Skip to content

Instantly share code, notes, and snippets.

@Micropathology

Micropathology/gist:bee4ac9601de5739445c3d3a595b606b

Created March 30, 2018 12:35
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save Micropathology/bee4ac9601de5739445c3d3a595b606b to your computer and use it in GitHub Desktop.
Save Micropathology/bee4ac9601de5739445c3d3a595b606b to your computer and use it in GitHub Desktop.
Download ZIP
30_03_18_conda_kraken_error
Raw
gistfile1.txt
galaxy.jobs.handler INFO 2018-03-30 12:31:10,366 (6088) Job dispatched
galaxy.tools.deps DEBUG 2018-03-30 12:31:10,560 Using dependency kraken version 0.10.6-eaf8fb68 of type tool_shed_package
galaxy.tools.deps DEBUG 2018-03-30 12:31:10,560 Using dependency kraken version 0.10.6_eaf8fb68 of type conda
galaxy.tools.deps.conda_util DEBUG 2018-03-30 12:31:10,560 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda list --name __kraken@0.10.6_eaf8fb68 --export > /mnt/galaxy/tmp/jobdepsUqR4RTea42a74b7bf23de1655065d377d25493f18569d396a2ca072edc0e3f40d60c43/__kraken@0.10.6_eaf8fb68
galaxy.tools.deps.conda_util DEBUG 2018-03-30 12:31:10,901 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --unknown --offline --prefix /mnt/galaxy/tmp/job_working_directory/006/6088/conda-env --file /mnt/galaxy/tmp/jobdepsUqR4RTea42a74b7bf23de1655065d377d25493f18569d396a2ca072edc0e3f40d60c43/__kraken@0.10.6_eaf8fb68 > /dev/null
94.125.130.125 - - [30/Mar/2018:12:31:13 +0000] "GET /api/histories/03552bdee8c8190f/contents?details=0d78ab6c212891ac%2C6dd5f6a56568a0ca&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-30T12%3A31%3A09.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?job_id=de3532e6c02adbd2&__identifer=rox6xy4edvs" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36"
94.125.130.125 - - [30/Mar/2018:12:31:14 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/devteam/kraken/kraken/1.2.1/build HTTP/1.0" 200 - "http://52.54.147.188/?job_id=de3532e6c02adbd2&__identifer=rox6xy4edvs" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36"
==> WARNING: A newer version of conda exists. <==
current version: 4.4.11
latest version: 4.5.0
Please update conda by running
$ conda update -n base conda
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/mnt/galaxy/tool_dependencies/_conda/lib/python2.7/site-packages/conda/exceptions.py", line 789, in __call__
return func(*args, **kwargs)
File "/mnt/galaxy/tool_dependencies/_conda/lib/python2.7/site-packages/conda/cli/main.py", line 78, in _main
exit_code = do_call(args, p)
File "/mnt/galaxy/tool_dependencies/_conda/lib/python2.7/site-packages/conda/cli/conda_argparse.py", line 77, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/mnt/galaxy/tool_dependencies/_conda/lib/python2.7/site-packages/conda/cli/main_create.py", line 11, in execute
install(args, parser, 'create')
File "/mnt/galaxy/tool_dependencies/_conda/lib/python2.7/site-packages/conda/cli/install.py", line 255, in install
handle_txn(progressive_fetch_extract, unlink_link_transaction, prefix, args, newenv)
File "/mnt/galaxy/tool_dependencies/_conda/lib/python2.7/site-packages/conda/cli/install.py", line 272, in handle_txn
unlink_link_transaction.display_actions(progressive_fetch_extract)
File "/mnt/galaxy/tool_dependencies/_conda/lib/python2.7/site-packages/conda/core/link.py", line 711, in display_actions
specs_to_remove=stp.remove_specs, specs_to_add=stp.update_specs)
File "/mnt/galaxy/tool_dependencies/_conda/lib/python2.7/site-packages/conda/plan.py", line 98, in display_actions
extra = '%15s' % human_bytes(info['size'])
File "/mnt/galaxy/tool_dependencies/_conda/lib/python2.7/site-packages/conda/_vendor/auxlib/entity.py", line 870, in __getitem__
return getattr(self, item)
File "/mnt/galaxy/tool_dependencies/_conda/lib/python2.7/site-packages/conda/_vendor/auxlib/entity.py", line 414, in __get__
raise AttributeError("A value for {0} has not been set".format(self.name))
AttributeError: A value for size has not been set
`$ /mnt/galaxy/tool_dependencies/_conda/bin/conda create -y --override-channels --channel iuc --channel bioconda --channel conda-forge --channel defaults --unknown --offline --prefix /mnt/galaxy/tmp/job_working_directory/006/6088/conda-env --file /mnt/galaxy/tmp/jobdepsUqR4RTea42a74b7bf23de1655065d377d25493f18569d396a2ca072edc0e3f40d60c43/__kraken@0.10.6_eaf8fb68`
environment variables:
CIO_TEST=
CONDARC=/mnt/galaxy/tools/_condarc
CONDA_ROOT=/mnt/galaxy/tool_dependencies/_conda
PATH=/mnt/galaxy/galaxy-app/.venv/bin:/mnt/galaxy/galaxy-app/.venv/bin:/usr
/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/java
-8-oracle/bin:/usr/lib/jvm/java-8-oracle/db/bin:/usr/lib/jvm/java-8-or
acle/jre/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
active environment : None
