From a8a70b4324f11489cfebe480f99b35efaa7d7445 Mon Sep 17 00:00:00 2001 From: "seqera-ai-agent[bot]" Date: Tue, 26 May 2026 13:30:08 +0000 Subject: [PATCH 1/2] Fix Nextflow I/O wiring: channels, lib imports, script execution - Fix channel types: use Channel.value(file(...)) for single-file inputs (FASTA, gene list) so they pair correctly with queue channels - Stage lib/ directory into each process and set PYTHONPATH so Python scripts can resolve `from lib import ...` inside Nextflow work dirs - Call bin/ scripts directly (not via `python ${projectDir}/bin/...`) since Nextflow adds bin/ to $PATH automatically - Make all bin/*.py scripts executable (required by Nextflow) - Fix output glob in LABEL_GENE_PAIRS to match actual filenames - Simplify publishDir syntax (remove closure wrappers) - Remove redundant `nextflow.enable.dsl = 2` from workflow files (already declared in nextflow.config) - Add --random-seqs flag pass-through to ENCODE_AND_SPLIT_PAIRS --- .nextflow.log | 73 +++++++++++++ .nextflow.log.1 | 102 ++++++++++++++++++ .../db/000003.log | Bin 0 -> 1048576 bytes .../db/CURRENT | 1 + .../db/LOCK | 0 .../db/MANIFEST-000002 | Bin 0 -> 1048576 bytes .../index.stupefied_lagrange | 0 .../db/000003.log | 0 .../db/CURRENT | 1 + .../db/LOCK | 0 .../db/MANIFEST-000002 | Bin 0 -> 50 bytes .../index.nasty_gilbert | 0 .nextflow/history | 2 + bin/compare_same_species_models.py | 0 bin/encode_split.py | 0 bin/label.py | 0 bin/model_processing.py | 0 bin/normalize.py | 0 bin/preprocess.py | 0 bin/profiling.py | 0 main.nf | 2 - modules/local/encode_and_split_pairs.nf | 10 +- modules/local/label_gene_pairs.nf | 8 +- modules/local/train_and_evaluate_model.nf | 9 +- workflows/main.nf | 42 +++++--- 25 files changed, 223 insertions(+), 27 deletions(-) create mode 100644 .nextflow.log create mode 100644 .nextflow.log.1 create mode 100644 .nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/db/000003.log create mode 100644 .nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/db/CURRENT create mode 100644 .nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/db/LOCK create mode 100644 .nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/db/MANIFEST-000002 create mode 100644 .nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/index.stupefied_lagrange create mode 100644 .nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/000003.log create mode 100644 .nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/CURRENT create mode 100644 .nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/LOCK create mode 100644 .nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/MANIFEST-000002 create mode 100644 .nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/index.nasty_gilbert create mode 100644 .nextflow/history mode change 100644 => 100755 bin/compare_same_species_models.py mode change 100644 => 100755 bin/encode_split.py mode change 100644 => 100755 bin/label.py mode change 100644 => 100755 bin/model_processing.py mode change 100644 => 100755 bin/normalize.py mode change 100644 => 100755 bin/preprocess.py mode change 100644 => 100755 bin/profiling.py diff --git a/.nextflow.log b/.nextflow.log new file mode 100644 index 0000000..b9f1720 --- /dev/null +++ b/.nextflow.log @@ -0,0 +1,73 @@ +May-26 13:27:01.370 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf --input data/merged_kinases_tpm_humanandmouse.tsv --name test_kinases --human_fasta data/promoter_kinases_human.fasta --mouse_fasta data/promoter_kinases_mouse.fasta -preview +May-26 13:27:01.498 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.10.4 +May-26 13:27:01.525 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/bedrock_agentcore/.nextflow/plugins; core-plugins: nf-amazon@3.4.4,nf-azure@1.20.2,nf-cloudcache@0.5.0,nf-codecommit@0.5.0,nf-console@1.3.0,nf-google@1.23.5,nf-k8s@1.2.2,nf-tower@1.17.5,nf-wave@1.16.1 +May-26 13:27:01.551 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] +May-26 13:27:01.552 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] +May-26 13:27:01.555 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode +May-26 13:27:01.574 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config +May-26 13:27:01.739 [main] INFO org.pf4j.AbstractPluginManager - No plugins +May-26 13:27:01.792 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /app/home/user/DeepBenchBioData/nextflow.config +May-26 13:27:01.798 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /app/home/user/DeepBenchBioData/nextflow.config +May-26 13:27:01.859 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +May-26 13:27:02.656 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] +May-26 13:27:02.656 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] +May-26 13:27:02.669 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/bedrock_agentcore/.nextflow/secrets/store.json +May-26 13:27:02.672 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6dc9da2d] - activable => nextflow.secret.LocalSecretsProvider@6dc9da2d +May-26 13:27:02.673 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from config declaration +May-26 13:27:02.692 [main] DEBUG nextflow.cli.CmdRun - * PREVIEW * null [nasty_gilbert] DSL2 - revision: 56fa9034c7 +May-26 13:27:02.753 [main] DEBUG nextflow.Session - Session UUID: 72910696-46c5-4a6f-bbf2-da0adb9f275b +May-26 13:27:02.754 [main] DEBUG nextflow.Session - Run name: nasty_gilbert +May-26 13:27:02.754 [main] DEBUG nextflow.Session - Executor pool size: 2 +May-26 13:27:02.764 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null +May-26 13:27:02.771 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false +May-26 13:27:02.799 [main] DEBUG nextflow.cli.CmdRun - + Version: 25.10.4 build 11177 + Created: 10-02-2026 17:12 UTC + System: Linux 6.1.158-15.288.amzn2023.aarch64 + Runtime: Groovy 4.0.28 on OpenJDK 64-Bit Server VM 17.0.18+8-Debian-1deb12u1 + Encoding: UTF-8 (UTF-8) + Process: 252@localhost [127.0.0.1] + CPUs: 2 - Mem: 7.8 GB (5.2 GB) - Swap: 0 (0) +May-26 13:27:02.827 [main] DEBUG nextflow.Session - Work-dir: /app/home/user/DeepBenchBioData/work [overlayfs] +May-26 13:27:02.861 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] +May-26 13:27:02.872 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory +May-26 13:27:02.875 [main] DEBUG nextflow.Session - Observer factory (v2): DefaultObserverFactory +May-26 13:27:02.962 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory +May-26 13:27:02.996 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 3; maxThreads: 1000 +May-26 13:27:03.046 [main] DEBUG nextflow.Session - Session start +May-26 13:27:03.052 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: results/nextflow_reports/trace.txt +May-26 13:27:03.056 [main] DEBUG nextflow.Session - Using default localLib path: /app/home/user/DeepBenchBioData/lib +May-26 13:27:03.060 [main] DEBUG nextflow.Session - Adding to the classpath library: /app/home/user/DeepBenchBioData/lib +May-26 13:27:03.158 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution +May-26 13:27:04.155 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:LABEL_GENE_PAIRS` matches process PROMOTER_SEQUENCE_PIPELINE:LABEL_GENE_PAIRS +May-26 13:27:04.164 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +May-26 13:27:04.164 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +May-26 13:27:04.180 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local +May-26 13:27:04.188 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=2; memory=7.8 GB; capacity=2; pollInterval=100ms; dumpInterval=5m +May-26 13:27:04.191 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) +May-26 13:27:04.220 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PROMOTER_SEQUENCE_PIPELINE:LABEL_GENE_PAIRS': maxForks=0; fair=false; array=0 +May-26 13:27:04.272 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:ENCODE_AND_SPLIT_PAIRS` matches process PROMOTER_SEQUENCE_PIPELINE:ENCODE_AND_SPLIT_PAIRS +May-26 13:27:04.276 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +May-26 13:27:04.276 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +May-26 13:27:04.278 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PROMOTER_SEQUENCE_PIPELINE:ENCODE_AND_SPLIT_PAIRS': maxForks=0; fair=false; array=0 +May-26 13:27:04.293 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:TRAIN_AND_EVALUATE_MODEL` matches process PROMOTER_SEQUENCE_PIPELINE:TRAIN_AND_EVALUATE_MODEL +May-26 13:27:04.295 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null +May-26 13:27:04.296 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' +May-26 13:27:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PROMOTER_SEQUENCE_PIPELINE:TRAIN_AND_EVALUATE_MODEL': maxForks=0; fair=false; array=0 +May-26 13:27:04.302 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: LABEL_GENE_PAIRS, ENCODE_AND_SPLIT_PAIRS, TRAIN_AND_EVALUATE_MODEL, PROMOTER_SEQUENCE_PIPELINE:TRAIN_AND_EVALUATE_MODEL, PROMOTER_SEQUENCE_PIPELINE:ENCODE_AND_SPLIT_PAIRS, PROMOTER_SEQUENCE_PIPELINE:LABEL_GENE_PAIRS +May-26 13:27:04.313 [main] WARN nextflow.Session - There's no process matching config selector: NORMALIZE_BENCHMARK +May-26 13:27:04.316 [main] WARN nextflow.Session - There's no process matching config selector: PROFILE_BENCHMARK +May-26 13:27:04.319 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: + Script_4306fb1ced06e867: /app/home/user/DeepBenchBioData/main.nf + Script_027f4e7f2cafe472: /app/home/user/DeepBenchBioData/workflows/main.nf + Script_df398b1bd6d6761e: /app/home/user/DeepBenchBioData/modules/local/encode_and_split_pairs.nf + Script_760e1ff7eba26d51: /app/home/user/DeepBenchBioData/modules/local/label_gene_pairs.nf + Script_7c3069c8f75e46f0: /app/home/user/DeepBenchBioData/modules/local/train_and_evaluate_model.nf +May-26 13:27:04.331 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ] +May-26 13:27:04.397 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop +May-26 13:27:04.498 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report +May-26 13:27:05.139 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline +May-26 13:27:05.205 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file +May-26 13:27:05.212 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done +May-26 13:27:05.228 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) +May-26 13:27:05.228 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye diff --git a/.nextflow.log.1 b/.nextflow.log.1 new file mode 100644 index 0000000..76a3801 --- /dev/null +++ b/.nextflow.log.1 @@ -0,0 +1,102 @@ +May-26 13:26:49.612 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf --help +May-26 13:26:49.696 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.10.4 +May-26 13:26:49.726 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/bedrock_agentcore/.nextflow/plugins; core-plugins: nf-amazon@3.4.4,nf-azure@1.20.2,nf-cloudcache@0.5.0,nf-codecommit@0.5.0,nf-console@1.3.0,nf-google@1.23.5,nf-k8s@1.2.2,nf-tower@1.17.5,nf-wave@1.16.1 +May-26 13:26:49.745 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] +May-26 13:26:49.746 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] +May-26 13:26:49.749 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode +May-26 13:26:49.769 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config +May-26 13:26:49.913 [main] INFO org.pf4j.AbstractPluginManager - No plugins +May-26 13:26:49.968 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /app/home/user/DeepBenchBioData/nextflow.config +May-26 13:26:49.973 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /app/home/user/DeepBenchBioData/nextflow.config +May-26 13:26:50.018 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` +May-26 13:26:50.879 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] +May-26 13:26:50.879 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] +May-26 13:26:50.900 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/bedrock_agentcore/.nextflow/secrets/store.json +May-26 13:26:50.904 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@34332b8d] - activable => nextflow.secret.LocalSecretsProvider@34332b8d +May-26 13:26:50.905 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from config declaration +May-26 13:26:50.917 [main] DEBUG nextflow.cli.CmdRun - Launching `main.nf` [stupefied_lagrange] DSL2 - revision: 56fa9034c7 +May-26 13:26:50.974 [main] DEBUG nextflow.Session - Session UUID: 64fbd765-7899-4c87-9543-37de66cb8d35 +May-26 13:26:50.975 [main] DEBUG nextflow.Session - Run name: stupefied_lagrange +May-26 13:26:50.975 [main] DEBUG nextflow.Session - Executor pool size: 2 +May-26 13:26:50.984 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null +May-26 13:26:50.991 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false +May-26 13:26:51.013 [main] DEBUG nextflow.cli.CmdRun - + Version: 25.10.4 build 11177 + Created: 10-02-2026 17:12 UTC + System: Linux 6.1.158-15.288.amzn2023.aarch64 + Runtime: Groovy 4.0.28 on OpenJDK 64-Bit Server VM 17.0.18+8-Debian-1deb12u1 + Encoding: UTF-8 (UTF-8) + Process: 166@localhost [127.0.0.1] + CPUs: 2 - Mem: 7.8 GB (5.2 GB) - Swap: 0 (0) +May-26 13:26:51.039 [main] DEBUG nextflow.Session - Work-dir: /app/home/user/DeepBenchBioData/work [overlayfs] +May-26 13:26:51.092 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] +May-26 13:26:51.106 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory +May-26 13:26:51.109 [main] DEBUG nextflow.Session - Observer factory (v2): DefaultObserverFactory +May-26 13:26:51.188 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory +May-26 13:26:51.201 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 3; maxThreads: 1000 +May-26 13:26:51.249 [main] DEBUG nextflow.Session - Session start +May-26 13:26:51.255 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: results/nextflow_reports/trace.txt +May-26 13:26:51.260 [main] DEBUG nextflow.Session - Using default localLib path: /app/home/user/DeepBenchBioData/lib +May-26 13:26:51.265 [main] DEBUG nextflow.Session - Adding to the classpath library: /app/home/user/DeepBenchBioData/lib +May-26 13:26:51.399 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution +May-26 13:26:52.060 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: + Script_4306fb1ced06e867: /app/home/user/DeepBenchBioData/main.nf + Script_df398b1bd6d6761e: /app/home/user/DeepBenchBioData/modules/local/encode_and_split_pairs.nf + Script_027f4e7f2cafe472: /app/home/user/DeepBenchBioData/workflows/main.nf + Script_760e1ff7eba26d51: /app/home/user/DeepBenchBioData/modules/local/label_gene_pairs.nf + Script_7c3069c8f75e46f0: /app/home/user/DeepBenchBioData/modules/local/train_and_evaluate_model.nf +May-26 13:26:52.061 [main] DEBUG nextflow.Session - Session aborted -- Cause: Missing required parameter: --input +May-26 13:26:52.079 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ] +May-26 13:26:52.272 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report +May-26 13:26:52.952 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline +May-26 13:26:53.011 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file +May-26 13:26:53.025 [main] ERROR nextflow.cli.Launcher - @unknown +nextflow.exception.WorkflowScriptErrorException: Missing required parameter: --input + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at nextflow.Nextflow.error(Nextflow.groovy:244) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at Script_027f4e7f2cafe472$_runScript_closure1$_closure2.doCall(Script_027f4e7f2cafe472:9) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:569) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + at groovy.lang.Closure.call(Closure.java:433) + at groovy.lang.Closure.call(Closure.java:412) + at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205) + at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189) + at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) + at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) + at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:105) + at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:651) + at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:392) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:331) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) + at Script_4306fb1ced06e867$_runScript_closure1$_closure2.doCall(Script_4306fb1ced06e867:6) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + at java.base/java.lang.reflect.Method.invoke(Method.java:569) + at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) + at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) + at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280) + at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) + at groovy.lang.Closure.call(Closure.java:433) + at groovy.lang.Closure.call(Closure.java:412) + at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205) + at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189) + at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) + at nextflow.script.BaseScript.run0(BaseScript.groovy:249) + at nextflow.script.BaseScript.run(BaseScript.groovy:260) + at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy:246) + at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy) + at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:246) + at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:139) + at nextflow.cli.CmdRun.run(CmdRun.groovy:429) + at nextflow.cli.Launcher.run(Launcher.groovy:515) + at nextflow.cli.Launcher.main(Launcher.groovy:675) diff --git a/.nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/db/000003.log b/.nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/db/000003.log new file mode 100644 index 0000000000000000000000000000000000000000..9e0f96a2a253b173cb45b41868209a5d043e1437 GIT binary patch literal 1048576 zcmeIuF#!Mo0K%a4Pi+Wah(KY$fB^#r3>YwAz<>b*1`HT5V8DO@0|pEjFkrxd0RsjM 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0000000..e69de29 diff --git a/.nextflow/history b/.nextflow/history new file mode 100644 index 0000000..2bc5d24 --- /dev/null +++ b/.nextflow/history @@ -0,0 +1,2 @@ +2026-05-26 13:26:51 - stupefied_lagrange - 56fa9034c79e186a8998623b4519b518 64fbd765-7899-4c87-9543-37de66cb8d35 nextflow run main.nf --help +2026-05-26 13:27:02 3.2s nasty_gilbert OK 56fa9034c79e186a8998623b4519b518 72910696-46c5-4a6f-bbf2-da0adb9f275b nextflow run main.nf --input data/merged_kinases_tpm_humanandmouse.tsv --name test_kinases --human_fasta data/promoter_kinases_human.fasta --mouse_fasta data/promoter_kinases_mouse.fasta -preview diff --git a/bin/compare_same_species_models.py b/bin/compare_same_species_models.py old mode 100644 new mode 100755 diff --git a/bin/encode_split.py b/bin/encode_split.py old mode 100644 new mode 100755 diff --git a/bin/label.py b/bin/label.py old mode 100644 new mode 100755 diff --git a/bin/model_processing.py b/bin/model_processing.py old mode 100644 new mode 100755 diff --git a/bin/normalize.py b/bin/normalize.py old mode 100644 new mode 100755 diff --git a/bin/preprocess.py b/bin/preprocess.py old mode 100644 new mode 100755 diff --git a/bin/profiling.py b/bin/profiling.py old mode 100644 new mode 100755 diff --git a/main.nf b/main.nf index 23ab463..b11f1b0 100644 --- a/main.nf +++ b/main.nf @@ -1,7 +1,5 @@ #!/usr/bin/env nextflow -nextflow.enable.dsl = 2 - include { PROMOTER_SEQUENCE_PIPELINE } from './workflows/main.nf' workflow { diff --git a/modules/local/encode_and_split_pairs.nf b/modules/local/encode_and_split_pairs.nf index 64665e8..2f3a4b3 100644 --- a/modules/local/encode_and_split_pairs.nf +++ b/modules/local/encode_and_split_pairs.nf @@ -1,20 +1,23 @@ process ENCODE_AND_SPLIT_PAIRS { tag { dataset_name } - publishDir { "${params.outdir}/${dataset_name}/Encoded" }, mode: params.publish_mode + publishDir "${params.outdir}/${dataset_name}/Encoded", mode: params.publish_mode input: tuple val(dataset_name), path(labeled_pairs) path human_fasta path mouse_fasta path original_gene_list + path project_lib output: tuple val(dataset_name), path("results/${dataset_name}/splits/${params.split_mode}"), emit: split_directory script: + def random_seqs_flag = params.random_seqs ? '--random-seqs' : '' """ - python ${projectDir}/bin/encode_split.py \ + export PYTHONPATH="${project_lib}/..:${project_lib}" + encode_split.py \ --input ${labeled_pairs} \ --name ${dataset_name} \ --human-fasta ${human_fasta} \ @@ -24,6 +27,7 @@ process ENCODE_AND_SPLIT_PAIRS { --gene-list ${original_gene_list} \ --val-frac ${params.val_frac} \ --test-frac ${params.test_frac} \ - --seed ${params.seed} + --seed ${params.seed} \ + ${random_seqs_flag} """ } diff --git a/modules/local/label_gene_pairs.nf b/modules/local/label_gene_pairs.nf index 85785f8..2b10421 100644 --- a/modules/local/label_gene_pairs.nf +++ b/modules/local/label_gene_pairs.nf @@ -1,17 +1,19 @@ process LABEL_GENE_PAIRS { tag { dataset_name } - publishDir { "${params.outdir}/${dataset_name}/Labeling" }, mode: params.publish_mode + publishDir "${params.outdir}/${dataset_name}/Labeling", mode: params.publish_mode input: tuple val(dataset_name), path(raw_expression_dataset) + path project_lib output: - tuple val(dataset_name), path("results/${dataset_name}/Labeling/${params.profiling}_labeling_*"), emit: labeled_pairs + tuple val(dataset_name), path("results/${dataset_name}/Labeling/*.tsv"), emit: labeled_pairs script: """ - python ${projectDir}/bin/label.py \ + export PYTHONPATH="${project_lib}/..:${project_lib}" + label.py \ --input ${raw_expression_dataset} \ --name ${dataset_name} \ --normalization ${params.normalization} \ diff --git a/modules/local/train_and_evaluate_model.nf b/modules/local/train_and_evaluate_model.nf index 7011eee..9995149 100644 --- a/modules/local/train_and_evaluate_model.nf +++ b/modules/local/train_and_evaluate_model.nf @@ -1,19 +1,20 @@ process TRAIN_AND_EVALUATE_MODEL { tag "${dataset_name}" - publishDir {"${params.outdir}/${dataset_name}/Model"}, mode: params.publish_mode + publishDir "${params.outdir}/${dataset_name}/Model", mode: params.publish_mode input: tuple val(dataset_name), path(split_directory) + path project_lib output: tuple val(dataset_name), path("results/${dataset_name}/Model"), emit: model_directory script: - optimize_argument = params.optimize ? '--optimize' : '' - + def optimize_argument = params.optimize ? '--optimize' : '' """ - python ${projectDir}/bin/model_processing.py \ + export PYTHONPATH="${project_lib}/..:${project_lib}" + model_processing.py \ --data ${split_directory} \ --name ${dataset_name} \ --metric ${params.profiling} \ diff --git a/workflows/main.nf b/workflows/main.nf index f98b93b..6b02c60 100644 --- a/workflows/main.nf +++ b/workflows/main.nf @@ -1,43 +1,55 @@ -nextflow.enable.dsl = 2 - include { LABEL_GENE_PAIRS } from '../modules/local/label_gene_pairs.nf' include { ENCODE_AND_SPLIT_PAIRS } from '../modules/local/encode_and_split_pairs.nf' include { TRAIN_AND_EVALUATE_MODEL } from '../modules/local/train_and_evaluate_model.nf' workflow PROMOTER_SEQUENCE_PIPELINE { + // --- Validate required parameters --- if (params.input == null) { error "Missing required parameter: --input" } - if (params.name == null) { error "Missing required parameter: --name" } - if (params.human_fasta == null) { error "Missing required parameter: --human_fasta" } - if (params.mouse_fasta == null) { error "Missing required parameter: --mouse_fasta" } - raw_expression_dataset_channel = Channel + // --- Stage the lib/ directory so Python scripts can import from it --- + ch_lib = Channel.value(file("${projectDir}/lib", checkIfExists: true)) + + // --- Input channels --- + // Queue channel: one tuple per dataset + ch_expression = Channel .fromPath(params.input, checkIfExists: true) - .map { raw_expression_dataset -> tuple(params.name, raw_expression_dataset) } + .map { f -> tuple(params.name, f) } - human_promoter_fasta_channel = Channel.fromPath(params.human_fasta, checkIfExists: true) - mouse_promoter_fasta_channel = Channel.fromPath(params.mouse_fasta, checkIfExists: true) - original_gene_list_channel = Channel.fromPath(params.input, checkIfExists: true) + // Value channels for single files (reusable across all items in the queue) + ch_human_fasta = Channel.value(file(params.human_fasta, checkIfExists: true)) + ch_mouse_fasta = Channel.value(file(params.mouse_fasta, checkIfExists: true)) + ch_gene_list = Channel.value(file(params.input, checkIfExists: true)) - LABEL_GENE_PAIRS(raw_expression_dataset_channel) + // --- Step 1: Label gene pairs --- + LABEL_GENE_PAIRS( + ch_expression, + ch_lib + ) + // --- Step 2: Encode sequences and split into train/val/test --- ENCODE_AND_SPLIT_PAIRS( LABEL_GENE_PAIRS.out.labeled_pairs, - human_promoter_fasta_channel, - mouse_promoter_fasta_channel, - original_gene_list_channel + ch_human_fasta, + ch_mouse_fasta, + ch_gene_list, + ch_lib ) - TRAIN_AND_EVALUATE_MODEL(ENCODE_AND_SPLIT_PAIRS.out.split_directory) + // --- Step 3: Train and evaluate the model --- + TRAIN_AND_EVALUATE_MODEL( + ENCODE_AND_SPLIT_PAIRS.out.split_directory, + ch_lib + ) } From 6689ff93105b75737feb5f3005301fcc12ee61d4 Mon Sep 17 00:00:00 2001 From: "seqera-ai-agent[bot]" Date: Tue, 26 May 2026 13:30:31 +0000 Subject: [PATCH 2/2] Remove Nextflow cache from tracking, add to .gitignore Remove accidentally committed .nextflow/ and .nextflow.log* files. Add Nextflow runtime artifacts (cache, work dir, logs) to .gitignore. --- .gitignore | 5 + .nextflow.log | 73 ------------- .nextflow.log.1 | 102 ------------------ .../db/000003.log | Bin 1048576 -> 0 bytes .../db/CURRENT | 1 - .../db/LOCK | 0 .../db/MANIFEST-000002 | Bin 1048576 -> 0 bytes .../index.stupefied_lagrange | 0 .../db/000003.log | 0 .../db/CURRENT | 1 - .../db/LOCK | 0 .../db/MANIFEST-000002 | Bin 50 -> 0 bytes .../index.nasty_gilbert | 0 .nextflow/history | 2 - 14 files changed, 5 insertions(+), 179 deletions(-) delete mode 100644 .nextflow.log delete mode 100644 .nextflow.log.1 delete mode 100644 .nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/db/000003.log delete mode 100644 .nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/db/CURRENT delete mode 100644 .nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/db/LOCK delete mode 100644 .nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/db/MANIFEST-000002 delete mode 100644 .nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/index.stupefied_lagrange delete mode 100644 .nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/000003.log delete mode 100644 .nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/CURRENT delete mode 100644 .nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/LOCK delete mode 100644 .nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/MANIFEST-000002 delete mode 100644 .nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/index.nasty_gilbert delete mode 100644 .nextflow/history diff --git a/.gitignore b/.gitignore index b7e83e9..8e696a6 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,8 @@ +# Nextflow runtime +.nextflow/ +.nextflow.log* +work/ + # Python cache __pycache__/ *.pyc diff --git a/.nextflow.log b/.nextflow.log deleted file mode 100644 index b9f1720..0000000 --- a/.nextflow.log +++ /dev/null @@ -1,73 +0,0 @@ -May-26 13:27:01.370 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf --input data/merged_kinases_tpm_humanandmouse.tsv --name test_kinases --human_fasta data/promoter_kinases_human.fasta --mouse_fasta data/promoter_kinases_mouse.fasta -preview -May-26 13:27:01.498 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.10.4 -May-26 13:27:01.525 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/bedrock_agentcore/.nextflow/plugins; core-plugins: nf-amazon@3.4.4,nf-azure@1.20.2,nf-cloudcache@0.5.0,nf-codecommit@0.5.0,nf-console@1.3.0,nf-google@1.23.5,nf-k8s@1.2.2,nf-tower@1.17.5,nf-wave@1.16.1 -May-26 13:27:01.551 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] -May-26 13:27:01.552 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] -May-26 13:27:01.555 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode -May-26 13:27:01.574 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config -May-26 13:27:01.739 [main] INFO org.pf4j.AbstractPluginManager - No plugins -May-26 13:27:01.792 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /app/home/user/DeepBenchBioData/nextflow.config -May-26 13:27:01.798 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /app/home/user/DeepBenchBioData/nextflow.config -May-26 13:27:01.859 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -May-26 13:27:02.656 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] -May-26 13:27:02.656 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] -May-26 13:27:02.669 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/bedrock_agentcore/.nextflow/secrets/store.json -May-26 13:27:02.672 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6dc9da2d] - activable => nextflow.secret.LocalSecretsProvider@6dc9da2d -May-26 13:27:02.673 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from config declaration -May-26 13:27:02.692 [main] DEBUG nextflow.cli.CmdRun - * PREVIEW * null [nasty_gilbert] DSL2 - revision: 56fa9034c7 -May-26 13:27:02.753 [main] DEBUG nextflow.Session - Session UUID: 72910696-46c5-4a6f-bbf2-da0adb9f275b -May-26 13:27:02.754 [main] DEBUG nextflow.Session - Run name: nasty_gilbert -May-26 13:27:02.754 [main] DEBUG nextflow.Session - Executor pool size: 2 -May-26 13:27:02.764 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null -May-26 13:27:02.771 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false -May-26 13:27:02.799 [main] DEBUG nextflow.cli.CmdRun - - Version: 25.10.4 build 11177 - Created: 10-02-2026 17:12 UTC - System: Linux 6.1.158-15.288.amzn2023.aarch64 - Runtime: Groovy 4.0.28 on OpenJDK 64-Bit Server VM 17.0.18+8-Debian-1deb12u1 - Encoding: UTF-8 (UTF-8) - Process: 252@localhost [127.0.0.1] - CPUs: 2 - Mem: 7.8 GB (5.2 GB) - Swap: 0 (0) -May-26 13:27:02.827 [main] DEBUG nextflow.Session - Work-dir: /app/home/user/DeepBenchBioData/work [overlayfs] -May-26 13:27:02.861 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] -May-26 13:27:02.872 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory -May-26 13:27:02.875 [main] DEBUG nextflow.Session - Observer factory (v2): DefaultObserverFactory -May-26 13:27:02.962 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory -May-26 13:27:02.996 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 3; maxThreads: 1000 -May-26 13:27:03.046 [main] DEBUG nextflow.Session - Session start -May-26 13:27:03.052 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: results/nextflow_reports/trace.txt -May-26 13:27:03.056 [main] DEBUG nextflow.Session - Using default localLib path: /app/home/user/DeepBenchBioData/lib -May-26 13:27:03.060 [main] DEBUG nextflow.Session - Adding to the classpath library: /app/home/user/DeepBenchBioData/lib -May-26 13:27:03.158 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution -May-26 13:27:04.155 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:LABEL_GENE_PAIRS` matches process PROMOTER_SEQUENCE_PIPELINE:LABEL_GENE_PAIRS -May-26 13:27:04.164 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -May-26 13:27:04.164 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -May-26 13:27:04.180 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local -May-26 13:27:04.188 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=2; memory=7.8 GB; capacity=2; pollInterval=100ms; dumpInterval=5m -May-26 13:27:04.191 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local) -May-26 13:27:04.220 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PROMOTER_SEQUENCE_PIPELINE:LABEL_GENE_PAIRS': maxForks=0; fair=false; array=0 -May-26 13:27:04.272 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:ENCODE_AND_SPLIT_PAIRS` matches process PROMOTER_SEQUENCE_PIPELINE:ENCODE_AND_SPLIT_PAIRS -May-26 13:27:04.276 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -May-26 13:27:04.276 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -May-26 13:27:04.278 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PROMOTER_SEQUENCE_PIPELINE:ENCODE_AND_SPLIT_PAIRS': maxForks=0; fair=false; array=0 -May-26 13:27:04.293 [main] DEBUG n.script.dsl.ProcessConfigBuilder - Config settings `withName:TRAIN_AND_EVALUATE_MODEL` matches process PROMOTER_SEQUENCE_PIPELINE:TRAIN_AND_EVALUATE_MODEL -May-26 13:27:04.295 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null -May-26 13:27:04.296 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local' -May-26 13:27:04.297 [main] DEBUG nextflow.processor.TaskProcessor - Creating process 'PROMOTER_SEQUENCE_PIPELINE:TRAIN_AND_EVALUATE_MODEL': maxForks=0; fair=false; array=0 -May-26 13:27:04.302 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: LABEL_GENE_PAIRS, ENCODE_AND_SPLIT_PAIRS, TRAIN_AND_EVALUATE_MODEL, PROMOTER_SEQUENCE_PIPELINE:TRAIN_AND_EVALUATE_MODEL, PROMOTER_SEQUENCE_PIPELINE:ENCODE_AND_SPLIT_PAIRS, PROMOTER_SEQUENCE_PIPELINE:LABEL_GENE_PAIRS -May-26 13:27:04.313 [main] WARN nextflow.Session - There's no process matching config selector: NORMALIZE_BENCHMARK -May-26 13:27:04.316 [main] WARN nextflow.Session - There's no process matching config selector: PROFILE_BENCHMARK -May-26 13:27:04.319 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: - Script_4306fb1ced06e867: /app/home/user/DeepBenchBioData/main.nf - Script_027f4e7f2cafe472: /app/home/user/DeepBenchBioData/workflows/main.nf - Script_df398b1bd6d6761e: /app/home/user/DeepBenchBioData/modules/local/encode_and_split_pairs.nf - Script_760e1ff7eba26d51: /app/home/user/DeepBenchBioData/modules/local/label_gene_pairs.nf - Script_7c3069c8f75e46f0: /app/home/user/DeepBenchBioData/modules/local/train_and_evaluate_model.nf -May-26 13:27:04.331 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ] -May-26 13:27:04.397 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop -May-26 13:27:04.498 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report -May-26 13:27:05.139 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline -May-26 13:27:05.205 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file -May-26 13:27:05.212 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done -May-26 13:27:05.228 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false) -May-26 13:27:05.228 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye diff --git a/.nextflow.log.1 b/.nextflow.log.1 deleted file mode 100644 index 76a3801..0000000 --- a/.nextflow.log.1 +++ /dev/null @@ -1,102 +0,0 @@ -May-26 13:26:49.612 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf --help -May-26 13:26:49.696 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 25.10.4 -May-26 13:26:49.726 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/bedrock_agentcore/.nextflow/plugins; core-plugins: nf-amazon@3.4.4,nf-azure@1.20.2,nf-cloudcache@0.5.0,nf-codecommit@0.5.0,nf-console@1.3.0,nf-google@1.23.5,nf-k8s@1.2.2,nf-tower@1.17.5,nf-wave@1.16.1 -May-26 13:26:49.745 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] -May-26 13:26:49.746 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] -May-26 13:26:49.749 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode -May-26 13:26:49.769 [main] DEBUG nextflow.util.RetryConfig - Missing nextflow session - using default retry config -May-26 13:26:49.913 [main] INFO org.pf4j.AbstractPluginManager - No plugins -May-26 13:26:49.968 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /app/home/user/DeepBenchBioData/nextflow.config -May-26 13:26:49.973 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /app/home/user/DeepBenchBioData/nextflow.config -May-26 13:26:50.018 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard` -May-26 13:26:50.879 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] -May-26 13:26:50.879 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[] -May-26 13:26:50.900 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/bedrock_agentcore/.nextflow/secrets/store.json -May-26 13:26:50.904 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@34332b8d] - activable => nextflow.secret.LocalSecretsProvider@34332b8d -May-26 13:26:50.905 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from config declaration -May-26 13:26:50.917 [main] DEBUG nextflow.cli.CmdRun - Launching `main.nf` [stupefied_lagrange] DSL2 - revision: 56fa9034c7 -May-26 13:26:50.974 [main] DEBUG nextflow.Session - Session UUID: 64fbd765-7899-4c87-9543-37de66cb8d35 -May-26 13:26:50.975 [main] DEBUG nextflow.Session - Run name: stupefied_lagrange -May-26 13:26:50.975 [main] DEBUG nextflow.Session - Executor pool size: 2 -May-26 13:26:50.984 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null -May-26 13:26:50.991 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=10; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false -May-26 13:26:51.013 [main] DEBUG nextflow.cli.CmdRun - - Version: 25.10.4 build 11177 - Created: 10-02-2026 17:12 UTC - System: Linux 6.1.158-15.288.amzn2023.aarch64 - Runtime: Groovy 4.0.28 on OpenJDK 64-Bit Server VM 17.0.18+8-Debian-1deb12u1 - Encoding: UTF-8 (UTF-8) - Process: 166@localhost [127.0.0.1] - CPUs: 2 - Mem: 7.8 GB (5.2 GB) - Swap: 0 (0) -May-26 13:26:51.039 [main] DEBUG nextflow.Session - Work-dir: /app/home/user/DeepBenchBioData/work [overlayfs] -May-26 13:26:51.092 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] -May-26 13:26:51.106 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory -May-26 13:26:51.109 [main] DEBUG nextflow.Session - Observer factory (v2): DefaultObserverFactory -May-26 13:26:51.188 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory -May-26 13:26:51.201 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 3; maxThreads: 1000 -May-26 13:26:51.249 [main] DEBUG nextflow.Session - Session start -May-26 13:26:51.255 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: results/nextflow_reports/trace.txt -May-26 13:26:51.260 [main] DEBUG nextflow.Session - Using default localLib path: /app/home/user/DeepBenchBioData/lib -May-26 13:26:51.265 [main] DEBUG nextflow.Session - Adding to the classpath library: /app/home/user/DeepBenchBioData/lib -May-26 13:26:51.399 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution -May-26 13:26:52.060 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files: - Script_4306fb1ced06e867: /app/home/user/DeepBenchBioData/main.nf - Script_df398b1bd6d6761e: /app/home/user/DeepBenchBioData/modules/local/encode_and_split_pairs.nf - Script_027f4e7f2cafe472: /app/home/user/DeepBenchBioData/workflows/main.nf - Script_760e1ff7eba26d51: /app/home/user/DeepBenchBioData/modules/local/label_gene_pairs.nf - Script_7c3069c8f75e46f0: /app/home/user/DeepBenchBioData/modules/local/train_and_evaluate_model.nf -May-26 13:26:52.061 [main] DEBUG nextflow.Session - Session aborted -- Cause: Missing required parameter: --input -May-26 13:26:52.079 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ] -May-26 13:26:52.272 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report -May-26 13:26:52.952 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline -May-26 13:26:53.011 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file -May-26 13:26:53.025 [main] ERROR nextflow.cli.Launcher - @unknown -nextflow.exception.WorkflowScriptErrorException: Missing required parameter: --input - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at nextflow.Nextflow.error(Nextflow.groovy:244) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at Script_027f4e7f2cafe472$_runScript_closure1$_closure2.doCall(Script_027f4e7f2cafe472:9) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:569) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - at groovy.lang.Closure.call(Closure.java:433) - at groovy.lang.Closure.call(Closure.java:412) - at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205) - at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189) - at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) - at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40) - at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:105) - at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:651) - at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:392) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:331) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321) - at Script_4306fb1ced06e867$_runScript_closure1$_closure2.doCall(Script_4306fb1ced06e867:6) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - at java.base/java.lang.reflect.Method.invoke(Method.java:569) - at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343) - at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328) - at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:280) - at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007) - at groovy.lang.Closure.call(Closure.java:433) - at groovy.lang.Closure.call(Closure.java:412) - at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:205) - at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:189) - at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51) - at nextflow.script.BaseScript.run0(BaseScript.groovy:249) - at nextflow.script.BaseScript.run(BaseScript.groovy:260) - at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy:246) - at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy) - at 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a/.nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/index.stupefied_lagrange b/.nextflow/cache/64fbd765-7899-4c87-9543-37de66cb8d35/index.stupefied_lagrange deleted file mode 100644 index e69de29..0000000 diff --git a/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/000003.log b/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/000003.log deleted file mode 100644 index e69de29..0000000 diff --git a/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/CURRENT b/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/CURRENT deleted file mode 100644 index 1a84852..0000000 --- a/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/CURRENT +++ /dev/null @@ -1 +0,0 @@ -MANIFEST-000002 diff --git a/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/LOCK b/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/LOCK deleted file mode 100644 index e69de29..0000000 diff --git a/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/MANIFEST-000002 b/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/db/MANIFEST-000002 deleted file mode 100644 index bbbc585686bcbcc33686059c69d80b7b4e1291cd..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 50 zcmWIhx#Ncn10$nUPHI_dPD+xVQ)NkNd1i5{bAE0?Vo_pAe$kRS-TOEg7@3$k8JJmE F7y#sj5K{mE diff --git a/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/index.nasty_gilbert b/.nextflow/cache/72910696-46c5-4a6f-bbf2-da0adb9f275b/index.nasty_gilbert deleted file mode 100644 index e69de29..0000000 diff --git a/.nextflow/history b/.nextflow/history deleted file mode 100644 index 2bc5d24..0000000 --- a/.nextflow/history +++ /dev/null @@ -1,2 +0,0 @@ -2026-05-26 13:26:51 - stupefied_lagrange - 56fa9034c79e186a8998623b4519b518 64fbd765-7899-4c87-9543-37de66cb8d35 nextflow run main.nf --help -2026-05-26 13:27:02 3.2s nasty_gilbert OK 56fa9034c79e186a8998623b4519b518 72910696-46c5-4a6f-bbf2-da0adb9f275b nextflow run main.nf --input data/merged_kinases_tpm_humanandmouse.tsv --name test_kinases --human_fasta data/promoter_kinases_human.fasta --mouse_fasta data/promoter_kinases_mouse.fasta -preview