Starting server in PID 14373. serving on 0.0.0.0:8000 view at http://127.0.0.1:8000 73.16.113.171 - - [27/Jun/2019:11:01:12 -0900] "GET /api/jobs/2ed853f7b5849b0f/build_for_rerun HTTP/1.0" 200 - "https://jetstream.lappsgrid.org/?job_id=2ed853f7b5849b0f&__identifer=ikxnyz3rtuo" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/11.1.2 Safari/605.1.15" 73.16.113.171 - - [27/Jun/2019:11:01:12 -0900] "GET /api/webhooks HTTP/1.0" 200 - "https://jetstream.lappsgrid.org/?job_id=2ed853f7b5849b0f&__identifer=ikxnyz3rtuo" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/11.1.2 Safari/605.1.15" galaxy.tools DEBUG 2019-06-27 11:01:23,131 Validated and populated state for tool request (26.379 ms) galaxy.tools.actions INFO 2019-06-27 11:01:23,234 Handled output named output_confusion for tool toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1 (60.782 ms) galaxy.tools.actions INFO 2019-06-27 11:01:23,256 Handled output named output_prf for tool toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1 (22.494 ms) galaxy.tools.actions INFO 2019-06-27 11:01:23,274 Handled output named output_roc for tool toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1 (18.009 ms) galaxy.tools.actions INFO 2019-06-27 11:01:23,298 Added output datasets to history (23.187 ms) galaxy.tools.actions INFO 2019-06-27 11:01:23,300 Setup for job Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1] complete, ready to be enqueued (2.547 ms) galaxy.util.handlers DEBUG 2019-06-27 11:01:23,301 (Job[unflushed,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1]) Selected handler 'main' by random choice from handler tag '_default_' galaxy.util.handlers INFO 2019-06-27 11:01:23,381 Flushed transaction for Job[id=1525,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1] (79.441 ms) galaxy.util.handlers INFO 2019-06-27 11:01:23,381 (Job[id=1525,tool_id=toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1]) Handler 'main' assigned using 'db-preassign' assignment method galaxy.tools.execute DEBUG 2019-06-27 11:01:23,381 Tool [toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1] created job [1525] (223.199 ms) galaxy.tools.execute DEBUG 2019-06-27 11:01:23,387 Executed 1 job(s) for tool toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1 request: (255.311 ms) 73.16.113.171 - - [27/Jun/2019:11:01:23 -0900] "POST /api/tools HTTP/1.0" 200 - "https://jetstream.lappsgrid.org/?job_id=2ed853f7b5849b0f&__identifer=ikxnyz3rtuo" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/11.1.2 Safari/605.1.15" 73.16.113.171 - - [27/Jun/2019:11:01:23 -0900] "GET /api/webhooks HTTP/1.0" 200 - "https://jetstream.lappsgrid.org/?job_id=2ed853f7b5849b0f&__identifer=ikxnyz3rtuo" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/11.1.2 Safari/605.1.15" 73.16.113.171 - - [27/Jun/2019:11:01:23 -0900] "GET /api/histories/3d7f8bc59d1f2d70/contents?details=7b468fe61035b1cd%2C3629acb5a2fd85b2%2C4159e5ff97210004%2Cbf331a3c13f57353&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2019-06-27T19%3A46%3A02.000Z&qv=False&qv=False HTTP/1.0" 200 - "https://jetstream.lappsgrid.org/?job_id=2ed853f7b5849b0f&__identifer=ikxnyz3rtuo" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/11.1.2 Safari/605.1.15" 73.16.113.171 - - [27/Jun/2019:11:01:23 -0900] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1/build HTTP/1.0" 200 - "https://jetstream.lappsgrid.org/?job_id=2ed853f7b5849b0f&__identifer=ikxnyz3rtuo" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/11.1.2 Safari/605.1.15" galaxy.jobs.mapper DEBUG 2019-06-27 11:01:23,987 (1525) Mapped job to destination id: local 73.16.113.171 - - [27/Jun/2019:11:01:23 -0900] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/bgruening/plotly_ml_performance_plots/plotly_ml_performance_plots/0.1/build HTTP/1.0" 200 - "https://jetstream.lappsgrid.org/?job_id=2ed853f7b5849b0f&__identifer=ikxnyz3rtuo" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/11.1.2 Safari/605.1.15" galaxy.jobs.handler DEBUG 2019-06-27 11:01:24,018 (1525) Dispatching to local runner galaxy.jobs DEBUG 2019-06-27 11:01:24,043 (1525) Persisting job destination (destination id: local) galaxy.jobs DEBUG 2019-06-27 11:01:24,045 (1525) Working directory for job is: /home/galaxy/galaxy/database/jobs_directory/001/1525 galaxy.jobs.runners DEBUG 2019-06-27 11:01:24,065 Job [1525] queued (47.108 ms) galaxy.jobs.handler INFO 2019-06-27 11:01:24,079 (1525) Job dispatched galaxy.tools.deps DEBUG 2019-06-27 11:01:24,268 Using dependency pandas version 0.22.0 of type conda galaxy.tools.deps DEBUG 2019-06-27 11:01:24,269 Using dependency scikit-learn version 0.19.1 of type conda galaxy.tools.deps.conda_util DEBUG 2019-06-27 11:01:24,270 Executing command: /home/galaxy/galaxy/database/dependencies/_conda/bin/conda list --name __pandas@0.22.0 --export > './database/tmp/jobdepspxLM53a5cc10bd2db8c3cc09fcfb66383a0dbdb32360bb1ee566b16b33514ebbfb623e/__pandas@0.22.0' galaxy.tools.deps.conda_util DEBUG 2019-06-27 11:01:24,998 Executing command: /home/galaxy/galaxy/database/dependencies/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /home/galaxy/galaxy/database/jobs_directory/001/1525/conda-env --file ./database/tmp/jobdepspxLM53a5cc10bd2db8c3cc09fcfb66383a0dbdb32360bb1ee566b16b33514ebbfb623e/__pandas@0.22.0 Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... done # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<< Traceback (most recent call last): File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/_vendor/auxlib/entity.py", line 411, in __get__ val = instance.__dict__[self.name] KeyError: 'size' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/exceptions.py", line 1043, in __call__ return func(*args, **kwargs) File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/cli/main.py", line 84, in _main exit_code = do_call(args, p) File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/cli/conda_argparse.py", line 82, in do_call exit_code = getattr(module, func_name)(args, parser) File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/cli/main_create.py", line 37, in execute install(args, parser, 'create') File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/cli/install.py", line 304, in install handle_txn(unlink_link_transaction, prefix, args, newenv) File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/cli/install.py", line 320, in handle_txn unlink_link_transaction.print_transaction_summary() File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/core/link.py", line 877, in print_transaction_summary change_report_str = self._change_report_str(change_report) File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/core/link.py", line 926, in _change_report_str size = prec.size File "/home/galaxy/galaxy/database/dependencies/_conda/lib/python3.6/site-packages/conda/_vendor/auxlib/entity.py", line 417, in __get__ raise AttributeError("A value for {0} has not been set".format(self.name)) AttributeError: A value for size has not been set `$ /home/galaxy/galaxy/database/dependencies/_conda/bin/conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --unknown --offline --prefix /home/galaxy/galaxy/database/jobs_directory/001/1525/conda-env --file ./database/tmp/jobdepspxLM53a5cc10bd2db8c3cc09fcfb66383a0dbdb32360bb1ee566b16b33514ebbfb623e/__pandas@0.22.0` environment variables: CIO_TEST= CONDARC=/home/galaxy/galaxy/database/dependencies/_condarc CONDA_ROOT=/home/galaxy/galaxy/database/dependencies/_conda NODE_PATH=/home/galaxy/galaxy/.venv/lib/node_modules PATH=/home/galaxy/galaxy/.venv/lib/node_modules/.bin:/home/galaxy/galaxy/.v env/bin:/home/galaxy/galaxy/.venv/bin:/usr/local/sbin:/usr/local/bin:/ usr/sbin:/usr/bin:/sbin:/bin:/snap/bin REQUESTS_CA_BUNDLE= SSL_CERT_FILE= SUDO_COMMAND=./run.sh SUDO_GID=0 SUDO_UID=0 SUDO_USER=root active environment : None user config file : /home/galaxy/galaxy/database/tmp/conda_exec_home_o4CNVp/.condarc populated config files : conda version : 4.7.5 conda-build version : 3.18.6 python version : 3.6.7.final.0 virtual packages : base environment : /home/galaxy/galaxy/database/dependencies/_conda (writable) channel URLs : https://conda.anaconda.org/iuc/linux-64 (offline) https://conda.anaconda.org/iuc/noarch (offline) https://conda.anaconda.org/conda-forge/linux-64 (offline) https://conda.anaconda.org/conda-forge/noarch (offline) https://conda.anaconda.org/bioconda/linux-64 (offline) https://conda.anaconda.org/bioconda/noarch (offline) https://repo.anaconda.com/pkgs/main/linux-64 (offline) https://repo.anaconda.com/pkgs/main/noarch (offline) https://repo.anaconda.com/pkgs/r/linux-64 (offline) https://repo.anaconda.com/pkgs/r/noarch (offline) package cache : /home/galaxy/galaxy/database/dependencies/_conda/pkgs /home/galaxy/galaxy/database/tmp/conda_exec_home_o4CNVp/.conda/pkgs envs directories : /home/galaxy/galaxy/database/dependencies/_conda/envs /home/galaxy/galaxy/database/tmp/conda_exec_home_o4CNVp/.conda/envs platform : linux-64 user-agent : conda/4.7.5 requests/2.18.4 CPython/3.6.7 Linux/4.15.0-47-generic ubuntu/18.04.2 glibc/2.27 UID:GID : 118:124 netrc file : None offline mode : True An unexpected error has occurred. Conda has prepared the above report. Upload successful. galaxy.tools.deps.conda_util DEBUG 2019-06-27 11:01:26,257 Executing command: /home/galaxy/galaxy/database/dependencies/_conda/bin/conda clean --tarballs -y Cache location: /home/galaxy/galaxy/database/dependencies/_conda/pkgs Will remove the following tarballs: /home/galaxy/galaxy/database/dependencies/_conda/pkgs ----------------------------------------------------- beautifulsoup4-4.7.1-py36_1001.tar.bz2 140 KB python-libarchive-c-2.8-py36_1004.tar.bz2 21 KB conda-build-3.18.6-py36_0.tar.bz2 505 KB filelock-3.0.10-py_0.tar.bz2 9 KB liblief-0.9.0-hf8a498c_1.tar.bz2 4.2 MB py-lief-0.9.0-py36he1b5a44_1.tar.bz2 1.4 MB libxml2-2.9.9-h13577e0_0.tar.bz2 2.0 MB conda-4.7.5-py36_0.tar.bz2 3.0 MB pytz-2019.1-py_0.tar.bz2 227 KB sqlite-3.28.0-h8b20d00_0.tar.bz2 1.9 MB zstd-1.4.0-h3b9ef0a_0.tar.bz2 928 KB libiconv-1.15-h516909a_1005.tar.bz2 2.0 MB soupsieve-1.9.2-py36_0.tar.bz2 59 KB conda-package-handling-1.3.10-py36_0.tar.bz2 257 KB cryptography-2.7-py36h72c5cf5_0.tar.bz2 607 KB pyyaml-5.1.1-py36h516909a_0.tar.bz2 184 KB patchelf-0.10-he1b5a44_0.tar.bz2 77 KB libarchive-3.3.3-hb44662c_1005.tar.bz2 1.4 MB markupsafe-1.1.1-py36h14c3975_0.tar.bz2 26 KB psutil-5.6.3-py36h516909a_0.tar.bz2 322 KB lz4-c-1.8.3-he1b5a44_1001.tar.bz2 187 KB glob2-0.7-py_0.tar.bz2 11 KB tqdm-4.32.2-py_0.tar.bz2 41 KB tk-8.6.9-hed695b0_1002.tar.bz2 3.2 MB lzo-2.10-h14c3975_1000.tar.bz2 319 KB pkginfo-1.5.0.1-py_0.tar.bz2 21 KB jinja2-2.10.1-py_0.tar.bz2 91 KB --------------------------------------------------- Total: 23.1 MB Removed beautifulsoup4-4.7.1-py36_1001.tar.bz2 Removed python-libarchive-c-2.8-py36_1004.tar.bz2 Removed conda-build-3.18.6-py36_0.tar.bz2 Removed filelock-3.0.10-py_0.tar.bz2 Removed liblief-0.9.0-hf8a498c_1.tar.bz2 Removed py-lief-0.9.0-py36he1b5a44_1.tar.bz2 Removed libxml2-2.9.9-h13577e0_0.tar.bz2 Removed conda-4.7.5-py36_0.tar.bz2 Removed pytz-2019.1-py_0.tar.bz2 Removed sqlite-3.28.0-h8b20d00_0.tar.bz2 Removed zstd-1.4.0-h3b9ef0a_0.tar.bz2 Removed libiconv-1.15-h516909a_1005.tar.bz2 Removed soupsieve-1.9.2-py36_0.tar.bz2 Removed conda-package-handling-1.3.10-py36_0.tar.bz2 Removed cryptography-2.7-py36h72c5cf5_0.tar.bz2 Removed pyyaml-5.1.1-py36h516909a_0.tar.bz2 Removed patchelf-0.10-he1b5a44_0.tar.bz2 Removed libarchive-3.3.3-hb44662c_1005.tar.bz2 Removed markupsafe-1.1.1-py36h14c3975_0.tar.bz2 Removed psutil-5.6.3-py36h516909a_0.tar.bz2 Removed lz4-c-1.8.3-he1b5a44_1001.tar.bz2 Removed glob2-0.7-py_0.tar.bz2 Removed tqdm-4.32.2-py_0.tar.bz2 Removed tk-8.6.9-hed695b0_1002.tar.bz2 Removed lzo-2.10-h14c3975_1000.tar.bz2 Removed pkginfo-1.5.0.1-py_0.tar.bz2 Removed jinja2-2.10.1-py_0.tar.bz2 galaxy.jobs.runners ERROR 2019-06-27 11:01:26,624 (1525) Failure preparing job Traceback (most recent call last): File "/home/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 223, in prepare_job modify_command_for_container=modify_command_for_container File "/home/galaxy/galaxy/lib/galaxy/jobs/runners/__init__.py", line 257, in build_command_line container=container File "/home/galaxy/galaxy/lib/galaxy/jobs/command_factory.py", line 69, in build_command __handle_dependency_resolution(commands_builder, job_wrapper, remote_command_params) File "/home/galaxy/galaxy/lib/galaxy/jobs/command_factory.py", line 162, in __handle_dependency_resolution if local_dependency_resolution and job_wrapper.dependency_shell_commands: File "/home/galaxy/galaxy/lib/galaxy/jobs/__init__.py", line 737, in dependency_shell_commands job_directory=self.working_directory File "/home/galaxy/galaxy/lib/galaxy/tools/__init__.py", line 1584, in build_dependency_shell_commands tool_instance=self File "/home/galaxy/galaxy/lib/galaxy/tools/deps/__init__.py", line 127, in dependency_shell_commands return [dependency.shell_commands() for dependency in ordered_dependencies if not isinstance(dependency, ContainerDependency)] File "/home/galaxy/galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 468, in shell_commands self.build_environment() File "/home/galaxy/galaxy/lib/galaxy/tools/deps/resolvers/conda.py", line 463, in build_environment raise DependencyException("Conda dependency seemingly installed but failed to build job environment.") DependencyException: Conda dependency seemingly installed but failed to build job environment. galaxy.tools.error_reports DEBUG 2019-06-27 11:01:26,918 Bug report plugin generated response None galaxy.tools.error_reports DEBUG 2019-06-27 11:01:26,918 Bug report plugin generated response None galaxy.tools.error_reports DEBUG 2019-06-27 11:01:26,918 Bug report plugin generated response None galaxy.model.metadata DEBUG 2019-06-27 11:01:26,921 Cleaning up external metadata files 73.16.113.171 - - [27/Jun/2019:11:01:27 -0900] "GET /api/histories/3d7f8bc59d1f2d70/contents?details=7b468fe61035b1cd%2C3629acb5a2fd85b2%2C4159e5ff97210004%2Cbf331a3c13f57353&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2019-06-27T20%3A01%3A23.000Z&qv=False&qv=False HTTP/1.0" 200 - "https://jetstream.lappsgrid.org/?job_id=2ed853f7b5849b0f&__identifer=ikxnyz3rtuo" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/11.1.2 Safari/605.1.15" 73.16.113.171 - - [27/Jun/2019:11:01:28 -0900] "GET /api/histories/3d7f8bc59d1f2d70?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "https://jetstream.lappsgrid.org/?job_id=2ed853f7b5849b0f&__identifer=ikxnyz3rtuo" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_6) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/11.1.2 Safari/605.1.15"