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bgruening / docker-galaxy

:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
http://bgruening.github.io/docker-galaxy
MIT License
226 stars 134 forks source link

Docker galaxy cannot be installed and started correctly #587

Closed shenweiyan closed 3 days ago

shenweiyan commented 3 years ago

I have tried to install docker-galaxy-stable, however, is there a problem that doesn't work correctly, it seems docker galaxy cannot start normally. The following is the log information at startup:

$ docker run -it -p 8090:80 -p 8091:21 -p 8092:22 -v /galaxy-dist/galaxy-store/:/export/ bgruening/galaxy-stable
Enable Galaxy reports authentification
Checking /export...
Disable Galaxy Interactive Environments. Start with --privileged to enable IE's.
Starting postgres
postgresql: started
Checking if database is up and running
Traceback (most recent call last):
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1284, in _execute_context
    cursor, statement, parameters, context
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 590, in do_execute
    cursor.execute(statement, parameters)
psycopg2.errors.UndefinedTable: relation "galaxy_user" does not exist
LINE 3: FROM galaxy_user
             ^

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/bin/check_database.py", line 25, in <module>
    query.count()
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3749, in count
    return self.from_self(col).scalar()
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3469, in scalar
    ret = self.one()
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3436, in one
    ret = self.one_or_none()
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3405, in one_or_none
    ret = list(self)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3481, in __iter__
    return self._execute_and_instances(context)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3506, in _execute_and_instances
    result = conn.execute(querycontext.statement, self._params)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1020, in execute
    return meth(self, multiparams, params)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 298, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_clauseelement
    distilled_params,
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1324, in _execute_context
    e, statement, parameters, cursor, context
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1518, in _handle_dbapi_exception
    sqlalchemy_exception, with_traceback=exc_info[2], from_=e
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise_
    raise exception
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1284, in _execute_context
    cursor, statement, parameters, context
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 590, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.ProgrammingError: (psycopg2.errors.UndefinedTable) relation "galaxy_user" does not exist
LINE 3: FROM galaxy_user
             ^

[SQL: SELECT count(*) AS count_1
FROM (SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.username AS galaxy_user_username, galaxy_user.password AS galaxy_user_password, galaxy_user.last_password_change AS galaxy_user_last_password_change, galaxy_user.external AS galaxy_user_external, galaxy_user.form_values_id AS galaxy_user_form_values_id, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged, galaxy_user.disk_usage AS galaxy_user_disk_usage, galaxy_user.active AS galaxy_user_active, galaxy_user.activation_token AS galaxy_user_activation_token
FROM galaxy_user
WHERE galaxy_user.email = %(email_1)s) AS anon_1]
[parameters: {'email_1': 'admin@galaxy.org'}]
(Background on this error at: http://sqlalche.me/e/f405)
Waiting for database
Traceback (most recent call last):
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1284, in _execute_context
    cursor, statement, parameters, context
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 590, in do_execute
    cursor.execute(statement, parameters)
psycopg2.errors.UndefinedTable: relation "galaxy_user" does not exist
LINE 3: FROM galaxy_user
             ^

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/local/bin/check_database.py", line 25, in <module>
    query.count()
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3749, in count
    return self.from_self(col).scalar()
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3469, in scalar
    ret = self.one()
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3436, in one
    ret = self.one_or_none()
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3405, in one_or_none
    ret = list(self)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3481, in __iter__
    return self._execute_and_instances(context)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/orm/query.py", line 3506, in _execute_and_instances
    result = conn.execute(querycontext.statement, self._params)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1020, in execute
    return meth(self, multiparams, params)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 298, in _execute_on_connection
    return connection._execute_clauseelement(self, multiparams, params)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1139, in _execute_clauseelement
    distilled_params,
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1324, in _execute_context
    e, statement, parameters, cursor, context
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1518, in _handle_dbapi_exception
    sqlalchemy_exception, with_traceback=exc_info[2], from_=e
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise_
    raise exception
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1284, in _execute_context
    cursor, statement, parameters, context
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 590, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.ProgrammingError: (psycopg2.errors.UndefinedTable) relation "galaxy_user" does not exist
LINE 3: FROM galaxy_user
             ^

[SQL: SELECT count(*) AS count_1
FROM (SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.username AS galaxy_user_username, galaxy_user.password AS galaxy_user_password, galaxy_user.last_password_change AS galaxy_user_last_password_change, galaxy_user.external AS galaxy_user_external, galaxy_user.form_values_id AS galaxy_user_form_values_id, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged, galaxy_user.disk_usage AS galaxy_user_disk_usage, galaxy_user.active AS galaxy_user_active, galaxy_user.activation_token AS galaxy_user_activation_token
FROM galaxy_user
WHERE galaxy_user.email = %(email_1)s) AS anon_1]
[parameters: {'email_1': 'admin@galaxy.org'}]
(Background on this error at: http://sqlalche.me/e/f405)
Waiting for database
Database connected
Starting cron
cron: started
Starting ProFTP
proftpd: started
Starting Galaxy reports webapp
reports: ERROR (spawn error)
Starting nodejs
galaxy:galaxy_nodejs_proxy: ERROR (spawn error)
Starting condor
condor: started
Starting slurmctld
Starting slurmd
Creating admin user admin with key fakekey and password password if not existing
==> /home/galaxy/logs/handler0.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,106 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,109 Adding inherited display application 'igv_fasta' to datatype 'fasta.gz'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,125 Adding inherited display application 'ensembl_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,125 Adding inherited display application 'igv_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,125 Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,125 Adding inherited display application 'igv_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,125 Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,126 Adding inherited display application 'igv_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,126 Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,126 Adding inherited display application 'igv_gff' to datatype 'gtf'

==> /home/galaxy/logs/handler1.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,817 Adding inherited display application 'igv_interval_as_bed' to datatype 'chrint'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,827 Adding inherited display application 'igv_fasta' to datatype 'fasta.gz'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,893 Adding inherited display application 'ensembl_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,898 Adding inherited display application 'igv_gff' to datatype 'gff3'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,898 Adding inherited display application 'ensembl_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,898 Adding inherited display application 'igv_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,899 Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,899 Adding inherited display application 'igv_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,912 Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:16,912 Adding inherited display application 'igv_gff' to datatype 'gtf'

==> /home/galaxy/logs/reports.log <==
galaxy.web.framework.base DEBUG 2021-09-28 01:38:09,887 Enabling 'jobs' controller, class: Jobs
galaxy.web.framework.base DEBUG 2021-09-28 01:38:09,894 Enabling 'users' controller, class: Users
galaxy.web.framework.base DEBUG 2021-09-28 01:38:09,899 Enabling 'system' controller, class: System
galaxy.webapps.util DEBUG 2021-09-28 01:38:09,902 Enabling 'paste.httpexceptions' middleware
galaxy.webapps.util DEBUG 2021-09-28 01:38:09,909 Enabling 'RecursiveMiddleware' middleware
galaxy.webapps.util DEBUG 2021-09-28 01:38:09,924 Enabling 'ErrorMiddleware' middleware
galaxy.webapps.util DEBUG 2021-09-28 01:38:09,927 Enabling 'TransLogger' middleware
galaxy.webapps.util DEBUG 2021-09-28 01:38:09,929 Enabling 'XForwardedHostMiddleware' middleware
Starting server in PID 563.
serving on http://127.0.0.1:9001

==> /home/galaxy/logs/slurmctld.log <==
[2021-09-28T01:37:38.894] No trigger state file (/tmp/slurm/trigger_state.old) to recover
[2021-09-28T01:37:38.894] _preserve_plugins: backup_controller not specified
[2021-09-28T01:37:38.894] Reinitializing job accounting state
[2021-09-28T01:37:38.894] cons_res: select_p_reconfigure
[2021-09-28T01:37:38.894] cons_res: select_p_node_init
[2021-09-28T01:37:38.894] cons_res: preparing for 1 partitions
[2021-09-28T01:37:38.895] Running as primary controller
[2021-09-28T01:37:38.898] No parameter for mcs plugin, default values set
[2021-09-28T01:37:38.898] mcs: MCSParameters = (null). ondemand set.
[2021-09-28T01:37:42.214] SchedulerParameters=default_queue_depth=100,max_rpc_cnt=0,max_sched_time=2,partition_job_depth=0,sched_max_job_start=0,sched_min_interval=2

==> /home/galaxy/logs/slurmd.log <==
[2021-09-28T01:37:40.709] error: Domain socket directory /var/spool/slurmd: No such file or directory
[2021-09-28T01:37:40.810] Message aggregation disabled
[2021-09-28T01:37:40.812] CPU frequency setting not configured for this node
[2021-09-28T01:37:41.015] slurmd version 17.11.2 started
[2021-09-28T01:37:41.093] slurmd started on Tue, 28 Sep 2021 01:37:41 +0000
[2021-09-28T01:37:41.112] CPUs=4 Boards=1 Sockets=4 Cores=1 Threads=1 Memory=15871 TmpDisk=1007799 Uptime=3224664 CPUSpecList=(null) FeaturesAvail=(null) FeaturesActive=(null)

==> /home/galaxy/logs/uwsgi.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:17,202 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.gz'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:17,202 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:17,203 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'igv_gff' to datatype 'gff3.bz2'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:17,204 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:17,204 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'igv_gff' to datatype 'gtf'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:17,289 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:17,289 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:17,289 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:17,290 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:17,291 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'igv_fasta' to datatype 'sequences'

==> /home/galaxy/logs/handler0.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,306 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,310 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,310 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,310 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,312 Adding inherited display application 'igv_fasta' to datatype 'sequences'

==> /home/galaxy/logs/handler1.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,133 Adding inherited display application 'ensembl_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,200 Adding inherited display application 'gbrowse_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,200 Adding inherited display application 'rviewer_interval' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,200 Adding inherited display application 'igv_interval_as_bed' to datatype 'encodepeak'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,202 Adding inherited display application 'igv_fasta' to datatype 'sequences'

==> /home/galaxy/logs/handler0.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,392 Adding inherited display application 'igv_fasta' to datatype 'mothur.align'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,507 Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,512 Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,518 Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,525 Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,530 Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,585 Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,592 Loaded converter: CONVERTER_cram_to_bam_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,597 Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,602 Loaded converter: CONVERTER_bed_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,607 Loaded converter: CONVERTER_bed_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,612 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,618 Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,624 Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,629 Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,684 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,691 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,696 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,708 Loaded converter: csv_to_tabular
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,713 Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,719 Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,725 Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,730 Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,786 Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,790 Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,795 Loaded converter: CONVERTER_fasta_to_fai
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,804 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,813 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,818 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,828 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,883 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,888 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,892 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,897 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,902 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,908 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,913 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,917 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,920 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,923 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,927 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,930 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,989 Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,005 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,012 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,025 Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,085 Loaded converter: CONVERTER_gff_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,091 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,096 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,102 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,106 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,112 Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,120 Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,129 Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,186 Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,194 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,200 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,211 Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,285 Loaded converter: CONVERTER_picard_interval_list_to_bed6
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,296 Loaded converter: CONVERTER_tar_to_directory
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,301 Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,304 Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,311 Loaded converter: CONVERTER_encodepeak_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,316 Loaded converter: CONVERTER_encodepeak_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,318 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,319 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,323 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,327 Loaded converter: CONVERTER_sam_to_unsorted_bam

==> /home/galaxy/logs/handler1.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,402 Adding inherited display application 'igv_fasta' to datatype 'mothur.align'
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,511 Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,516 Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,521 Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,525 Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,605 Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,609 Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,612 Loaded converter: CONVERTER_cram_to_bam_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,615 Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,620 Loaded converter: CONVERTER_bed_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,624 Loaded converter: CONVERTER_bed_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,628 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,687 Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,698 Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,703 Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,710 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,716 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,720 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,726 Loaded converter: csv_to_tabular
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,730 Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,784 Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,787 Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,790 Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,794 Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,797 Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,805 Loaded converter: CONVERTER_fasta_to_fai
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,814 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,822 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,827 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,887 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,893 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,896 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,900 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,906 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,910 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,914 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,919 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,922 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,926 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,928 Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,931 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,985 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:32,992 Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,006 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,013 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,027 Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,087 Loaded converter: CONVERTER_gff_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,093 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,099 Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,104 Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,108 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,114 Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,124 Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,131 Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,189 Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,195 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,200 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,212 Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,223 Loaded converter: CONVERTER_picard_interval_list_to_bed6
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,283 Loaded converter: CONVERTER_tar_to_directory
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,286 Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,289 Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,292 Loaded converter: CONVERTER_encodepeak_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,295 Loaded converter: CONVERTER_encodepeak_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,297 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,299 Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,301 Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,304 Loaded converter: CONVERTER_sam_to_unsorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,307 Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,310 Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,315 Loaded converter: CONVERTER_sam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,318 Loaded converter: tabular_to_dbnsfp
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,323 Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,326 Loaded converter: CONVERTER_gz_to_uncompressed

==> /home/galaxy/logs/handler0.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,330 Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,384 Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,388 Loaded converter: CONVERTER_sam_to_bigwig_0

==> /home/galaxy/logs/handler1.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,387 Loaded converter: CONVERTER_vcf_to_bgzip_0

==> /home/galaxy/logs/handler0.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,393 Loaded converter: tabular_to_dbnsfp
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,396 Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,399 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,408 Loaded converter: CONVERTER_vcf_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,416 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,425 Loaded converter: CONVERTER_vcf_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,429 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,492 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,500 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,519 Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,530 Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,588 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,591 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,599 Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,611 Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,615 Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,620 Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,623 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,627 Loaded converter: CONVERTER_biom1_to_biom2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,631 Loaded converter: CONVERTER_biom2_to_biom1
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,705 Loaded converter: CONVERTER_SMILES_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,713 Loaded converter: CONVERTER_SMILES_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,723 Loaded converter: CONVERTER_SMILES_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,729 Loaded converter: CONVERTER_SMILES_to_MOL
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,735 Loaded converter: CONVERTER_SMILES_to_MOL2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,741 Loaded converter: CONVERTER_smiles_to_smiles
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,746 Loaded converter: CONVERTER_sdf_to_smiles
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,751 Loaded converter: CONVERTER_sdf_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,791 Loaded converter: CONVERTER_sdf_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,797 Loaded converter: CONVERTER_sdf_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,807 Loaded converter: CONVERTER_inchi_to_smi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,812 Loaded converter: CONVERTER_inchi_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,822 Loaded converter: CONVERTER_inchi_to_mol
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,828 Loaded converter: CONVERTER_inchi_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,898 Loaded converter: CONVERTER_inchi_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,905 Loaded converter: CONVERTER_mol_to_smi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,911 Loaded converter: CONVERTER_mol_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,916 Loaded converter: CONVERTER_mol_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,921 Loaded converter: CONVERTER_mol_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,927 Loaded converter: CONVERTER_mol2_to_smi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,984 Loaded converter: CONVERTER_mol2_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,994 Loaded converter: CONVERTER_mol2_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,000 Loaded converter: CONVERTER_mol2_to_mol
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,004 Loaded converter: CONVERTER_mol2_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,018 Loaded converter: CONVERTER_cml_to_smiles
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,026 Loaded converter: CONVERTER_cml_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,084 Loaded converter: CONVERTER_cml_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,092 Loaded converter: CONVERTER_cml_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,098 Loaded converter: CONVERTER_ref_to_seq_taxomony
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,106 Loaded converter: CONVERTER_neostorezip_to_neostore
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,212 Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2021-09-28 01:38:34,227 Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2021-09-28 01:38:34,233 Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2021-09-28 01:38:34,287 Loaded data fetch tool: __DATA_FETCH__
sqlitedict INFO 2021-09-28 01:38:34,307 opening Sqlite table 'unnamed' in '/galaxy-central/database/tool_cache/tmp7itu8yt3cache.sqlite.tmp'
sqlitedict.SqliteMultithread DEBUG 2021-09-28 01:38:34,324 received: --close--, send: --no more--
sqlitedict INFO 2021-09-28 01:38:34,385 opening Sqlite table 'unnamed' in '/galaxy-central/database/tool_cache/cache.sqlite'

==> /home/galaxy/logs/handler1.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,396 Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,410 Loaded converter: CONVERTER_vcf_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,416 Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,425 Loaded converter: CONVERTER_bcf_to_bcf_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,431 Loaded converter: CONVERTER_bcf_uncompressed_to_bcf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,484 Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,494 Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,517 Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,527 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,590 Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,599 Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,606 Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,641 Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,707 Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,714 Loaded converter: CONVERTER_biom1_to_biom2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,721 Loaded converter: CONVERTER_biom2_to_biom1
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,725 Loaded converter: CONVERTER_SMILES_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,730 Loaded converter: CONVERTER_SMILES_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,734 Loaded converter: CONVERTER_SMILES_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,787 Loaded converter: CONVERTER_SMILES_to_MOL
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,795 Loaded converter: CONVERTER_SMILES_to_MOL2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,805 Loaded converter: CONVERTER_smiles_to_smiles
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,813 Loaded converter: CONVERTER_sdf_to_smiles
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,818 Loaded converter: CONVERTER_sdf_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,823 Loaded converter: CONVERTER_sdf_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,827 Loaded converter: CONVERTER_sdf_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,895 Loaded converter: CONVERTER_inchi_to_smi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,902 Loaded converter: CONVERTER_inchi_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,910 Loaded converter: CONVERTER_inchi_to_mol
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,915 Loaded converter: CONVERTER_inchi_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,920 Loaded converter: CONVERTER_inchi_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,928 Loaded converter: CONVERTER_mol_to_smi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,934 Loaded converter: CONVERTER_mol_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,993 Loaded converter: CONVERTER_mol_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:33,997 Loaded converter: CONVERTER_mol_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,008 Loaded converter: CONVERTER_mol2_to_smi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,014 Loaded converter: CONVERTER_mol2_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,023 Loaded converter: CONVERTER_mol2_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,029 Loaded converter: CONVERTER_mol2_to_mol
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,083 Loaded converter: CONVERTER_mol2_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,094 Loaded converter: CONVERTER_cml_to_smiles
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,102 Loaded converter: CONVERTER_cml_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,108 Loaded converter: CONVERTER_cml_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,111 Loaded converter: CONVERTER_cml_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,113 Loaded converter: CONVERTER_ref_to_seq_taxomony
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,115 Loaded converter: CONVERTER_neostorezip_to_neostore
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:34,202 Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2021-09-28 01:38:34,221 Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2021-09-28 01:38:34,226 Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2021-09-28 01:38:34,232 Loaded data fetch tool: __DATA_FETCH__
sqlitedict INFO 2021-09-28 01:38:34,307 opening Sqlite table 'unnamed' in '/galaxy-central/database/tool_cache/tmpj1v_0tyxcache.sqlite.tmp'
sqlitedict.SqliteMultithread DEBUG 2021-09-28 01:38:34,324 received: --close--, send: --no more--
sqlitedict INFO 2021-09-28 01:38:34,331 opening Sqlite table 'unnamed' in '/galaxy-central/database/tool_cache/cache.sqlite'
sqlitedict.SqliteMultithread DEBUG 2021-09-28 01:38:34,400 received: --close--, send: --no more--
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,402 VisualizationsRegistry, loaded plugin: aequatus

==> /home/galaxy/logs/handler0.log <==
sqlitedict.SqliteMultithread DEBUG 2021-09-28 01:38:34,423 received: --close--, send: --no more--
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,428 VisualizationsRegistry, loaded plugin: aequatus
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,482 VisualizationsRegistry, loaded plugin: annotate_image
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,484 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,484 VisualizationsRegistry, loaded plugin: chiraviz
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,485 Visualizations plugin disabled: Circster. Skipping...
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,486 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,487 VisualizationsRegistry, loaded plugin: csg
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,488 VisualizationsRegistry, loaded plugin: cytoscape
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,493 VisualizationsRegistry, loaded plugin: drawrna
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,495 VisualizationsRegistry, loaded plugin: editor
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,584 VisualizationsRegistry, loaded plugin: example
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,588 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,590 VisualizationsRegistry, loaded plugin: graphviz
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,700 VisualizationsRegistry, loaded plugin: heatmap_cluster
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,724 VisualizationsRegistry, loaded plugin: heatmap_default
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,726 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,733 VisualizationsRegistry, loaded plugin: hivtrace
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,789 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,789 VisualizationsRegistry, loaded plugin: hyphyvision
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,886 VisualizationsRegistry, loaded plugin: jqplot_bar
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,917 VisualizationsRegistry, loaded plugin: jqplot_box
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,986 VisualizationsRegistry, loaded plugin: jqplot_histogram
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,009 VisualizationsRegistry, loaded plugin: jqplot_line
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,030 VisualizationsRegistry, loaded plugin: jqplot_scatter
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:35,032 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,084 VisualizationsRegistry, loaded plugin: audio_player
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:35,086 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,088 VisualizationsRegistry, loaded plugin: video_player
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,090 VisualizationsRegistry, loaded plugin: msa
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:35,092 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,093 VisualizationsRegistry, loaded plugin: mvpapp
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,097 VisualizationsRegistry, loaded plugin: ngl
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,109 VisualizationsRegistry, loaded plugin: nvd3_bar
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,119 VisualizationsRegistry, loaded plugin: nvd3_bar_stacked
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,128 VisualizationsRegistry, loaded plugin: nvd3_histogram
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,184 VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,193 VisualizationsRegistry, loaded plugin: nvd3_horizontal
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,200 VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,209 VisualizationsRegistry, loaded plugin: nvd3_line
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,217 VisualizationsRegistry, loaded plugin: nvd3_line_focus
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,221 VisualizationsRegistry, loaded plugin: nvd3_pie
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,229 VisualizationsRegistry, loaded plugin: nvd3_scatter
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,285 VisualizationsRegistry, loaded plugin: nvd3_stackedarea
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,298 VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,310 VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,316 VisualizationsRegistry, loaded plugin: openlayers
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,320 VisualizationsRegistry, loaded plugin: phylocanvas
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,323 VisualizationsRegistry, loaded plugin: phyloviz
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,326 VisualizationsRegistry, loaded plugin: pv
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,330 VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:35,397 Visualizations plugin disabled: Sweepster. Skipping...
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,399 VisualizationsRegistry, loaded plugin: trackster
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:35,400 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,401 VisualizationsRegistry, loaded plugin: unipept
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,404 VisualizationsRegistry, loaded plugin: venn

==> /home/galaxy/logs/handler1.log <==
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,410 VisualizationsRegistry, loaded plugin: annotate_image
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,414 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,417 VisualizationsRegistry, loaded plugin: chiraviz
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,421 Visualizations plugin disabled: Circster. Skipping...
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,425 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,426 VisualizationsRegistry, loaded plugin: csg
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,430 VisualizationsRegistry, loaded plugin: cytoscape
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,483 VisualizationsRegistry, loaded plugin: drawrna
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,488 VisualizationsRegistry, loaded plugin: editor
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,507 VisualizationsRegistry, loaded plugin: example
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,528 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,537 VisualizationsRegistry, loaded plugin: graphviz
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,632 VisualizationsRegistry, loaded plugin: heatmap_cluster
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,639 VisualizationsRegistry, loaded plugin: heatmap_default
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,642 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,643 VisualizationsRegistry, loaded plugin: hivtrace
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,645 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,647 VisualizationsRegistry, loaded plugin: hyphyvision
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,655 VisualizationsRegistry, loaded plugin: jqplot_bar
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,697 VisualizationsRegistry, loaded plugin: jqplot_box
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,791 VisualizationsRegistry, loaded plugin: jqplot_histogram
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,829 VisualizationsRegistry, loaded plugin: jqplot_line
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,902 VisualizationsRegistry, loaded plugin: jqplot_scatter
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,907 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,917 VisualizationsRegistry, loaded plugin: audio_player
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,919 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,920 VisualizationsRegistry, loaded plugin: video_player
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,923 VisualizationsRegistry, loaded plugin: msa
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:34,927 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,929 VisualizationsRegistry, loaded plugin: mvpapp
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,933 VisualizationsRegistry, loaded plugin: ngl
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:34,997 VisualizationsRegistry, loaded plugin: nvd3_bar
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,009 VisualizationsRegistry, loaded plugin: nvd3_bar_stacked
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,020 VisualizationsRegistry, loaded plugin: nvd3_histogram
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,112 VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,131 VisualizationsRegistry, loaded plugin: nvd3_horizontal
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,201 VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,209 VisualizationsRegistry, loaded plugin: nvd3_line
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,287 VisualizationsRegistry, loaded plugin: nvd3_line_focus
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,292 VisualizationsRegistry, loaded plugin: nvd3_pie
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,302 VisualizationsRegistry, loaded plugin: nvd3_scatter
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,312 VisualizationsRegistry, loaded plugin: nvd3_stackedarea
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,321 VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,330 VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,331 VisualizationsRegistry, loaded plugin: openlayers
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,386 VisualizationsRegistry, loaded plugin: phylocanvas
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,387 VisualizationsRegistry, loaded plugin: phyloviz
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,390 VisualizationsRegistry, loaded plugin: pv
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,391 VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:35,393 Visualizations plugin disabled: Sweepster. Skipping...
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,398 VisualizationsRegistry, loaded plugin: trackster
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:35,399 template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,400 VisualizationsRegistry, loaded plugin: unipept
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:35,403 VisualizationsRegistry, loaded plugin: venn

==> /home/galaxy/logs/handler0.log <==
galaxy.tours INFO 2021-09-28 01:38:35,426 Loaded tour 'core.scratchbook'
galaxy.tours INFO 2021-09-28 01:38:35,519 Loaded tour 'core.history'
galaxy.tours INFO 2021-09-28 01:38:36,312 Loaded tour 'core.galaxy_ui'

==> /home/galaxy/logs/handler1.log <==
galaxy.tours INFO 2021-09-28 01:38:35,518 Loaded tour 'core.scratchbook'
galaxy.tours INFO 2021-09-28 01:38:35,908 Loaded tour 'core.history'

==> /home/galaxy/logs/uwsgi.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,199 [p:121,w:0,m:0] [MainThread] Adding inherited display application 'igv_fasta' to datatype 'mothur.align'

==> /home/galaxy/logs/handler0.log <==
galaxy.jobs.manager DEBUG 2021-09-28 01:38:37,005 Initializing job handler
galaxy.jobs INFO 2021-09-28 01:38:37,005 Handler 'handler0' will load all configured runner plugins
galaxy.jobs.runners DEBUG 2021-09-28 01:38:37,011 Loading SlurmRunner with params: {'drmaa_library_path': '/usr/lib/slurm-drmaa/lib/libdrmaa.so'}
galaxy.jobs.runners.state_handler_factory DEBUG 2021-09-28 01:38:37,016 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners.drmaa INFO 2021-09-28 01:38:37,016 Overriding DRMAA_LIBRARY_PATH due to runner plugin parameter: /usr/lib/slurm-drmaa/lib/libdrmaa.so
pulsar.managers.util.drmaa DEBUG 2021-09-28 01:38:37,131 Initializing DRMAA session from thread MainThread

==> /home/galaxy/logs/handler1.log <==
galaxy.tours INFO 2021-09-28 01:38:36,494 Loaded tour 'core.galaxy_ui'
galaxy.jobs.manager DEBUG 2021-09-28 01:38:36,819 Initializing job handler
galaxy.jobs INFO 2021-09-28 01:38:36,819 Handler 'handler1' will load all configured runner plugins
galaxy.jobs.runners DEBUG 2021-09-28 01:38:36,908 Loading SlurmRunner with params: {'drmaa_library_path': '/usr/lib/slurm-drmaa/lib/libdrmaa.so'}
galaxy.jobs.runners.state_handler_factory DEBUG 2021-09-28 01:38:36,982 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners.drmaa INFO 2021-09-28 01:38:36,983 Overriding DRMAA_LIBRARY_PATH due to runner plugin parameter: /usr/lib/slurm-drmaa/lib/libdrmaa.so
pulsar.managers.util.drmaa DEBUG 2021-09-28 01:38:37,128 Initializing DRMAA session from thread MainThread

==> /home/galaxy/logs/uwsgi.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,501 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_Bam_Bai_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,522 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,530 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,592 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,617 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,620 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,626 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_cram_to_bam_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,690 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_to_gff_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,704 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,723 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,726 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,811 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_to_fli_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,823 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bedgraph_to_bigwig
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,835 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_len_to_linecount
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,899 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,913 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,920 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,924 [p:121,w:0,m:0] [MainThread] Loaded converter: csv_to_tabular
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,985 [p:121,w:0,m:0] [MainThread] Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:36,998 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_tabular
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,006 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_base_index
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,010 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_bowtie_color_index
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,014 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_2bit
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,021 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_len
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,031 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fasta_to_fai
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,085 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,091 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,096 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,103 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,108 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,112 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,117 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,123 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,128 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,132 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,197 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,202 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,206 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,210 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_fastq_to_fqtoc0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,217 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,223 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,232 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gff_to_bed_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,284 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,291 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,302 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gff_to_fli_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,309 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gff_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,313 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,316 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bz2_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,320 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gff_to_interval_index_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,324 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,331 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bed_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,389 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bedstrict_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,393 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bed6_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,397 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bed12_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,400 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,402 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,409 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,417 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_picard_interval_list_to_bed6

==> /home/galaxy/logs/handler0.log <==
galaxy.jobs.runners DEBUG 2021-09-28 01:38:37,508 Starting 2 SlurmRunner workers
galaxy.jobs DEBUG 2021-09-28 01:38:37,510 Loaded job runner 'galaxy.jobs.runners.slurm:SlurmJobRunner' as 'slurm'
galaxy.jobs.runners.state_handler_factory DEBUG 2021-09-28 01:38:37,520 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2021-09-28 01:38:37,520 Starting 2 LocalRunner workers
galaxy.jobs DEBUG 2021-09-28 01:38:37,521 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.handler DEBUG 2021-09-28 01:38:37,522 Loaded job runners plugins: slurm:local
galaxy.jobs.handler INFO 2021-09-28 01:38:37,526 job handler stop queue started
galaxy.jobs.handler DEBUG 2021-09-28 01:38:37,526 Handler queue starting for jobs assigned to handler: handler0
galaxy.web_stack.message DEBUG 2021-09-28 01:38:38,030 Bound default message handler 'JobHandlerMessage.default_handler' to <bound method TaskMessage.default_handler of <galaxy.jobs.handler.JobHandlerQueue object at 0x7f526835b400>>
galaxy.jobs.handler INFO 2021-09-28 01:38:38,038 job handler queue started
galaxy.jobs.handler INFO 2021-09-28 01:38:38,124 job handler stop queue started

==> /home/galaxy/logs/handler1.log <==
galaxy.jobs.runners DEBUG 2021-09-28 01:38:37,511 Starting 2 SlurmRunner workers
galaxy.jobs DEBUG 2021-09-28 01:38:37,515 Loaded job runner 'galaxy.jobs.runners.slurm:SlurmJobRunner' as 'slurm'
galaxy.jobs.runners.state_handler_factory DEBUG 2021-09-28 01:38:37,520 Loaded 'failure' state handler from module galaxy.jobs.runners.state_handlers.resubmit
galaxy.jobs.runners DEBUG 2021-09-28 01:38:37,520 Starting 2 LocalRunner workers
galaxy.jobs DEBUG 2021-09-28 01:38:37,523 Loaded job runner 'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
galaxy.jobs.handler DEBUG 2021-09-28 01:38:37,523 Loaded job runners plugins: slurm:local
galaxy.jobs.handler INFO 2021-09-28 01:38:37,527 job handler stop queue started
galaxy.jobs.handler DEBUG 2021-09-28 01:38:37,527 Handler queue starting for jobs assigned to handler: handler1
galaxy.web_stack.message DEBUG 2021-09-28 01:38:38,087 Bound default message handler 'JobHandlerMessage.default_handler' to <bound method TaskMessage.default_handler of <galaxy.jobs.handler.JobHandlerQueue object at 0x7f0f1055ab00>>
galaxy.jobs.handler INFO 2021-09-28 01:38:38,090 job handler queue started
galaxy.jobs.handler INFO 2021-09-28 01:38:38,094 job handler stop queue started

==> /home/galaxy/logs/uwsgi.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,422 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_tar_to_directory
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,426 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_maf_to_fasta_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,429 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_maf_to_interval_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,486 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_encodepeak_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,492 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_encodepeak_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,497 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,500 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,505 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_interval_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,512 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sam_to_unsorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,517 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_coodinate_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,521 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bam_to_qname_sorted_bam
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,528 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sam_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,587 [p:121,w:0,m:0] [MainThread] Loaded converter: tabular_to_dbnsfp
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,593 [p:121,w:0,m:0] [MainThread] Loaded converter: tabular_to_csv
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,599 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,623 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_vcf_to_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,630 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_vcf_to_vcf_bgzip_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,690 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_vcf_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,696 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bed_gff_or_vcf_to_bigwig_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,705 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bcf_to_bcf_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,712 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_bcf_uncompressed_to_bcf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,716 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_wig_to_bigwig
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,723 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_wiggle_to_interval_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,729 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_vcf_bgzip_to_tabix_0
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,783 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,787 [p:121,w:0,m:0] [MainThread] Loaded converter: lped2fpedconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,800 [p:121,w:0,m:0] [MainThread] Loaded converter: lped2pbedconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,805 [p:121,w:0,m:0] [MainThread] Loaded converter: pbed2lpedconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,809 [p:121,w:0,m:0] [MainThread] Loaded converter: pbed2ldindepconvert
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,817 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_gz_to_uncompressed
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,824 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_biom1_to_biom2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,836 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_biom2_to_biom1
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,843 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_SMILES_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,900 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_SMILES_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,908 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_SMILES_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,917 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_SMILES_to_MOL
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,927 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_SMILES_to_MOL2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,938 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_smiles_to_smiles
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:37,986 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sdf_to_smiles
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,120 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sdf_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,183 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sdf_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,194 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_sdf_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,207 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_inchi_to_smi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,384 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_inchi_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,403 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_inchi_to_mol
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,419 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_inchi_to_mol2

==> /home/galaxy/logs/handler0.log <==
galaxy.workflow.scheduling_manager INFO 2021-09-28 01:38:38,590 No workflow schedulers plugin config file defined, using default scheduler.
galaxy.workflow.scheduling_manager DEBUG 2021-09-28 01:38:38,591 Starting workflow schedulers
galaxy.queue_worker INFO 2021-09-28 01:38:39,212 Binding and starting galaxy control worker for handler0

==> /home/galaxy/logs/handler1.log <==
galaxy.workflow.scheduling_manager INFO 2021-09-28 01:38:38,618 No workflow schedulers plugin config file defined, using default scheduler.
galaxy.workflow.scheduling_manager DEBUG 2021-09-28 01:38:38,624 Starting workflow schedulers
galaxy.queue_worker INFO 2021-09-28 01:38:39,204 Binding and starting galaxy control worker for handler1

==> /home/galaxy/logs/uwsgi.log <==
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,497 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_inchi_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,508 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol_to_smi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,521 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,524 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,588 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,605 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol2_to_smi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,695 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol2_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,714 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol2_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,725 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol2_to_mol
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,784 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_mol2_to_cml
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,805 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_cml_to_smiles
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,823 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_cml_to_inchi
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,832 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_cml_to_sdf
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,894 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_cml_to_mol2
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,898 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_ref_to_seq_taxomony
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,909 [p:121,w:0,m:0] [MainThread] Loaded converter: CONVERTER_neostorezip_to_neostore
galaxy.datatypes.registry DEBUG 2021-09-28 01:38:38,982 [p:121,w:0,m:0] [MainThread] Loaded external metadata tool: __SET_METADATA__
galaxy.tools.special_tools DEBUG 2021-09-28 01:38:39,009 [p:121,w:0,m:0] [MainThread] Loaded history export tool: __EXPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2021-09-28 01:38:39,029 [p:121,w:0,m:0] [MainThread] Loaded history import tool: __IMPORT_HISTORY__
galaxy.tools.special_tools DEBUG 2021-09-28 01:38:39,035 [p:121,w:0,m:0] [MainThread] Loaded data fetch tool: __DATA_FETCH__
sqlitedict INFO 2021-09-28 01:38:39,123 [p:121,w:0,m:0] [MainThread] opening Sqlite table 'unnamed' in '/galaxy-central/database/tool_cache/tmp_ny5cqgzcache.sqlite.tmp'
sqlitedict.SqliteMultithread DEBUG 2021-09-28 01:38:39,223 [p:121,w:0,m:0] [Thread-3] received: --close--, send: --no more--
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,298 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: aequatus
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,312 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: annotate_image
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:39,316 [p:121,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,318 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: chiraviz
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:39,320 [p:121,w:0,m:0] [MainThread] Visualizations plugin disabled: Circster. Skipping...
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:39,383 [p:121,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,384 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: csg
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,399 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: cytoscape
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,402 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: drawrna
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,407 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: editor
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,410 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: example
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:39,413 [p:121,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,414 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: graphviz

==> /home/galaxy/logs/handler0.log <==
galaxy.queue_worker INFO 2021-09-28 01:38:39,797 Queuing async task rebuild_toolbox_search_index for handler0.

==> /home/galaxy/logs/handler1.log <==
galaxy.queue_worker INFO 2021-09-28 01:38:39,519 Queuing async task rebuild_toolbox_search_index for handler1.
galaxy.model.database_heartbeat DEBUG 2021-09-28 01:38:39,916 handler1 is config watcher
galaxy.util.watcher DEBUG 2021-09-28 01:38:40,187 Watching for changes in directory (recursively): /galaxy-central/tool-data

==> /home/galaxy/logs/uwsgi.log <==
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,429 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: heatmap_cluster
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,598 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: heatmap_default
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:39,600 [p:121,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,600 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: hivtrace
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:39,601 [p:121,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,602 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: hyphyvision
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,609 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: jqplot_bar
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,615 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: jqplot_box
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,701 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: jqplot_histogram
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,717 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: jqplot_line
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,726 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: jqplot_scatter
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:39,728 [p:121,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,729 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: audio_player
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:39,730 [p:121,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,730 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: video_player
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,732 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: msa
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:39,734 [p:121,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,734 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: mvpapp
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,739 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: ngl
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,800 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,810 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_bar_stacked
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,818 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,831 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_histogram_discrete
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,882 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,907 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_horizontal_stacked
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,918 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_line
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:39,997 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_line_focus
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,025 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_pie
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,102 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_scatter
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,115 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,192 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_full
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,209 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: nvd3_stackedarea_stream
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,212 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: openlayers
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,218 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: phylocanvas
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,220 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: phyloviz
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,225 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: pv
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,232 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: scatterplot
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:40,283 [p:121,w:0,m:0] [MainThread] Visualizations plugin disabled: Sweepster. Skipping...
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,287 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: trackster
galaxy.visualization.plugins.config_parser INFO 2021-09-28 01:38:40,293 [p:121,w:0,m:0] [MainThread] template syntax is deprecated: use entry_point instead
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,295 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: unipept
galaxy.visualization.plugins.registry INFO 2021-09-28 01:38:40,314 [p:121,w:0,m:0] [MainThread] VisualizationsRegistry, loaded plugin: venn

==> /home/galaxy/logs/handler0.log <==
galaxy.queue_worker ERROR 2021-09-28 01:38:41,307 Error queueing async task: '{'task': 'rebuild_toolbox_search_index', 'kwargs': {}}'. for control.handler0@662fc7812edb
Traceback (most recent call last):
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1284, in _execute_context
    cursor, statement, parameters, context
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 590, in do_execute
    cursor.execute(statement, parameters)
psycopg2.errors.UniqueViolation: duplicate key value violates unique constraint "pg_type_typname_nsp_index"
DETAIL:  Key (typname, typnamespace)=(kombu_message, 2200) already exists.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/galaxy-central/lib/galaxy/queue_worker.py", line 126, in send_task
    headers={'epoch': time.time()},
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/messaging.py", line 181, in publish
    exchange_name, declare,
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/connection.py", line 533, in _ensured
    return fun(*args, **kwargs)
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/messaging.py", line 194, in _publish
    [maybe_declare(entity) for entity in declare]
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/messaging.py", line 194, in <listcomp>
    [maybe_declare(entity) for entity in declare]
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/messaging.py", line 102, in maybe_declare
    return maybe_declare(entity, self.channel, retry, **retry_policy)
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/common.py", line 121, in maybe_declare
    return _maybe_declare(entity, channel)
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/common.py", line 161, in _maybe_declare
    entity.declare(channel=channel)
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/entity.py", line 611, in declare
    self._create_queue(nowait=nowait, channel=channel)
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/entity.py", line 620, in _create_queue
    self.queue_declare(nowait=nowait, passive=False, channel=channel)
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/entity.py", line 655, in queue_declare
    nowait=nowait,
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/transport/virtual/base.py", line 531, in queue_declare
    self._new_queue(queue, **kwargs)
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/transport/sqlalchemy/__init__.py", line 101, in _new_queue
    self._get_or_create(queue)
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/transport/sqlalchemy/__init__.py", line 80, in _get_or_create
    obj = self.session.query(self.queue_cls) \
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/transport/sqlalchemy/__init__.py", line 75, in session
    _, Session = self._open()
  File "/galaxy_venv/lib/python3.7/site-packages/kombu/transport/sqlalchemy/__init__.py", line 67, in _open
    metadata.create_all(engine)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/sql/schema.py", line 4465, in create_all
    ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2104, in _run_visitor
    conn._run_visitor(visitorcallable, element, **kwargs)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1663, in _run_visitor
    visitorcallable(self.dialect, self, **kwargs).traverse_single(element)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 144, in traverse_single
    return meth(obj, **kw)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 787, in visit_metadata
    _is_metadata_operation=True,
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/sql/visitors.py", line 144, in traverse_single
    return meth(obj, **kw)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 832, in visit_table
    include_foreign_key_constraints,  # noqa
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1020, in execute
    return meth(self, multiparams, params)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/sql/ddl.py", line 72, in _execute_on_connection
    return connection._execute_ddl(self, multiparams, params)
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1082, in _execute_ddl
    compiled,
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1324, in _execute_context
    e, statement, parameters, cursor, context
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1518, in _handle_dbapi_exception
    sqlalchemy_exception, with_traceback=exc_info[2], from_=e
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise_
    raise exception
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1284, in _execute_context
    cursor, statement, parameters, context
  File "/galaxy_venv/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 590, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.IntegrityError: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "pg_type_typname_nsp_index"
DETAIL:  Key (typname, typnamespace)=(kombu_message, 2200) already exists.

[SQL:
CREATE TABLE kombu_message (
        id INTEGER NOT NULL,
        visible BOOLEAN,
        timestamp TIMESTAMP WITHOUT TIME ZONE,
        payload TEXT NOT NULL,
        version SMALLINT NOT NULL,
        queue_id INTEGER,
        PRIMARY KEY (id),
        CONSTRAINT "FK_kombu_message_queue" FOREIGN KEY(queue_id) REFERENCES kombu_queue (id)
)

]
(Background on this error at: http://sqlalche.me/e/gkpj)
galaxy.app INFO 2021-09-28 01:38:41,317 Galaxy app startup finished (51405.335 ms)
galaxy.web_stack INFO 2021-09-28 01:38:41,317 Galaxy server instance 'handler0' is running

==> /home/galaxy/logs/uwsgi.log <==
galaxy.tours INFO 2021-09-28 01:38:40,486 [p:121,w:0,m:0] [MainThread] Loaded tour 'core.scratchbook'
galaxy.tours INFO 2021-09-28 01:38:40,589 [p:121,w:0,m:0] [MainThread] Loaded tour 'core.history'
galaxy.tours INFO 2021-09-28 01:38:40,625 [p:121,w:0,m:0] [MainThread] Loaded tour 'core.galaxy_ui'
galaxy.workflow.scheduling_manager INFO 2021-09-28 01:38:40,798 [p:121,w:0,m:0] [MainThread] No workflow schedulers plugin config file defined, using default scheduler.
galaxy.app INFO 2021-09-28 01:38:41,087 [p:121,w:0,m:0] [MainThread] Galaxy app startup finished (125169.027 ms)
galaxy.web.framework.base DEBUG 2021-09-28 01:38:41,211 [p:121,w:0,m:0] [MainThread] Enabling 'interactive_environments' controller, class: InteractiveEnvironmentsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:41,311 [p:121,w:0,m:0] [MainThread] Enabling 'dataset' controller, class: DatasetInterface

==> /home/galaxy/logs/handler1.log <==
galaxy.app INFO 2021-09-28 01:38:41,601 Galaxy app startup finished (53270.256 ms)
galaxy.web_stack INFO 2021-09-28 01:38:41,602 Galaxy server instance 'handler1' is running
galaxy.queue_worker INFO 2021-09-28 01:38:41,727 Instance 'handler1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.queue_worker DEBUG 2021-09-28 01:38:41,728 App is not a webapp, not building a search index

==> /home/galaxy/logs/uwsgi.log <==
galaxy.web.framework.base DEBUG 2021-09-28 01:38:43,698 [p:121,w:0,m:0] [MainThread] Enabling 'admin_toolshed' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2021-09-28 01:38:43,699 [p:121,w:0,m:0] [MainThread] Enabling 'admin_toolshed' controller, class: AdminToolshed
galaxy.web.framework.base DEBUG 2021-09-28 01:38:43,704 [p:121,w:0,m:0] [MainThread] Enabling 'shed_tool_static' controller, class: ShedToolStatic
galaxy.web.framework.base DEBUG 2021-09-28 01:38:44,515 [p:121,w:0,m:0] [MainThread] Enabling 'openid' controller, class: OpenID
galaxy.web.framework.base DEBUG 2021-09-28 01:38:44,518 [p:121,w:0,m:0] [MainThread] Enabling 'interactivetool' controller, class: InteractiveTool
galaxy.web.framework.base DEBUG 2021-09-28 01:38:44,525 [p:121,w:0,m:0] [MainThread] Enabling 'data_manager' controller, class: DataManager
galaxy.web.framework.base DEBUG 2021-09-28 01:38:44,530 [p:121,w:0,m:0] [MainThread] Enabling 'userskeys' controller, class: User
galaxy.web.framework.base DEBUG 2021-09-28 01:38:44,535 [p:121,w:0,m:0] [MainThread] Enabling 'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2021-09-28 01:38:44,586 [p:121,w:0,m:0] [MainThread] Enabling 'tool_runner' controller, class: ToolRunner
galaxy.web.framework.base DEBUG 2021-09-28 01:38:44,589 [p:121,w:0,m:0] [MainThread] Enabling 'error' controller, class: Error
galaxy.web.framework.base DEBUG 2021-09-28 01:38:44,687 [p:121,w:0,m:0] [MainThread] Enabling 'visualization' controller, class: VisualizationController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:44,810 [p:121,w:0,m:0] [MainThread] Enabling 'history' controller, class: HistoryController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:46,015 [p:121,w:0,m:0] [MainThread] Enabling 'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:46,109 [p:121,w:0,m:0] [MainThread] Enabling 'authnz' controller, class: JSAppLauncher
galaxy.web.framework.base DEBUG 2021-09-28 01:38:46,109 [p:121,w:0,m:0] [MainThread] Enabling 'authnz' controller, class: OIDC
galaxy.web.framework.base DEBUG 2021-09-28 01:38:46,116 [p:121,w:0,m:0] [MainThread] Enabling 'root' controller, class: RootController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:46,117 [p:121,w:0,m:0] [MainThread] Enabling 'library' controller, class: Library
galaxy.web.framework.base DEBUG 2021-09-28 01:38:46,117 [p:121,w:0,m:0] [MainThread] Enabling 'admin' controller, class: AdminGalaxy
galaxy.web.framework.base DEBUG 2021-09-28 01:38:46,314 [p:121,w:0,m:0] [MainThread] Enabling 'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,054 [p:121,w:0,m:0] [MainThread] Enabling 'page' controller, class: PageController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,059 [p:121,w:0,m:0] [MainThread] Enabling 'tag' controller, class: TagsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,063 [p:121,w:0,m:0] [MainThread] Enabling 'user' controller, class: User
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,085 [p:121,w:0,m:0] [MainThread] Enabling 'roles' API controller, class: RoleAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,087 [p:121,w:0,m:0] [MainThread] Enabling 'tags' API controller, class: TagsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,095 [p:121,w:0,m:0] [MainThread] Enabling 'tool_shed_repositories' API controller, class: ToolShedRepositoriesController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,097 [p:121,w:0,m:0] [MainThread] Enabling 'trs_consumer' API controller, class: TrsConsumeAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,100 [p:121,w:0,m:0] [MainThread] Enabling 'groups' API controller, class: GroupAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,102 [p:121,w:0,m:0] [MainThread] Enabling 'webhooks' API controller, class: WebhooksController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,106 [p:121,w:0,m:0] [MainThread] Enabling 'dataset_collections' API controller, class: DatasetCollectionsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,115 [p:121,w:0,m:0] [MainThread] Enabling 'remote_files' API controller, class: RemoteFilesAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,121 [p:121,w:0,m:0] [MainThread] Enabling 'folders' API controller, class: FoldersController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,123 [p:121,w:0,m:0] [MainThread] Enabling 'tool_entry_points' API controller, class: ToolEntryPointsAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:51,125 [p:121,w:0,m:0] [MainThread] Enabling 'authenticate' API controller, class: AuthenticationController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,895 [p:121,w:0,m:0] [MainThread] Enabling 'search' API controller, class: SearchController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,901 [p:121,w:0,m:0] [MainThread] Enabling 'folder_contents' API controller, class: FolderContentsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,905 [p:121,w:0,m:0] [MainThread] Enabling 'history_content_provenance' API controller, class: HDAProvenanceController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,905 [p:121,w:0,m:0] [MainThread] Enabling 'ldda_provenance' API controller, class: LDDAProvenanceController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,908 [p:121,w:0,m:0] [MainThread] Enabling 'page_revisions' API controller, class: PageRevisionsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,923 [p:121,w:0,m:0] [MainThread] Enabling 'tools' API controller, class: ToolsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,925 [p:121,w:0,m:0] [MainThread] Enabling 'metrics' API controller, class: MetricsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,929 [p:121,w:0,m:0] [MainThread] Enabling 'job_files' API controller, class: JobFilesAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,931 [p:121,w:0,m:0] [MainThread] Enabling 'quotas' API controller, class: QuotaAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,934 [p:121,w:0,m:0] [MainThread] Enabling 'display_applications' API controller, class: DisplayApplicationsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,942 [p:121,w:0,m:0] [MainThread] Enabling 'cloudauthz' API controller, class: CloudAuthzController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:53,984 [p:121,w:0,m:0] [MainThread] Enabling 'configuration' API controller, class: ConfigurationController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,028 [p:121,w:0,m:0] [MainThread] Enabling 'cloud' API controller, class: CloudController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,037 [p:121,w:0,m:0] [MainThread] Enabling 'history_content_tags' API controller, class: HistoryContentTagsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,038 [p:121,w:0,m:0] [MainThread] Enabling 'history_tags' API controller, class: HistoryTagsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,038 [p:121,w:0,m:0] [MainThread] Enabling 'workflow_tags' API controller, class: WorkflowTagsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,090 [p:121,w:0,m:0] [MainThread] Enabling 'history_contents' API controller, class: HistoryContentsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,093 [p:121,w:0,m:0] [MainThread] Enabling 'datatypes' API controller, class: DatatypesController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,099 [p:121,w:0,m:0] [MainThread] Enabling 'visualizations' API controller, class: VisualizationsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,103 [p:121,w:0,m:0] [MainThread] Enabling 'genomes' API controller, class: GenomesController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,113 [p:121,w:0,m:0] [MainThread] Enabling 'job_ports' API controller, class: JobPortsAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,117 [p:121,w:0,m:0] [MainThread] Enabling 'libraries' API controller, class: LibrariesController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,119 [p:121,w:0,m:0] [MainThread] Enabling 'group_users' API controller, class: GroupUsersAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,121 [p:121,w:0,m:0] [MainThread] Enabling 'tours' API controller, class: ToursController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,128 [p:121,w:0,m:0] [MainThread] Enabling 'histories' API controller, class: HistoriesController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,199 [p:121,w:0,m:0] [MainThread] Enabling 'workflows' API controller, class: WorkflowsAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,210 [p:121,w:0,m:0] [MainThread] Enabling 'library_datasets' API controller, class: LibraryDatasetsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,211 [p:121,w:0,m:0] [MainThread] Enabling 'history_annotations' API controller, class: HistoryAnnotationsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,211 [p:121,w:0,m:0] [MainThread] Enabling 'history_content_annotations' API controller, class: HistoryContentAnnotationsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,211 [p:121,w:0,m:0] [MainThread] Enabling 'workflow_annotations' API controller, class: WorkflowAnnotationsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,216 [p:121,w:0,m:0] [MainThread] Enabling 'jobs' API controller, class: JobController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,220 [p:121,w:0,m:0] [MainThread] Enabling 'group_roles' API controller, class: GroupRolesAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,228 [p:121,w:0,m:0] [MainThread] Enabling 'forms' API controller, class: FormDefinitionAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,230 [p:121,w:0,m:0] [MainThread] Enabling 'trs_search' API controller, class: TrsSearchAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,290 [p:121,w:0,m:0] [MainThread] Enabling 'users' API controller, class: UserAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,292 [p:121,w:0,m:0] [MainThread] Enabling 'history_dataset_extended_metadata' API controller, class: HistoryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,292 [p:121,w:0,m:0] [MainThread] Enabling 'library_dataset_extended_metadata' API controller, class: LibraryDatasetExtendMetadataController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,294 [p:121,w:0,m:0] [MainThread] Enabling 'container_resolution' API controller, class: ContainerResolutionAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,295 [p:121,w:0,m:0] [MainThread] Enabling 'uploads' API controller, class: UploadsAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,298 [p:121,w:0,m:0] [MainThread] Enabling 'pages' API controller, class: PagesController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,300 [p:121,w:0,m:0] [MainThread] Enabling 'toolshed' API controller, class: ToolShedController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,303 [p:121,w:0,m:0] [MainThread] Enabling 'tool_dependencies' API controller, class: ToolDependenciesAPIController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,306 [p:121,w:0,m:0] [MainThread] Enabling 'tool_data' API controller, class: ToolData
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,308 [p:121,w:0,m:0] [MainThread] Enabling 'plugins' API controller, class: PluginsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,312 [p:121,w:0,m:0] [MainThread] Enabling 'library_contents' API controller, class: LibraryContentsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,317 [p:121,w:0,m:0] [MainThread] Enabling 'datasets' API controller, class: DatasetsController
galaxy.web.framework.base DEBUG 2021-09-28 01:38:54,319 [p:121,w:0,m:0] [MainThread] Enabling 'dynamic_tools' API controller, class: DynamicToolsController
galaxy.webapps.util DEBUG 2021-09-28 01:38:55,819 [p:121,w:0,m:0] [MainThread] Enabling 'paste.httpexceptions' middleware
galaxy.webapps.util DEBUG 2021-09-28 01:38:55,828 [p:121,w:0,m:0] [MainThread] Enabling 'RecursiveMiddleware' middleware
galaxy.webapps.util DEBUG 2021-09-28 01:38:55,828 [p:121,w:0,m:0] [MainThread] Enabling 'ErrorMiddleware' middleware
galaxy.webapps.util DEBUG 2021-09-28 01:38:55,899 [p:121,w:0,m:0] [MainThread] Enabling 'TransLogger' middleware
galaxy.webapps.util DEBUG 2021-09-28 01:38:55,902 [p:121,w:0,m:0] [MainThread] Enabling 'XForwardedHostMiddleware' middleware
galaxy.webapps.util DEBUG 2021-09-28 01:38:55,902 [p:121,w:0,m:0] [MainThread] Enabling 'RequestIDMiddleware' middleware
galaxy.webapps.util DEBUG 2021-09-28 01:38:55,902 [p:121,w:0,m:0] [MainThread] Enabling 'BatchMiddleware' middleware
galaxy.webapps.galaxy.buildapp DEBUG 2021-09-28 01:38:55,907 [p:121,w:0,m:0] [MainThread] Prior to webapp return, Galaxy thread <_MainThread(MainThread, started 139750565128000)> is alive.
galaxy.webapps.galaxy.buildapp DEBUG 2021-09-28 01:38:55,908 [p:121,w:0,m:0] [MainThread] Prior to webapp return, Galaxy thread <SqliteMultithread(Thread-4, started daemon 139750363531008)> is alive.
Tue Sep 28 01:38:55 2021 - WSGI app 0 (mountpoint='') ready in 205 seconds on interpreter 0x558a0d901dc0 pid: 121 (default app)
Tue Sep 28 01:38:55 2021 - *** uWSGI is running in multiple interpreter mode ***
Tue Sep 28 01:38:55 2021 - spawned uWSGI master process (pid: 121)
Tue Sep 28 01:38:55 2021 - spawned uWSGI worker 1 (pid: 789, cores: 4)
Tue Sep 28 01:38:55 2021 - spawned 2 offload threads for uWSGI worker 1
Tue Sep 28 01:38:56 2021 - spawned uWSGI worker 2 (pid: 792, cores: 4)
Tue Sep 28 01:38:56 2021 - spawned 2 offload threads for uWSGI worker 2
Tue Sep 28 01:38:56 2021 - *** Stats server enabled on 127.0.0.1:9191 fd: 17 ***
galaxy.web_stack DEBUG 2021-09-28 01:38:56,016 [p:789,w:1,m:0] [MainThread] Calling postfork function: <bound method ApplicationStack.set_postfork_server_name of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f1a11a76400>>
Tue Sep 28 01:38:56 2021 - spawned uWSGI http 1 (pid: 795)
Tue Sep 28 01:38:56 2021 - running "unix_signal:2 gracefully_kill_them_all" (master-start)...
Tue Sep 28 01:38:56 2021 - running "unix_signal:15 gracefully_kill_them_all" (master-start)...
galaxy.web_stack DEBUG 2021-09-28 01:38:56,197 [p:792,w:2,m:0] [MainThread] Calling postfork function: <bound method ApplicationStack.set_postfork_server_name of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f1a11a76400>>
galaxy.web_stack DEBUG 2021-09-28 01:38:56,828 [p:789,w:1,m:0] [MainThread] server_name set to: main.web.1
galaxy.web_stack DEBUG 2021-09-28 01:38:56,831 [p:789,w:1,m:0] [MainThread] Calling postfork function: <bound method ToolDocumentCache.reopen_ro of <galaxy.tools.cache.ToolDocumentCache object at 0x7f1a110e86a0>>
sqlitedict INFO 2021-09-28 01:38:56,906 [p:789,w:1,m:0] [MainThread] opening Sqlite table 'unnamed' in '/galaxy-central/database/tool_cache/cache.sqlite'
galaxy.web_stack DEBUG 2021-09-28 01:38:57,020 [p:792,w:2,m:0] [MainThread] server_name set to: main.web.2
galaxy.web_stack DEBUG 2021-09-28 01:38:57,021 [p:792,w:2,m:0] [MainThread] Calling postfork function: <bound method ToolDocumentCache.reopen_ro of <galaxy.tools.cache.ToolDocumentCache object at 0x7f1a110e86a0>>
sqlitedict INFO 2021-09-28 01:38:57,033 [p:792,w:2,m:0] [MainThread] opening Sqlite table 'unnamed' in '/galaxy-central/database/tool_cache/cache.sqlite'
galaxy.web_stack DEBUG 2021-09-28 01:38:57,121 [p:789,w:1,m:0] [MainThread] Calling postfork function: <bound method JobManager.start of <galaxy.jobs.manager.JobManager object at 0x7f1a100a90b8>>
galaxy.web_stack DEBUG 2021-09-28 01:38:57,123 [p:789,w:1,m:0] [MainThread] Calling postfork function: <bound method DatabaseHeartbeat.start of <galaxy.model.database_heartbeat.DatabaseHeartbeat object at 0x7f1a100b3828>>
galaxy.web_stack DEBUG 2021-09-28 01:38:57,214 [p:789,w:1,m:0] [MainThread] Calling postfork function: <bound method UWSGIApplicationStack.start of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f1a11a76400>>
galaxy.web_stack DEBUG 2021-09-28 01:38:57,217 [p:789,w:1,m:0] [MainThread] Calling postfork function: <bound method GalaxyQueueWorker.bind_and_start of <GalaxyQueueWorker(Thread-1, initial daemon)>>
galaxy.queue_worker INFO 2021-09-28 01:38:57,223 [p:789,w:1,m:0] [MainThread] Binding and starting galaxy control worker for main.web.1
galaxy.web_stack DEBUG 2021-09-28 01:38:57,290 [p:792,w:2,m:0] [MainThread] Calling postfork function: <bound method JobManager.start of <galaxy.jobs.manager.JobManager object at 0x7f1a100a90b8>>
galaxy.web_stack DEBUG 2021-09-28 01:38:57,299 [p:792,w:2,m:0] [MainThread] Calling postfork function: <bound method DatabaseHeartbeat.start of <galaxy.model.database_heartbeat.DatabaseHeartbeat object at 0x7f1a100b3828>>
galaxy.web_stack DEBUG 2021-09-28 01:38:57,339 [p:792,w:2,m:0] [MainThread] Calling postfork function: <bound method UWSGIApplicationStack.start of <galaxy.web_stack.UWSGIApplicationStack object at 0x7f1a11a76400>>
galaxy.web_stack DEBUG 2021-09-28 01:38:57,341 [p:792,w:2,m:0] [MainThread] Calling postfork function: <bound method GalaxyQueueWorker.bind_and_start of <GalaxyQueueWorker(Thread-1, initial daemon)>>
galaxy.queue_worker INFO 2021-09-28 01:38:57,343 [p:792,w:2,m:0] [MainThread] Binding and starting galaxy control worker for main.web.2
galaxy.web_stack DEBUG 2021-09-28 01:38:57,504 [p:789,w:1,m:0] [MainThread] Calling postfork function: <function UniverseApplication.__init__.<locals>.<lambda> at 0x7f1a1009c158>
galaxy.queue_worker INFO 2021-09-28 01:38:57,511 [p:789,w:1,m:0] [MainThread] Queuing async task rebuild_toolbox_search_index for main.web.1.
galaxy.web_stack DEBUG 2021-09-28 01:38:57,502 [p:792,w:2,m:0] [MainThread] Calling postfork function: <function UniverseApplication.__init__.<locals>.<lambda> at 0x7f1a1009c158>
galaxy.queue_worker INFO 2021-09-28 01:38:57,514 [p:792,w:2,m:0] [MainThread] Queuing async task rebuild_toolbox_search_index for main.web.2.
galaxy.model.database_heartbeat DEBUG 2021-09-28 01:39:01,365 [p:789,w:1,m:0] [database_heartbeart_main.web.1.thread] main.web.1 is config watcher
galaxy.model.database_heartbeat DEBUG 2021-09-28 01:39:01,383 [p:792,w:2,m:0] [database_heartbeart_main.web.2.thread] main.web.2 is config watcher
galaxy.util.watcher DEBUG 2021-09-28 01:39:02,786 [p:792,w:2,m:0] [database_heartbeart_main.web.2.thread] Watching for changes in directory (recursively): /galaxy-central/tool-data
galaxy.util.watcher DEBUG 2021-09-28 01:39:02,793 [p:789,w:1,m:0] [database_heartbeart_main.web.1.thread] Watching for changes in directory (recursively): /galaxy-central/tool-data
galaxy.web_stack DEBUG 2021-09-28 01:39:02,799 [p:789,w:1,m:0] [MainThread] Calling postfork function: <built-in function register>
galaxy.web_stack DEBUG 2021-09-28 01:39:02,805 [p:789,w:1,m:0] [MainThread] Calling postfork function: <function postfork_setup at 0x7f1a11a5bd90>
galaxy.web_stack DEBUG 2021-09-28 01:39:02,807 [p:792,w:2,m:0] [MainThread] Calling postfork function: <built-in function register>
galaxy.web_stack DEBUG 2021-09-28 01:39:02,809 [p:792,w:2,m:0] [MainThread] Calling postfork function: <function postfork_setup at 0x7f1a11a5bd90>
galaxy.web_stack INFO 2021-09-28 01:39:02,809 [p:789,w:1,m:0] [MainThread] Galaxy server instance 'main.web.1' is running
Starting server in PID 121.
serving on http://127.0.0.1:8080
serving on uwsgi://127.0.0.1:4001
galaxy.web_stack INFO 2021-09-28 01:39:02,810 [p:792,w:2,m:0] [MainThread] Galaxy server instance 'main.web.2' is running
galaxy.queue_worker INFO 2021-09-28 01:39:03,299 [p:792,w:2,m:0] [Thread-1] Instance 'main.web.2' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2021-09-28 01:39:03,304 [p:792,w:2,m:0] [Thread-1] Starting to build toolbox index.
galaxy.queue_worker INFO 2021-09-28 01:39:03,407 [p:789,w:1,m:0] [Thread-1] Instance 'main.web.1' received 'rebuild_toolbox_search_index' task, executing now.
galaxy.tools.search DEBUG 2021-09-28 01:39:03,409 [p:789,w:1,m:0] [Thread-1] Starting to build toolbox index.
galaxy.tools.search DEBUG 2021-09-28 01:39:04,202 [p:792,w:2,m:0] [Thread-1] Toolbox index finished (900.223 ms)
galaxy.tools.search DEBUG 2021-09-28 01:39:06,315 [p:789,w:1,m:0] [Thread-1] Toolbox index finished (2905.242 ms)

==> /home/galaxy/logs/handler1.log <==
galaxy.model.database_heartbeat DEBUG 2021-09-28 01:39:40,316 handler1 is not config watcher

==> /home/galaxy/logs/uwsgi.log <==
galaxy.model.database_heartbeat DEBUG 2021-09-28 01:40:03,000 [p:789,w:1,m:0] [database_heartbeart_main.web.1.thread] main.web.1 is not config watcher

==> /home/galaxy/logs/slurmctld.log <==
[2021-09-28T01:42:38.254] error: Could not open job state file /tmp/slurm/job_state: No such file or directory
[2021-09-28T01:42:38.255] error: NOTE: Trying backup state save file. Jobs may be lost!
[2021-09-28T01:42:38.255] No job state file (/tmp/slurm/job_state.old) found

any idea what happens? Thanks so much

Kenzo52YZ commented 3 years ago

Hey I have been having similar issues but managed to fix it recently, can I have more information on your host distribution ? Personal experience was : Ubuntu-20.04 WSL2 (no GUI) : worked (Docker run) Ubuntu-20.04 VMWare on ESXi (Gnome GUI) : didn't work (Docker run and Docker-compose up -d) Debian 10 VMWare on ESXi (no GUI) : worked (Docker-compose up -d) I can share my docker-compose.yml if needed

Possible reasons : VMWare machines' way of interacting with assembly to build GUI might interfere with Docker's build. 有问题的话 中文也行 *if there is any trouble, chinese is also ok

shenweiyan commented 3 years ago

Hey I have been having similar issues but managed to fix it recently, can I have more information on your host distribution ? Personal experience was : Ubuntu-20.04 WSL2 (no GUI) : worked (Docker run) Ubuntu-20.04 VMWare on ESXi (Gnome GUI) : didn't work (Docker run and Docker-compose up -d) Debian 10 VMWare on ESXi (no GUI) : worked (Docker-compose up -d) I can share my docker-compose.yml if needed

Possible reasons : VMWare machines' way of interacting with assembly to build GUI might interfere with Docker's build. 有问题的话 中文也行 *if there is any trouble, chinese is also ok

It's great. Below is my host distribution information, maybe I should make some test on Ubuntu/Debian.

$ cat /proc/version
Linux version 3.10.0-957.el7.x86_64 (mockbuild@kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) ) #1 SMP Thu Nov 8 23:39:32 UTC 2018
$ lsb_release -a
LSB Version:    :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distributor ID: CentOS
Description:    CentOS Linux release 7.6.1810 (Core)
Release:        7.6.1810
Codename:       Core

By the way, you can speak Chinese?

Kenzo52YZ commented 3 years ago

会讲中文

Yes in my opinion Debian 10 with no GUI is the most straightforward installation that might work on many hardware installations (tried on ESXi and a PC both were smooth)

shenweiyan commented 3 years ago

会讲中文

Yes in my opinion Debian 10 with no GUI is the most straightforward installation that might work on many hardware installations (tried on ESXi and a PC both were smooth)

谢谢。难得在这里还能遇到一个可以中文交流的热心维护者，您是中国人也在国内做 Galaxy 的一些开发吗？

Fmrhj commented 3 years ago

I am having the same problem in two trials with Ubuntu and CentOs VMs. Trying docker-compose on the base compose yaml I get the error related to issue 588. Any news on that?

hexylena commented 3 years ago

@martinbsurfsara and I are seeing the same, it looks like a database migration issue. I see this above here

sqlalchemy.exc.IntegrityError: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "pg_type_typname_nsp_index"
DETAIL:  Key (typname, typnamespace)=(kombu_message, 2200) already exists.

[SQL:
CREATE TABLE kombu_message (
        id INTEGER NOT NULL,
        visible BOOLEAN,
        timestamp TIMESTAMP WITHOUT TIME ZONE,
        payload TEXT NOT NULL,
        version SMALLINT NOT NULL,
        queue_id INTEGER,
        PRIMARY KEY (id),
        CONSTRAINT "FK_kombu_message_queue" FOREIGN KEY(queue_id) REFERENCES kombu_queue (id)
)

And locally running the container and checking the uwsgi.log file I see

migrate.versioning.script.base DEBUG 2021-11-09 12:42:13,036 [p:1430,w:0,m:0] [MainThread] Loading script lib/galaxy/model/migrate/versions/0162_job_only_pjas.py...
migrate.versioning.script.base DEBUG 2021-11-09 12:42:13,036 [p:1430,w:0,m:0] [MainThread] Script lib/galaxy/model/migrate/versions/0162_job_only_pjas.py loaded successfully
migrate.versioning.repository DEBUG 2021-11-09 12:42:13,036 [p:1430,w:0,m:0] [MainThread] Repository lib/galaxy/model/migrate loaded successfully
migrate.versioning.repository DEBUG 2021-11-09 12:42:13,037 [p:1430,w:0,m:0] [MainThread] Config: OrderedDict([('db_settings', OrderedDict([('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))])
Traceback (most recent call last):
  File "lib/galaxy/webapps/galaxy/buildapp.py", line 48, in app_factory
    app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs)
  File "lib/galaxy/app.py", line 97, in __init__
    self._configure_models(check_migrate_databases=self.config.check_migrate_databases, check_migrate_tools=check_migrate_tools, config_file=config_file)
  File "lib/galaxy/config/__init__.py", line 1226, in _configure_models
    create_or_verify_database(db_url, config_file, self.config.database_engine_options, app=self, map_install_models=combined_install_database)
  File "lib/galaxy/model/migrate/check.py", line 140, in create_or_verify_database
    raise Exception("{}. {}{}".format(expect_msg, instructions, backup_msg))
Exception: Your database has version '1' but this code expects version '170'. Please backup your database and then migrate the database schema by running 'sh manage_db.sh upgrade'.
hexylena commented 2 years ago

@bgruening not sure if you've seen this?

hexylena commented 2 years ago

potential duplicate of https://github.com/bgruening/docker-galaxy-stable/issues/575

bgruening commented 3 days ago

Thanks to @jyotipm29 we are back on track :smile: The new 24.1 image contains a lot of changes and reflects the latest developments in Galaxy. I would like to close this PR, but please feel free to reopen and rebase against the latest version.

Please give it a try:

docker run -p 8080:80 -p 8021:21 -p 4002:4002 --privileged=true -e "GALAXY_DESTINATIONS_DEFAULT=slurm_cluster_docker"   -v /tmp/galaxy-data/:/export/ quay.io/bgruening/galaxy:24.1

... or any other combination. The readme has been updated. Please add any useful tip to it.

For a list of changes, see the Changelog.