.0 11710 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11659 cat1 1.0.0 11711 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11617 cat1 1.0.0 11712 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11663 Remove_ending 1.0.0 11716 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11662 Remove_ending 1.0.0 11717 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11669 Remove_ending 1.0.0 11718 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11659 cat1 1.0.0 11723 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11756 Remove_ending 1.0.0 11725 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11648 Remove_ending 1.0.0 11726 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11588 Remove_ending 1.0.0 11728 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11659 cat1 1.0.0 11729 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11572 Remove beginning1 1.0.0 11731 heatmapper 1.3 -578 2013-10-21 10:57:00 11761 Remove beginning1 1.0.0 11738 heatmapper 1.3 -578 2013-10-21 10:57:00 11768 Remove beginning1 1.0.0 11741 heatmapper 1.3 -578 2013-10-21 10:57:00 11765 Remove beginning1 1.0.0 11742 heatmapper 1.3 -578 2013-10-21 10:57:00 11770 Remove beginning1 1.0.0 11743 heatmapper 1.3 -578 2013-10-21 10:57:00 11767 Remove beginning1 1.0.0 11744 heatmapper 1.3 -578 2013-10-21 10:57:00 11751 cshl_word_list_grep 1.0.0 11746 Cut1 1.0.2 -578 2013-10-21 10:57:00 11753 cshl_word_list_grep 1.0.0 11748 Cut1 1.0.2 -578 2013-10-21 10:57:00 11569 cshl_word_list_grep 1.0.0 11750 Cut1 1.0.2 -578 2013-10-21 10:57:00 11564 Filter1 1.1.0 11751 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11681 Filter1 1.1.0 11751 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11682 Filter1 1.1.0 11751 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11683 Filter1 1.1.0 11751 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11610 Filter1 1.1.0 11753 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11788 Filter1 1.1.0 11753 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11790 Filter1 1.1.0 11753 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11791 Filter1 1.1.0 11753 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11793 Filter1 1.1.0 11753 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11678 Filter1 1.1.0 11754 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11679 Filter1 1.1.0 11754 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11680 Filter1 1.1.0 11754 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11684 Filter1 1.1.0 11754 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11686 Filter1 1.1.0 11754 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11687 Filter1 1.1.0 11754 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11794 Filter1 1.1.0 11754 cshl_word_list_grep 1.0.0 -578 2013-10-21 10:57:00 11622 Remove beginning1 1.0.0 11755 heatmapper 1.3 -578 2013-10-21 10:57:00 11627 Remove beginning1 1.0.0 11757 heatmapper 1.3 -578 2013-10-21 10:57:00 11545 Remove_ending 1.0.0 11761 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11544 Remove_ending 1.0.0 11762 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11543 Remove_ending 1.0.0 11763 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11542 Remove_ending 1.0.0 11764 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11541 Remove_ending 1.0.0 11765 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11552 Remove_ending 1.0.0 11767 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11583 Cut1 1.0.2 11771 cat1 1.0.0 -578 2013-10-21 10:57:00 11585 Paste1 1.0.0 11775 Cut1 1.0.2 -578 2013-10-21 10:57:00 11599 Remove_ending 1.0.0 11776 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11758 Remove_ending 1.0.0 11778 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11659 cat1 1.0.0 11784 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11585 Paste1 1.0.0 11785 Cut1 1.0.2 -578 2013-10-21 10:57:00 11664 heatmapper 1.3 11791 Filter1 1.1.0 -578 2013-10-21 10:57:00 11677 heatmapper 1.3 11792 Filter1 1.1.0 -578 2013-10-21 10:57:00 11674 heatmapper 1.3 11793 Filter1 1.1.0 -578 2013-10-21 10:57:00 11671 heatmapper 1.3 11794 Filter1 1.1.0 -578 2013-10-21 10:57:00 11676 heatmapper 1.3 11795 Filter1 1.1.0 -578 2013-10-21 10:57:00 11748 Cut1 1.0.2 11796 Filter1 1.1.0 -578 2013-10-21 10:57:00 11752 Cut1 1.0.2 11797 Filter1 1.1.0 -578 2013-10-21 10:57:00 11775 Cut1 1.0.2 11798 cat1 1.0.0 -578 2013-10-21 10:57:00 11808 Remove beginning1 1.0.0 11799 heatmapper 1.3 -578 2013-10-21 10:57:00 11710 Remove beginning1 1.0.0 11806 heatmapper 1.3 -578 2013-10-21 10:57:00 11827 Remove_ending 1.0.0 11808 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11547 