user config file : /mnt/galaxy/tmp/conda_exec_home_ViulbK/.condarc
populated config files : /mnt/galaxy/tools/_condarc
conda version : 4.4.11
conda-build version : not installed
python version : 2.7.14.final.0
base environment : /mnt/galaxy/tool_dependencies/_conda (writable)
channel URLs : https://conda.anaconda.org/iuc/linux-64 (offline)
https://conda.anaconda.org/iuc/noarch (offline)
https://conda.anaconda.org/bioconda/linux-64 (offline)
https://conda.anaconda.org/bioconda/noarch (offline)
https://conda.anaconda.org/conda-forge/linux-64 (offline)
https://conda.anaconda.org/conda-forge/noarch (offline)
https://repo.continuum.io/pkgs/main/linux-64 (offline)
https://repo.continuum.io/pkgs/main/noarch (offline)
https://repo.continuum.io/pkgs/free/linux-64 (offline)
https://repo.continuum.io/pkgs/free/noarch (offline)
https://repo.continuum.io/pkgs/r/linux-64 (offline)
https://repo.continuum.io/pkgs/r/noarch (offline)
https://repo.continuum.io/pkgs/pro/linux-64 (offline)
https://repo.continuum.io/pkgs/pro/noarch (offline)
package cache : /mnt/galaxy/tool_dependencies/_conda/pkgs
/mnt/galaxy/tmp/conda_exec_home_ViulbK/.conda/pkgs
envs directories : /mnt/galaxy/tool_dependencies/_conda/envs
/mnt/galaxy/tmp/conda_exec_home_ViulbK/.conda/envs
platform : linux-64
user-agent : conda/4.4.11 requests/2.18.4 CPython/2.7.14 Linux/3.13.0-100-generic ubuntu/14.04 glibc/2.19
UID:GID : 1001:100
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 2018-03-30 12:31:14,527 Executing command: /mnt/galaxy/tool_dependencies/_conda/bin/conda clean --tarballs -y
94.125.130.125 - - [30/Mar/2018:12:31:14 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/devteam/kraken/kraken/1.2.1/build HTTP/1.0" 200 - "http://52.54.147.188/?job_id=de3532e6c02adbd2&__identifer=rox6xy4edvs" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36"
Cache location:
There are no tarballs to remove
galaxy.jobs.runners ERROR 2018-03-30 12:31:14,964 (6088) Failure preparing job
Traceback (most recent call last):
File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job
job_wrapper.prepare()
File "/mnt/galaxy/galaxy-app/lib/galaxy/jobs/__init__.py", line 886, in prepare
self.dependency_shell_commands = self.tool.build_dependency_shell_commands(job_directory=self.working_directory)
File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 1450, in build_dependency_shell_commands
tool_instance=self
File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/deps/__init__.py", line 113, in dependency_shell_commands
return [dependency.shell_commands(requirement) for requirement, dependency in requirement_to_dependency.items()]
File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/deps/resolvers/conda.py", line 470, in shell_commands
self.build_environment()
File "/mnt/galaxy/galaxy-app/lib/galaxy/tools/deps/resolvers/conda.py", line 465, 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 2018-03-30 12:31:15,173 Bug report plugin generated response None
galaxy.tools.error_reports DEBUG 2018-03-30 12:31:15,173 Bug report plugin generated response None
galaxy.tools.error_reports DEBUG 2018-03-30 12:31:15,173 Bug report plugin generated response None
94.125.130.125 - - [30/Mar/2018:12:31:18 +0000] "GET /api/histories/03552bdee8c8190f/contents?details=0d78ab6c212891ac%2C6dd5f6a56568a0ca&order=hid&v=dev&q=update_time-ge&q=deleted&q=purged&qv=2018-03-30T12%3A31%3A14.000Z&qv=False&qv=False HTTP/1.0" 200 - "http://52.54.147.188/?job_id=de3532e6c02adbd2&__identifer=rox6xy4edvs" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36"
94.125.130.125 - - [30/Mar/2018:12:31:18 +0000] "GET /api/histories/03552bdee8c8190f?keys=size%2Cnon_ready_jobs%2Ccontents_active%2Chid_counter HTTP/1.0" 200 - "http://52.54.147.188/?job_id=de3532e6c02adbd2&__identifer=rox6xy4edvs" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36"
94.125.130.125 - - [30/Mar/2018:12:31:18 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/devteam/kraken/kraken/1.2.1/build HTTP/1.0" 200 - "http://52.54.147.188/?job_id=de3532e6c02adbd2&__identifer=rox6xy4edvs" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36"
94.125.130.125 - - [30/Mar/2018:12:31:18 +0000] "POST /api/tools/toolshed.g2.bx.psu.edu/repos/devteam/kraken/kraken/1.2.1/build HTTP/1.0" 200 - "http://52.54.147.188/?job_id=de3532e6c02adbd2&__identifer=rox6xy4edvs" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36"
94.125.130.125 - - [30/Mar/2018:12:31:19 +0000] "GET /api/histories/03552bdee8c8190f/contents/datasets/26eb5a373342f1e1 HTTP/1.0" 200 - "http://52.54.147.188/?job_id=de3532e6c02adbd2&__identifer=rox6xy4edvs" "Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/65.0.3325.181 Safari/537.36"
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment