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mulled enabled destination Chronos: command outputs and file
docker run --name mesos-99ec34b0-982a-4f18-888f-0435a5d73d9a --runtime runc -v /export/galaxy/database/:/export/galaxy/database/:rw -v /var/lib/mesos/slaves/89907619-076f-4f00-8bfd-67a1bbd599a6-S1/docker/links/99ec34b0-982a-4f18-888f-0435a5d73d9a:/mnt/mesos/sandbox --net host --restart no -h vnode-0.localdomain -e 'MESOS_SANDBOX=/mnt/mesos/sandbox' -e 'MESOS_TASK_ID=ct:1557825422389:0:galaxy-chronos-134:' -e 'mesos_task_id=ct:1557825422389:0:galaxy-chronos-134:' -e 'CHRONOS_JOB_RUN_ATTEMPT=0' -e 'CHRONOS_RESOURCE_CPU=2.0' -e 'CHRONOS_RESOURCE_MEM=512.0' -e 'MESOS_CONTAINER_NAME=mesos-99ec34b0-982a-4f18-888f-0435a5d73d9a' -e 'CHRONOS_RESOURCE_GPU=0' -e 'HOST=90.147.188.117' -e 'CHRONOS_JOB_NAME=galaxy-chronos-134' -e 'CHRONOS_JOB_OWNER=pietro.mandreoli@gmail.com' -e 'CHRONOS_JOB_RUN_TIME=1557825422389' -e 'CHRONOS_RESOURCE_DISK=256.0' -e 'PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin' -a stdout -a stderr --entrypoint "/bin/sh" quay.io/biocontainers/fastqc:0.11.8--1 -c rm -rf working; mkdir -p working; cd working; /export/galaxy/database/job_working_directory/000/134/tool_script.sh; return_code=$?; if [ -f /export/galaxy/database/job_working_directory/000/134/working/output.html ] ; then cp /export/galaxy/database/job_working_directory/000/134/working/output.html /export/galaxy/database/files/000/dataset_188.dat ; fi; if [ -f /export/galaxy/database/job_working_directory/000/134/working/output.txt ] ; then cp /export/galaxy/database/job_working_directory/000/134/working/output.txt /export/galaxy/database/files/000/dataset_189.dat ; fi; sh -c "exit $return_code"
~$tail -f /var/log/handler0.log
galaxy.jobs DEBUG 2019-05-14 09:16:59,863 (134) Working directory for job is: /export/galaxy/database/job_working_directory/000/134
galaxy.jobs.handler DEBUG 2019-05-14 09:16:59,881 (134) Dispatching to chronos runner
galaxy.jobs DEBUG 2019-05-14 09:16:59,900 (134) Persisting job destination (destination id: chronos_dest)
galaxy.jobs.runners DEBUG 2019-05-14 09:16:59,938 Job [134] queued (56.920 ms)
galaxy.jobs.handler INFO 2019-05-14 09:16:59,971 (134) Job dispatched
galaxy.jobs.runners.chronos DEBUG 2019-05-14 09:16:59,977 Starting queue_job for job 134
galaxy.tools.deps DEBUG 2019-05-14 09:17:00,171 Using dependency fastqc version 0.11.8 of type conda
galaxy.tools.deps.containers INFO 2019-05-14 09:17:00,196 Checking with container resolver [ExplicitContainerResolver[]] found description [None]
galaxy.tools.deps.containers INFO 2019-05-14 09:17:00,464 Checking with container resolver [CachedMulledDockerContainerResolver[namespace=biocontainers]] found description [None]
galaxy.tools.deps.containers INFO 2019-05-14 09:17:01,283 Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.8--1,type=docker]]
galaxy.jobs.command_factory INFO 2019-05-14 09:17:01,319 Built script [/export/galaxy/database/job_working_directory/000/134/tool_script.sh] for tool command [ln -s '/export/galaxy/database/files/000/dataset_90.dat' 'Sc_IP _1__fastq' && mkdir -p '/export/galaxy/database/job_working_directory/000/134/dataset_188_files' && fastqc --outdir '/export/galaxy/database/job_working_directory/000/134/dataset_188_files' --quiet --extract --kmers 7 -f 'fastq' 'Sc_IP _1__fastq' && cp '/export/galaxy/database/job_working_directory/000/134/dataset_188_files'/*/fastqc_data.txt output.txt && cp '/export/galaxy/database/job_working_directory/000/134/dataset_188_files'/*\.html output.html]
galaxy.tools.deps.containers INFO 2019-05-14 09:17:01,400 Checking with container resolver [ExplicitContainerResolver[]] found description [None]
galaxy.tools.deps.containers INFO 2019-05-14 09:17:01,550 Checking with container resolver [CachedMulledDockerContainerResolver[namespace=biocontainers]] found description [None]
galaxy.tools.deps.containers INFO 2019-05-14 09:17:02,257 Checking with container resolver [MulledDockerContainerResolver[namespace=biocontainers]] found description [ContainerDescription[identifier=quay.io/biocontainers/fastqc:0.11.8--1,type=docker]]
galaxy.jobs INFO 2019-05-14 09:17:21,359 Collecting metrics for Job 134
galaxy.jobs DEBUG 2019-05-14 09:17:21,379 job 134 ended (finish() executed in (754.287 ms))
ls -lh /export/galaxy/database/job_working_directory/000/132
drwxr-xr-x. 3 root root 4,0K 13 mag 15.27 dataset_184_files
-rw-r--r--. 1 galaxy galaxy 0 13 mag 15.27 galaxy_132.e
-rw-r--r--. 1 galaxy galaxy 46 13 mag 15.27 galaxy_132.o
-rwxr-xr-x. 1 galaxy galaxy 733 13 mag 15.26 tool_script.sh
drwxr-xr-x. 2 galaxy galaxy 4,0K 13 mag 15.26 working
ls -lh /export/galaxy/database/job_working_directory/000/132/working
totale 0
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