Remove_ending 1.0.0 11810 Remove beginning1 1.0.0 -578 2013-10-21 10:57:00 11561 heatmapper 1.3 11811 Filter1 1.1.0 -578 2013-10-21 10:57:00 11562 heatmapper 1.3 11812 Filter1 1.1.0 -578 2013-10-21 10:57:00 11557 heatmapper 1.3 11813 Filter1 1.1.0 -578 2013-10-21 10:57:00 11558 heatmapper 1.3 11814 Filter1 1.1.0 -578 2013-10-21 10:57:00 11560 heatmapper 1.3 11816 Filter1 1.1.0 -578 2013-10-21 10:57:00 11553 heatmapper 1.3 11817 Filter1 1.1.0 -578 2013-10-21 10:57:00 11554 heatmapper 1.3 11818 Filter1 1.1.0 -578 2013-10-21 10:57:00 11582 Cut1 1.0.2 11819 cat1 1.0.0 -578 2013-10-21 10:57:00 11805 heatmapper 1.3 11821 Filter1 1.1.0 -578 2013-10-21 10:57:00 11659 cat1 1.0.0 11825 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11617 cat1 1.0.0 11827 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11580 Remove beginning1 1.0.0 11829 heatmapper 1.3 -578 2013-10-21 10:57:00 11617 cat1 1.0.0 11830 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11617 cat1 1.0.0 11831 Remove_ending 1.0.0 -578 2013-10-21 10:57:00 11553 heatmapper 1.3 11832 -578 2013-10-21 10:57:00 11554 heatmapper 1.3 11832 -578 2013-10-21 10:57:00 11555 heatmapper 1.3 11832 -578 2013-10-21 10:57:00 11556 heatmapper 1.3 11832 -578 2013-10-21 10:57:00 11557 heatmapper 1.3 11832 -578 2013-10-21 10:57:00 11558 heatmapper 1.3 11832 -578 2013-10-21 10:57:00 11560 heatmapper 1.3 11832 -578 2013-10-21 10:57:00 11561 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85 addValue 1.0.0 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 85 addValue 1.0.0 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 85 addValue 1.0.0 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 85 addValue 1.0.0 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 85 addValue 1.0.0 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 85 addValue 1.0.0 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 85 addValue 1.0.0 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 85 addValue 1.0.0 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 t f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f t f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 86 Cut1 1.0.1 88 Paste1 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 t f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f t f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 88 Paste1 1.0.0 87 addValue 1.0.0 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 t f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f t f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +9 2013-02-07 16:59:41.215802 89 82 Grep1 1.0.1 f f f +11 2013-02-07 17:03:54.795316 135 addValue 1.0.0 136 cat1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 136 cat1 1.0.0 145 barchart_gnuplot 1.0.0 f t f +11 2013-02-07 17:03:54.795316 137 Cut1 1.0.1 170 Paste1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 138 Cut1 1.0.1 170 Paste1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 139 Cut1 1.0.1 177 Paste1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 140 Cut1 1.0.1 177 Paste1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 141 Cut1 1.0.1 147 Paste1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 142 Cut1 1.0.1 147 Paste1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 143 Cut1 1.0.1 171 Paste1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 144 Cut1 1.0.1 171 Paste1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 146 Paste1 1.0.0 176 Add_a_column1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 147 Paste1 1.0.0 175 Add_a_column1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 148 addValue 1.0.0 136 cat1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 149 addValue 1.0.0 136 cat1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 150 Filter1 1.1.0 157 Summary_Statistics1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 150 Filter1 1.1.0 156 Summary_Statistics1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 151 gops_coverage_1 1.0.0 155 Filter1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 151 gops_coverage_1 1.0.0 154 Filter1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 151 gops_coverage_1 1.0.0 153 Filter1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 151 gops_coverage_1 1.0.0 152 cshl_grep_tool 1.0.0 f t f +11 2013-02-07 17:03:54.795316 151 gops_coverage_1 1.0.0 150 Filter1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 152 cshl_grep_tool 1.0.0 163 Summary_Statistics1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 152 cshl_grep_tool 1.0.0 162 Summary_Statistics1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 153 Filter1 1.1.0 161 Summary_Statistics1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 153 Filter1 1.1.0 160 Summary_Statistics1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 154 Filter1 1.1.0 167 Summary_Statistics1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 154 Filter1 1.1.0 166 Summary_Statistics1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 155 Filter1 1.1.0 165 Summary_Statistics1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 155 Filter1 1.1.0 164 Summary_Statistics1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 156 Summary_Statistics1 1.1.0 168 Cut1 1.0.1 f t f +11 2013-02-07 17:03:54.795316 157 Summary_Statistics1 1.1.0 169 Cut1 1.0.1 f t f +11 2013-02-07 17:03:54.795316 158 addValue 1.0.0 136 cat1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 159 addValue 1.0.0 136 cat1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 160 Summary_Statistics1 1.1.0 142 Cut1 1.0.1 f t f +11 2013-02-07 17:03:54.795316 161 Summary_Statistics1 1.1.0 141 Cut1 1.0.1 f t f +11 2013-02-07 17:03:54.795316 162 Summary_Statistics1 1.1.0 144 Cut1 1.0.1 f t f +11 2013-02-07 17:03:54.795316 163 Summary_Statistics1 1.1.0 143 Cut1 1.0.1 f t f +11 2013-02-07 17:03:54.795316 164 Summary_Statistics1 1.1.0 138 Cut1 1.0.1 f t f +11 2013-02-07 17:03:54.795316 165 Summary_Statistics1 1.1.0 137 Cut1 1.0.1 f t f +11 2013-02-07 17:03:54.795316 166 Summary_Statistics1 1.1.0 140 Cut1 1.0.1 f t f +11 2013-02-07 17:03:54.795316 167 Summary_Statistics1 1.1.0 139 Cut1 1.0.1 f t f +11 2013-02-07 17:03:54.795316 168 Cut1 1.0.1 146 Paste1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 169 Cut1 1.0.1 146 Paste1 1.0.0 f t f +11 2013-02-07 17:03:54.795316 170 Paste1 1.0.0 173 Add_a_column1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 171 Paste1 1.0.0 174 Add_a_column1 1.1.0 f t f +11 2013-02-07 17:03:54.795316 172 Add_a_column1 1.1.0 135 addValue 1.0.0 f t f +11 2013-02-07 17:03:54.795316 173 Add_a_column1 1.1.0 149 addValue 1.0.0 f t f +11 2013-02-07 17:03:54.795316 174 Add_a_column1 1.1.0 148 addValue 1.0.0 f t f +11 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2013-02-07 17:04:38.354863 184 sort1 1.0.1 186 cshl_awk_tool t t f +12 2013-02-07 17:04:38.354863 184 sort1 1.0.1 186 cshl_awk_tool f t f +12 2013-02-07 17:04:38.354863 185 addValue 1.0.0 180 cat1 1.0.0 t t f +12 2013-02-07 17:04:38.354863 185 addValue 1.0.0 180 cat1 1.0.0 f t f +12 2013-02-07 17:04:38.354863 186 cshl_awk_tool 188 cshl_uniq_tool 1.0.0 t t f +12 2013-02-07 17:04:38.354863 186 cshl_awk_tool 188 cshl_uniq_tool 1.0.0 f t f +12 2013-02-07 17:04:38.354863 187 Count1 1.0.0 180 cat1 1.0.0 t t f +12 2013-02-07 17:04:38.354863 187 Count1 1.0.0 180 cat1 1.0.0 f t f +12 2013-02-07 17:04:38.354863 188 cshl_uniq_tool 1.0.0 187 Count1 1.0.0 t t f +12 2013-02-07 17:04:38.354863 188 cshl_uniq_tool 1.0.0 187 Count1 1.0.0 f t f +12 2013-02-07 17:04:38.354863 190 182 bedtools_intersectBed t t f +12 2013-02-07 17:04:38.354863 190 182 bedtools_intersectBed f t f +12 2013-02-07 17:04:38.354863 190 181 bedtools_intersectBed t t f +12 2013-02-07 17:04:38.354863 190 181 bedtools_intersectBed f t f +12 2013-02-07 17:04:38.354863 191 182 bedtools_intersectBed t t f +12 2013-02-07 17:04:38.354863 191 182 bedtools_intersectBed f t f +12 2013-02-07 17:04:38.354863 191 181 bedtools_intersectBed t t f +12 2013-02-07 17:04:38.354863 191 181 bedtools_intersectBed f t f +19 2013-02-14 15:51:02.598429 193 194 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 f t f +19 2013-02-14 15:51:02.598429 193 194 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 f t f +19 2013-02-14 15:51:02.598429 193 194 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 f t f +19 2013-02-14 15:51:02.598429 193 194 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 f t f +19 2013-02-14 15:51:02.598429 195 194 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 f t f +19 2013-02-14 15:51:02.598429 195 194 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 f t f +19 2013-02-14 15:51:02.598429 195 194 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 f t f +19 2013-02-14 15:51:02.598429 195 194 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 f t f +19 2013-02-14 15:51:02.598429 199 205 gops_subtract_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 199 205 gops_subtract_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 199 205 gops_subtract_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 199 205 gops_subtract_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 199 200 gops_intersect_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 199 200 gops_intersect_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 199 200 gops_intersect_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 199 200 gops_intersect_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 200 gops_intersect_1 1.0.0 215 Count1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 200 gops_intersect_1 1.0.0 215 Count1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 200 gops_intersect_1 1.0.0 215 Count1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 200 gops_intersect_1 1.0.0 215 Count1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 200 gops_intersect_1 1.0.0 210 cshl_awk_tool f t f +19 2013-02-14 15:51:02.598429 200 gops_intersect_1 1.0.0 210 cshl_awk_tool f t f +19 2013-02-14 15:51:02.598429 200 gops_intersect_1 1.0.0 210 cshl_awk_tool f t f +19 2013-02-14 15:51:02.598429 200 gops_intersect_1 1.0.0 210 cshl_awk_tool f t f +19 2013-02-14 15:51:02.598429 201 cshl_find_and_replace 1.0.0 205 gops_subtract_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 201 cshl_find_and_replace 1.0.0 205 gops_subtract_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 201 cshl_find_and_replace 1.0.0 205 gops_subtract_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 201 cshl_find_and_replace 1.0.0 205 gops_subtract_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 201 cshl_find_and_replace 1.0.0 200 gops_intersect_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 201 cshl_find_and_replace 1.0.0 200 gops_intersect_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 201 cshl_find_and_replace 1.0.0 200 gops_intersect_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 201 cshl_find_and_replace 1.0.0 200 gops_intersect_1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 202 get_flanks1 1.0.0 201 cshl_find_and_replace 1.0.0 f t f +19 2013-02-14 15:51:02.598429 202 get_flanks1 1.0.0 201 cshl_find_and_replace 1.0.0 f t f +19 2013-02-14 15:51:02.598429 202 get_flanks1 1.0.0 201 cshl_find_and_replace 1.0.0 f t f +19 2013-02-14 15:51:02.598429 202 get_flanks1 1.0.0 201 cshl_find_and_replace 1.0.0 f t f +19 2013-02-14 15:51:02.598429 203 204 cshl_grep_tool 1.0.0 f t f +19 2013-02-14 15:51:02.598429 203 204 cshl_grep_tool 1.0.0 f t f +19 2013-02-14 15:51:02.598429 203 204 cshl_grep_tool 1.0.0 f t f +19 2013-02-14 15:51:02.598429 203 204 cshl_grep_tool 1.0.0 f t f +19 2013-02-14 15:51:02.598429 203 202 get_flanks1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 203 202 get_flanks1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 203 202 get_flanks1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 203 202 get_flanks1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 205 gops_subtract_1 1.0.0 206 cshl_awk_tool f t f +19 2013-02-14 15:51:02.598429 205 gops_subtract_1 1.0.0 206 cshl_awk_tool f t f +19 2013-02-14 15:51:02.598429 205 gops_subtract_1 1.0.0 206 cshl_awk_tool f t f +19 2013-02-14 15:51:02.598429 205 gops_subtract_1 1.0.0 206 cshl_awk_tool f t f +19 2013-02-14 15:51:02.598429 206 cshl_awk_tool 207 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 206 cshl_awk_tool 207 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 206 cshl_awk_tool 207 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 206 cshl_awk_tool 207 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 207 Extract genomic DNA 1 2.2.2 214 Show beginning1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 207 Extract genomic DNA 1 2.2.2 214 Show beginning1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 207 Extract genomic DNA 1 2.2.2 214 Show beginning1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 207 Extract genomic DNA 1 2.2.2 214 Show beginning1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 208 213 trap f t f +19 2013-02-14 15:51:02.598429 208 213 trap f t f +19 2013-02-14 15:51:02.598429 208 213 trap f t f +19 2013-02-14 15:51:02.598429 208 213 trap f t f +19 2013-02-14 15:51:02.598429 208 209 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 208 209 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 208 209 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 208 209 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 208 207 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 208 207 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 208 207 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 208 207 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 209 Extract genomic DNA 1 2.2.2 211 Show beginning1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 209 Extract genomic DNA 1 2.2.2 211 Show beginning1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 209 Extract genomic DNA 1 2.2.2 211 Show beginning1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 209 Extract genomic DNA 1 2.2.2 211 Show beginning1 1.0.0 f t f +19 2013-02-14 15:51:02.598429 210 cshl_awk_tool 209 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 210 cshl_awk_tool 209 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 210 cshl_awk_tool 209 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 210 cshl_awk_tool 209 Extract genomic DNA 1 2.2.2 f t f +19 2013-02-14 15:51:02.598429 211 Show beginning1 1.0.0 212 meme_meme 1.0.0 f t f +19 2013-02-14 15:51:02.598429 211 Show beginning1 1.0.0 212 meme_meme 1.0.0 f t f +19 2013-02-14 15:51:02.598429 211 Show beginning1 1.0.0 212 meme_meme 1.0.0 f t f +19 2013-02-14 15:51:02.598429 211 Show beginning1 1.0.0 212 meme_meme 1.0.0 f t f +19 2013-02-14 15:51:02.598429 215 Count1 1.0.0 216 barchart_gnuplot 1.0.0 f t f +19 2013-02-14 15:51:02.598429 215 Count1 1.0.0 216 barchart_gnuplot 1.0.0 f t f +19 2013-02-14 15:51:02.598429 215 Count1 1.0.0 216 barchart_gnuplot 1.0.0 f t f +19 2013-02-14 15:51:02.598429 215 Count1 1.0.0 216 barchart_gnuplot 1.0.0 f t f +28 2013-02-14 16:08:08.300397 242 243 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 1.4.1 f t f +28 2013-02-14 16:08:08.300397 244 243 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 1.4.1 f t f +29 2013-02-14 17:12:23.558236 245 246 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 1.4.1 f t f +29 2013-02-14 17:12:23.558236 247 246 toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/peakcalling_macs14/1.4.1 1.4.1 f t f +29 2013-02-14 17:12:23.558236 251 257 gops_subtract_1 1.0.0 f t f +29 2013-02-14 17:12:23.558236 251 252 gops_intersect_1 1.0.0 f t f +29 2013-02-14 17:12:23.558236 252 gops_intersect_1 1.0.0 267 Count1 1.0.0 f t f +29 2013-02-14 17:12:23.558236 252 gops_intersect_1 1.0.0 262 cshl_awk_tool f t f +29 2013-02-14 17:12:23.558236 253 cshl_find_and_replace 1.0.0 257 gops_subtract_1 1.0.0 f t f +29 2013-02-14 17:12:23.558236 253 cshl_find_and_replace 1.0.0 252 gops_intersect_1 1.0.0 f t f +29 2013-02-14 17:12:23.558236 254 get_flanks1 1.0.0 253 cshl_find_and_replace 1.0.0 f t f +29 2013-02-14 17:12:23.558236 255 256 cshl_grep_tool 1.0.0 f t f +29 2013-02-14 17:12:23.558236 255 254 get_flanks1 1.0.0 f t f +29 2013-02-14 17:12:23.558236 257 gops_subtract_1 1.0.0 258 cshl_awk_tool f t f +29 2013-02-14 17:12:23.558236 258 cshl_awk_tool 259 Extract genomic DNA 1 2.2.2 f t f +29 2013-02-14 17:12:23.558236 259 Extract genomic DNA 1 2.2.2 266 Show beginning1 1.0.0 f t f +29 2013-02-14 17:12:23.558236 260 265 trap f t f +29 2013-02-14 17:12:23.558236 260 261 Extract genomic DNA 1 2.2.2 f t f +29 2013-02-14 17:12:23.558236 260 259 Extract genomic DNA 1 2.2.2 f t f +29 2013-02-14 17:12:23.558236 261 Extract genomic DNA 1 2.2.2 263 Show beginning1 1.0.0 f t f +29 2013-02-14 17:12:23.558236 262 cshl_awk_tool 261 Extract genomic DNA 1 2.2.2 f t f +29 2013-02-14 17:12:23.558236 263 Show beginning1 1.0.0 264 meme_meme 1.0.0 f t f +29 2013-02-14 17:12:23.558236 267 Count1 1.0.0 268 barchart_gnuplot 1.0.0 f t f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f t f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f t f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f t f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f t f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f t f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 274 275 addValue 1.0.0 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f t f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f t f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f t f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f t f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f t f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 275 addValue 1.0.0 276 mergeCols1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f t f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f t f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f t f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f t f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f t f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 2013-02-18 11:33:27.210212 276 mergeCols1 1.0.1 277 Cut1 1.0.1 f f f +31 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2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f t f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 708 gops_intersect_1 1.0.0 t t f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f t f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 705 cshl_awk_tool 1.0.0 704 gops_subtract_1 1.0.0 t t f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f t f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 f f f +97 2013-02-20 10:11:21.312214 706 get_flanks1 1.0.0 705 cshl_awk_tool 1.0.0 t t f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f t f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 707 706 get_flanks1 1.0.0 t t f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f t f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 720 Count1 1.0.0 t t f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f t f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 708 gops_intersect_1 1.0.0 709 Extract genomic DNA 1 2.2.2 t t f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f t f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 709 Extract genomic DNA 1 2.2.2 716 fasta2tab 1.1.0 t t f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f t f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 711 Extract genomic DNA 1 2.2.2 t t f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f t f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 f f f +97 2013-02-20 10:11:21.312214 710 709 Extract genomic DNA 1 2.2.2 t t f +97 2013-02-20 10:11:21.312214 711 Extract genomic DNA 1 2.2.2 712 fasta2tab 1.1.0 f f f +97 2013-02-20 10:11:21.312214 711 Extract genomic DNA 1 2.2.2 712 fasta2tab 1.1.0 f f f
--- a/utils.py Wed Sep 25 06:42:18 2019 -0400 +++ b/utils.py Sat May 09 09:38:04 2020 +0000 @@ -2,12 +2,8 @@ import numpy as np import json import h5py +import random -from keras.models import model_from_json, Sequential -from keras.layers import Dense, GRU, Dropout -from keras.layers.embeddings import Embedding -from keras.layers.core import SpatialDropout1D -from keras.optimizers import RMSprop from keras import backend as K @@ -20,34 +16,6 @@ return file_content -def write_file(file_path, content): - """ - Write a file - """ - remove_file(file_path) - with open(file_path, "w") as json_file: - json_file.write(json.dumps(content)) - - -def save_processed_workflows(file_path, unique_paths): - workflow_paths_unique = "" - for path in unique_paths: - workflow_paths_unique += path + "\n" - with open(file_path, "w") as workflows_file: - workflows_file.write(workflow_paths_unique) - - -def load_saved_model(model_config, model_weights): - """ - Load the saved trained model using the saved network and its weights - """ - # load the network - loaded_model = model_from_json(model_config) - # load the saved weights into the model - loaded_model.set_weights(model_weights) - return loaded_model - - def format_tool_id(tool_link): """ Extract tool id from tool link @@ -57,22 +25,6 @@ return tool_id -def get_HDF5(hf, d_key): - """ - Read h5 file to get train and test data - """ - return hf.get(d_key).value - - -def save_HDF5(hf_file, d_key, data, d_type=""): - """ - Save datasets as h5 file - """ - if (d_type == 'json'): - data = json.dumps(data) - hf_file.create_dataset(d_key, data=data) - - def set_trained_model(dump_file, model_values): """ Create an h5 file with the trained weights and associated dicts @@ -95,55 +47,13 @@ hf_file.close() -def remove_file(file_path): - if os.path.exists(file_path): - os.remove(file_path) - - -def extract_configuration(config_object): - config_loss = dict() - for index, item in enumerate(config_object): - config_loss[index] = list() - d_config = dict() - d_config['loss'] = item['result']['loss'] - d_config['params_config'] = item['misc']['vals'] - config_loss[index].append(d_config) - return config_loss - - -def get_best_parameters(mdl_dict): - """ - Get param values (defaults as well) - """ - lr = float(mdl_dict.get("learning_rate", "0.001")) - embedding_size = int(mdl_dict.get("embedding_size", "512")) - dropout = float(mdl_dict.get("dropout", "0.2")) - recurrent_dropout = float(mdl_dict.get("recurrent_dropout", "0.2")) - spatial_dropout = float(mdl_dict.get("spatial_dropout", "0.2")) - units = int(mdl_dict.get("units", "512")) - batch_size = int(mdl_dict.get("batch_size", "512")) - activation_recurrent = mdl_dict.get("activation_recurrent", "elu") - activation_output = mdl_dict.get("activation_output", "sigmoid") - - return { - "lr": lr, - "embedding_size": embedding_size, - "dropout": dropout, - "recurrent_dropout": recurrent_dropout, - "spatial_dropout": spatial_dropout, - "units": units, - "batch_size": batch_size, - "activation_recurrent": activation_recurrent, - "activation_output": activation_output, - } - - def weighted_loss(class_weights): """ Create a weighted loss function. Penalise the misclassification of classes more with the higher usage """ weight_values = list(class_weights.values()) + weight_values.extend(weight_values) def weighted_binary_crossentropy(y_true, y_pred): # add another dimension to compute dot product @@ -152,67 +62,101 @@ return weighted_binary_crossentropy -def set_recurrent_network(mdl_dict, reverse_dictionary, class_weights): - """ - Create a RNN network and set its parameters - """ - dimensions = len(reverse_dictionary) + 1 - model_params = get_best_parameters(mdl_dict) - - # define the architecture of the neural network - model = Sequential() - model.add(Embedding(dimensions, model_params["embedding_size"], mask_zero=True)) - model.add(SpatialDropout1D(model_params["spatial_dropout"])) - model.add(GRU(model_params["units"], dropout=model_params["spatial_dropout"], recurrent_dropout=model_params["recurrent_dropout"], activation=model_params["activation_recurrent"], return_sequences=True)) - model.add(Dropout(model_params["dropout"])) - model.add(GRU(model_params["units"], dropout=model_params["spatial_dropout"], recurrent_dropout=model_params["recurrent_dropout"], activation=model_params["activation_recurrent"], return_sequences=False)) - model.add(Dropout(model_params["dropout"])) - model.add(Dense(dimensions, activation=model_params["activation_output"])) - optimizer = RMSprop(lr=model_params["lr"]) - model.compile(loss=weighted_loss(class_weights), optimizer=optimizer) - return model, model_params +def balanced_sample_generator(train_data, train_labels, batch_size, l_tool_tr_samples): + while True: + dimension = train_data.shape[1] + n_classes = train_labels.shape[1] + tool_ids = list(l_tool_tr_samples.keys()) + generator_batch_data = np.zeros([batch_size, dimension]) + generator_batch_labels = np.zeros([batch_size, n_classes]) + for i in range(batch_size): + random_toolid_index = random.sample(range(0, len(tool_ids)), 1)[0] + random_toolid = tool_ids[random_toolid_index] + sample_indices = l_tool_tr_samples[str(random_toolid)] + random_index = random.sample(range(0, len(sample_indices)), 1)[0] + random_tr_index = sample_indices[random_index] + generator_batch_data[i] = train_data[random_tr_index] + generator_batch_labels[i] = train_labels[random_tr_index] + yield generator_batch_data, generator_batch_labels -def compute_precision(model, x, y, reverse_data_dictionary, next_compatible_tools, usage_scores, actual_classes_pos, topk): +def compute_precision(model, x, y, reverse_data_dictionary, usage_scores, actual_classes_pos, topk, standard_conn, last_tool_id, lowest_tool_ids): """ Compute absolute and compatible precision """ - absolute_precision = 0.0 + pred_t_name = "" + top_precision = 0.0 + mean_usage = 0.0 + usage_wt_score = list() + pub_precision = 0.0 + lowest_pub_prec = 0.0 + lowest_norm_prec = 0.0 + pub_tools = list() + actual_next_tool_names = list() test_sample = np.reshape(x, (1, len(x))) # predict next tools for a test path prediction = model.predict(test_sample, verbose=0) + # divide the predicted vector into two halves - one for published and + # another for normal workflows nw_dimension = prediction.shape[1] - - # remove the 0th position as there is no tool at this index - prediction = np.reshape(prediction, (nw_dimension,)) + half_len = int(nw_dimension / 2) - prediction_pos = np.argsort(prediction, axis=-1) - topk_prediction_pos = prediction_pos[-topk:] + # predict tools + prediction = np.reshape(prediction, (nw_dimension,)) + # get predictions of tools from published workflows + standard_pred = prediction[:half_len] + # get predictions of tools from normal workflows + normal_pred = prediction[half_len:] - # remove the wrong tool position from the predicted list of tool positions - topk_prediction_pos = [x for x in topk_prediction_pos if x > 0] + standard_prediction_pos = np.argsort(standard_pred, axis=-1) + standard_topk_prediction_pos = standard_prediction_pos[-topk] + + normal_prediction_pos = np.argsort(normal_pred, axis=-1) + normal_topk_prediction_pos = normal_prediction_pos[-topk] - # read tool names using reverse dictionary - actual_next_tool_names = [reverse_data_dictionary[int(tool_pos)] for tool_pos in actual_classes_pos] - top_predicted_next_tool_names = [reverse_data_dictionary[int(tool_pos)] for tool_pos in topk_prediction_pos] - - # compute the class weights of predicted tools - mean_usg_score = 0 - usg_wt_scores = list() - for t_id in topk_prediction_pos: - t_name = reverse_data_dictionary[int(t_id)] - if t_id in usage_scores and t_name in actual_next_tool_names: - usg_wt_scores.append(np.log(usage_scores[t_id] + 1.0)) - if len(usg_wt_scores) > 0: - mean_usg_score = np.sum(usg_wt_scores) / float(topk) - false_positives = [tool_name for tool_name in top_predicted_next_tool_names if tool_name not in actual_next_tool_names] - absolute_precision = 1 - (len(false_positives) / float(topk)) - return mean_usg_score, absolute_precision + # get true tools names + for a_t_pos in actual_classes_pos: + if a_t_pos > half_len: + t_name = reverse_data_dictionary[int(a_t_pos - half_len)] + else: + t_name = reverse_data_dictionary[int(a_t_pos)] + actual_next_tool_names.append(t_name) + last_tool_name = reverse_data_dictionary[x[-1]] + # compute scores for published recommendations + if standard_topk_prediction_pos in reverse_data_dictionary: + pred_t_name = reverse_data_dictionary[int(standard_topk_prediction_pos)] + if last_tool_name in standard_conn: + pub_tools = standard_conn[last_tool_name] + if pred_t_name in pub_tools: + pub_precision = 1.0 + if last_tool_id in lowest_tool_ids: + lowest_pub_prec = 1.0 + if standard_topk_prediction_pos in usage_scores: + usage_wt_score.append(np.log(usage_scores[standard_topk_prediction_pos] + 1.0)) + # compute scores for normal recommendations + if normal_topk_prediction_pos in reverse_data_dictionary: + pred_t_name = reverse_data_dictionary[int(normal_topk_prediction_pos)] + if pred_t_name in actual_next_tool_names: + if normal_topk_prediction_pos in usage_scores: + usage_wt_score.append(np.log(usage_scores[normal_topk_prediction_pos] + 1.0)) + top_precision = 1.0 + if last_tool_id in lowest_tool_ids: + lowest_norm_prec = 1.0 + if len(usage_wt_score) > 0: + mean_usage = np.mean(usage_wt_score) + return mean_usage, top_precision, pub_precision, lowest_pub_prec, lowest_norm_prec -def verify_model(model, x, y, reverse_data_dictionary, next_compatible_tools, usage_scores, topk_list=[1, 2, 3]): +def get_lowest_tools(l_tool_freq, fraction=0.25): + l_tool_freq = dict(sorted(l_tool_freq.items(), key=lambda kv: kv[1], reverse=True)) + tool_ids = list(l_tool_freq.keys()) + lowest_ids = tool_ids[-int(len(tool_ids) * fraction):] + return lowest_ids + + +def verify_model(model, x, y, reverse_data_dictionary, usage_scores, standard_conn, lowest_tool_ids, topk_list=[1, 2, 3]): """ Verify the model on test data """ @@ -221,31 +165,49 @@ size = y.shape[0] precision = np.zeros([len(y), len(topk_list)]) usage_weights = np.zeros([len(y), len(topk_list)]) + epo_pub_prec = np.zeros([len(y), len(topk_list)]) + epo_lowest_tools_pub_prec = list() + epo_lowest_tools_norm_prec = list() + # loop over all the test samples and find prediction precision for i in range(size): + lowest_pub_topk = list() + lowest_norm_topk = list() actual_classes_pos = np.where(y[i] > 0)[0] + test_sample = x[i, :] + last_tool_id = str(int(test_sample[-1])) for index, abs_topk in enumerate(topk_list): - abs_mean_usg_score, absolute_precision = compute_precision(model, x[i, :], y, reverse_data_dictionary, next_compatible_tools, usage_scores, actual_classes_pos, abs_topk) + usg_wt_score, absolute_precision, pub_prec, lowest_p_prec, lowest_n_prec = compute_precision(model, test_sample, y, reverse_data_dictionary, usage_scores, actual_classes_pos, abs_topk, standard_conn, last_tool_id, lowest_tool_ids) precision[i][index] = absolute_precision - usage_weights[i][index] = abs_mean_usg_score + usage_weights[i][index] = usg_wt_score + epo_pub_prec[i][index] = pub_prec + if last_tool_id in lowest_tool_ids: + lowest_pub_topk.append(lowest_p_prec) + lowest_norm_topk.append(lowest_n_prec) + if last_tool_id in lowest_tool_ids: + epo_lowest_tools_pub_prec.append(lowest_pub_topk) + epo_lowest_tools_norm_prec.append(lowest_norm_topk) mean_precision = np.mean(precision, axis=0) mean_usage = np.mean(usage_weights, axis=0) - return mean_precision, mean_usage + mean_pub_prec = np.mean(epo_pub_prec, axis=0) + mean_lowest_pub_prec = np.mean(epo_lowest_tools_pub_prec, axis=0) + mean_lowest_norm_prec = np.mean(epo_lowest_tools_norm_prec, axis=0) + return mean_usage, mean_precision, mean_pub_prec, mean_lowest_pub_prec, mean_lowest_norm_prec, len(epo_lowest_tools_pub_prec) -def save_model(results, data_dictionary, compatible_next_tools, trained_model_path, class_weights): +def save_model(results, data_dictionary, compatible_next_tools, trained_model_path, class_weights, standard_connections): # save files trained_model = results["model"] best_model_parameters = results["best_parameters"] model_config = trained_model.to_json() model_weights = trained_model.get_weights() - model_values = { 'data_dictionary': data_dictionary, 'model_config': model_config, 'best_parameters': best_model_parameters, 'model_weights': model_weights, "compatible_tools": compatible_next_tools, - "class_weights": class_weights + "class_weights": class_weights, + "standard_connections": standard_connections } set_trained_model(trained_model_path, model_values)