Philip Mabon Takadonet
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| "Traceback (most recent call last):", | |
| " File \"/Galaxy/scripts/manage_db.py\", line 28, in <module>", | |
| " invoke_migrate_main()", | |
| " File \"/Galaxy/scripts/manage_db.py\", line 24, in invoke_migrate_main", | |
| " main(repository=repo, url=db_url)", | |
| " File \"/Galaxy/.venv/lib/python2.7/site-packages/migrate/versioning/shell.py\", line 209, in main", | |
| " ret = command_func(**kwargs)", | |
| " File \"</Galaxy/.venv/lib/python2.7/site-packages/decorator.pyc:decorator-gen-6>\", line 2, in db_version", | |
| " File \"/Galaxy/.venv/lib/python2.7/site-packages/migrate/versioning/util/__init__.py\", line 167, in with_engine", | |
| " return f(*a, **kw)", |
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| MN908947.3 7203 . C CT 133.0 PASS BaseCalledReadsWithVariant=64;BaseCalledFraction=0.160804;TotalReads=364;AlleleCount=1;SupportFraction=0.59658;SupportFractionByStrand=0.591949,0.60116;StrandSupport=74,73,107,110;StrandFisherTest=0;SOR=0.708369;RefContext=TTCATCTTTTA GT 1 |
Takadonet
/ gist:669f927e2151c053093d621921d38e61
Created
April 5, 2020 15:04
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| [samfaipath] build FASTA index... | |
| INFO [2020-04-04 22:34:36,482]: Using 32 threads with following basic args: lofreq call --verbose --ref reference.fa --call-indels --min-cov 50 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --def-alt-bq 0 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic reads.bam | |
| WARNING [2020-04-04 22:34:36,504]: Looks like the index for reads.bam is a bit old (idxstats reports no reads mapped). Reindexing should solve this. Will continue by calling samtools, so no need to worry for now though. | |
| Traceback (most recent call last): | |
| File /Galaxy/deps/_conda/envs/__lofreq@2.1.3.1/bin/lofreq2_call_pparallel.py", line 746, in <module> | |
| main() | |
| File /Galaxy/deps/_conda/envs/__lofreq@2.1.3.1/bin/lofreq2_call_pparallel.py", line 557, in main | |
| bam_bins = [Region._make(x) for x in bins_from_bamheader(bam)] | |
| File /Galaxy/deps/_conda/envs/__lofreq@2.1.3.1/bin/lofreq2_call_pparallel.py", line 283, in bins_from_bamheader |
Takadonet
/ gist:2ad91e273171c1daac6cb120ebfd19a3
Created
June 21, 2018 16:39
Cannot run : sh manage_db.sh db_version
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| sh manage_db.sh db_version | |
| stracetrace : | |
| Traceback (most recent call last): | |
| File "./scripts/manage_db.py", line 24, in <module> | |
| invoke_migrate_main() | |
| File "./scripts/manage_db.py", line 20, in invoke_migrate_main | |
| main(repository=repo, url=db_url) | |
| File "/Galaxy/galaxy-prod/venv/lib/python2.7/site-packages/migrate/versioning/shell.py", line 209, in main |
Takadonet
/ gist:808e67c946bf68f29025
Last active
August 29, 2015 14:16
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| Traceback (most recent call last): | |
| File "/galaxy/production/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 565, in finish_job | |
| job_state.job_wrapper.finish( stdout, stderr, exit_code ) | |
| File "/galaxy/production/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1250, in finish | |
| self.sa_session.flush() | |
| File "/galaxy/production/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do | |
| return getattr(self.registry(), name)(*args, **kwargs) | |
| File "/galaxy/production/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush | |
| self._flush(objects) | |
| File "/galaxy/production/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1789, in _flush |
Takadonet
/ gist:66100393301dfd71ed08
Created
September 30, 2014 18:43
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| <tool id="smalt_map" name="smalt map" version="0.0.3" > | |
| <requirements> | |
| <requirement type="package" version="1.1">smalt</requirement> | |
| </requirements> | |
| <command interpreter="bash"> | |
| smalt_map.sh $smi $sma | |
| #if $singlePaired.sPaired == "single": | |
| 1 $singlePaired.sInput1 |
Takadonet
/ gist:567a34f4b7e463faab2a
Created
September 30, 2014 18:37
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| <tool id="spades_header_fixer2" name="SPAdes fasta header fixer2" version="1.1.2"> | |
| <description>Fixes Spades Fasta ids</description> | |
| <command >#for $f in $inputs.keys# sed -r "s/>NODE(_[0-9]+)_(.*)/>$f\1 \2/g" $inputs[$f] >$output; #end for# </command> | |
| <inputs> | |
| <param name="inputs" type="data_collection" format="fasta" label="Collection of Spades Fasta file(s)" collection_type="list"/> | |
| </inputs> |
Takadonet
/ gist:053337a2a8f645bb52fb
Created
September 30, 2014 16:25
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| <tool id="spades_header_fixer" name="SPAdes fasta header fixer" version="1.1.1"> | |
| <description>Fixes Spades Fasta ids</description> | |
| <command >sed -r "s/>NODE(_[0-9]+)_(.*)/>${input.name}\1 \2/g" $input >$output</command> | |
| <inputs> | |
| <param name="input" type="data" format="fasta" label="fix these fasta headers"/> | |
| </inputs> | |
| <outputs> | |
| <data name="output" format="fasta"/> | |
| </outputs> | |
| <help> |
Takadonet
/ gist:ba21ca26748a459615e3
Created
September 3, 2014 18:43
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| "GET /tool_runner/rerun?id=dac0095901af192f HTTP/1.0" 500 - "http://galaxy.badd.ca/" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/36.0.1985.143 Safari/537.36" | |
| Error - <class 'sqlalchemy.exc.DataError'>: (DataError) invalid input syntax for integer: "hdca:567" | |
| LINE 3: WHERE history_dataset_collection_association.id = E'hdca:567... | |
| ^ | |
| 'SELECT history_dataset_collection_association.id AS history_dataset_collection_association_id, history_dataset_collection_association.collection_id AS history_dataset_collection_association_collection_id, history_dataset_collection_association.history_id AS history_dataset_collection_association_history_id, history_dataset_collection_association.name AS history_dataset_collection_association_name, history_dataset_collection_association.hid AS history_dataset_collection_association_hid, history_dataset_collection_association.visible AS history_dataset_collection_association_visible, history |
Takadonet
/ gist:7361fa11b6cfb97d9266
Created
June 10, 2014 14:29
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| ew python executable in /BADD/Applications/galaxy/tool_dependencies/snptools/1.0.0/phil/snptools/1b6ec80fe8e8/venv/bin/python | |
| install_environment.STDOUT DEBUG 2014-06-10 09:24:24,658 Installing setuptools............done. | |
| Installing setuptools............done. | |
| Installing pip...............done. | |
| Downloading/unpacking requirements.txt (from -r /BADD/Applications/galaxy/tool_dependencies/snptools/1.0.0/phil/snptools/1b6ec80fe8e8/requirements.txt (line 1)) | |
| Real name of requirement requirements.txt is requirements.txt | |
| Could not find any downloads that satisfy the requirement requirements.txt (from -r /BADD/Applications/galaxy/tool_dependencies/snptools/1.0.0/phil/snptools/1b6ec80fe8e8/requirements.txt (line 1)) | |
| No distributions at all found for requirements.txt (from -r /BADD/Applications/galaxy/tool_dependencies/snptools/1.0.0/phil/snptools/1b6ec80fe8e8/requirements.txt (line 1)) | |
| Storing complete log in /home/badd-galaxy/.pip/pip.log | |
| Traceback (most recent call last): |
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