Created
May 14, 2019 11:40
-
-
Save pmandreoli/bbbeb2eab5c1d1772872220c01678e15 to your computer and use it in GitHub Desktop.
mulled enabled destination Chronos: command outputs and file
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 $return_code" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ~$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)) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment