[0KRunning with gitlab-runner 12.9.0 (4c96e5ad)
[0;m[0K on Runner_GUDMAP.RBK zQsjNk-Q
[0;msection_start:1634274196:prepare_executor
[0K[0K[36;1mPreparing the "shell" executor[0;m
[0;m[0KUsing Shell executor...
[0;msection_end:1634274196:prepare_executor
[0Ksection_start:1634274196:prepare_script
[0K[0K[36;1mPreparing environment[0;m
[0;mRunning on Nucleus009...
section_end:1634274196:prepare_script
[0Ksection_start:1634274196:get_sources
[0K[0K[36;1mGetting source from Git repository[0;m
[0;m[32;1mFetching changes...[0;m
Initialized empty Git repository in /project/BICF/BICF_Core/shared/gudmap/runner/zQsjNk-Q/rna-seq/11218/148910/.git/
[32;1mCreated fresh repository.[0;m
From https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq
* [new ref] f9ecbb83c686046f1a688f74eb63dffec8b19527 -> refs/pipelines/11218
* [new branch] develop -> origin/develop
* [new branch] master -> origin/master
* [new tag] 0.0.2 -> 0.0.2
* [new tag] 0.0.3 -> 0.0.3
* [new tag] 0.0.4_indev -> 0.0.4_indev
* [new tag] 0.1.0 -> 0.1.0
* [new tag] aws -> aws
* [new tag] v0.0.1 -> v0.0.1
* [new tag] v1.0.0 -> v1.0.0
* [new tag] v1.0.1 -> v1.0.1
* [new tag] v1.0.2 -> v1.0.2
* [new tag] v2.0.0 -> v2.0.0
* [new tag] v2.0.0rc01 -> v2.0.0rc01
* [new tag] v2.0.0rc02 -> v2.0.0rc02
* [new tag] v2.0.1 -> v2.0.1
[32;1mChecking out f9ecbb83 as master...[0;m
Removing .tmp/
[32;1mSkipping Git submodules setup[0;m
section_end:1634274199:get_sources
[0Ksection_start:1634274199:restore_cache
[0K[0K[36;1mRestoring cache[0;m
[0;msection_end:1634274199:restore_cache
[0Ksection_start:1634274199:download_artifacts
[0K[0K[36;1mDownloading artifacts[0;m
[0;msection_end:1634274199:download_artifacts
[0Ksection_start:1634274199:build_script
[0K[0K[36;1mRunning before_script and script[0;m
[0;m[32;1m$ module load python/3.6.4-anaconda[0;m
[32;1m$ pip install --user attrs==20.3.0 pytest==6.2.2 pytest-pythonpath==0.7.3 pytest-cov==2.11.1[0;m
Requirement already satisfied: attrs==20.3.0 in /home2/bicf_user/.local/lib/python3.6/site-packages
Requirement already satisfied: pytest==6.2.2 in /home2/bicf_user/.local/lib/python3.6/site-packages
Requirement already satisfied: pytest-pythonpath==0.7.3 in /home2/bicf_user/.local/lib/python3.6/site-packages
Requirement already satisfied: pytest-cov==2.11.1 in /home2/bicf_user/.local/lib/python3.6/site-packages
Requirement already satisfied: toml in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: iniconfig in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: pluggy<1.0.0a1,>=0.12 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: py>=1.8.2 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: importlib-metadata>=0.12; python_version < "3.8" in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: packaging in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest==6.2.2)
Requirement already satisfied: coverage>=5.2.1 in /home2/bicf_user/.local/lib/python3.6/site-packages (from pytest-cov==2.11.1)
Requirement already satisfied: zipp>=0.5 in /home2/bicf_user/.local/lib/python3.6/site-packages (from importlib-metadata>=0.12; python_version < "3.8"->pytest==6.2.2)
Requirement already satisfied: six in /home2/bicf_user/.local/lib/python3.6/site-packages (from packaging->pytest==6.2.2)
Requirement already satisfied: pyparsing>=2.0.2 in /home2/bicf_user/.local/lib/python3.6/site-packages (from packaging->pytest==6.2.2)
You are using pip version 9.0.1, however version 21.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
[32;1m$ module load singularity/3.5.3[0;m
[32;1m$ export SINGULARITY_CACHEDIR=${dir}cache/[0;m
[32;1m$ module load nextflow/20.01.0[0;m
[32;1m$ ln -sfn /project/BICF/BICF_Core/shared/gudmap/test_data/* ./test_data/[0;m
[32;1m$ mkdir -p ~/.deriva[0;m
[32;1m$ mkdir -p ~/.bdbag[0;m
[32;1m$ hostname[0;m
Nucleus009
[32;1m$ ulimit -a[0;m
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 1031304
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files (-n) 131072
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) unlimited
cpu time (seconds, -t) unlimited
max user processes (-u) 16384
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
[32;1m$ mkdir -p ./badges/env[0;m
[32;1m$ curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-inactive-critical?style=flat > ./badges/env/aws.svg[0;m
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1191 0 1191 0 0 7089 0 --:--:-- --:--:-- --:--:-- 7089
[32;1m$ module load awscli/1.11.139[0;m
[32;1m$ export AWS_ACCESS_KEY_ID=${aws_accesskeyid}[0;m
[32;1m$ export AWS_SECRET_ACCESS_KEY=${aws_secretaccesskey}[0;m
[32;1m$ aws configure set region ${aws_region}[0;m
[32;1m$ aws s3 cp ./test_data/auth/ s3://bicf-nf-output/ci-env/auth/ --exclude "*" --include "c*" --recursive[0;m
Completed 210 Bytes/456 Bytes (708 Bytes/s) with 2 file(s) remaining
Completed 456 Bytes/456 Bytes (1.5 KiB/s) with 2 file(s) remaining
upload: test_data/auth/cookies.txt to s3://bicf-nf-output/ci-env/auth/cookies.txt
Completed 456 Bytes/456 Bytes (1.5 KiB/s) with 1 file(s) remaining
upload: test_data/auth/credential.json to s3://bicf-nf-output/ci-env/auth/credential.json
[32;1m$ aws s3 cp ./test_data/fastq/xsmall/ s3://bicf-nf-output/ci-env/input/ --exclude "*" --include "Q-Y5F6_10K.R*.fastq.gz" --recursive[0;m
Completed 256.0 KiB/1.0 MiB (1.1 MiB/s) with 2 file(s) remaining
Completed 512.0 KiB/1.0 MiB (1.7 MiB/s) with 2 file(s) remaining
Completed 768.0 KiB/1.0 MiB (1.8 MiB/s) with 2 file(s) remaining
Completed 789.6 KiB/1.0 MiB (1.6 MiB/s) with 2 file(s) remaining
upload: test_data/fastq/xsmall/Q-Y5F6_10K.R2.fastq.gz to s3://bicf-nf-output/ci-env/input/Q-Y5F6_10K.R2.fastq.gz
Completed 789.6 KiB/1.0 MiB (1.6 MiB/s) with 1 file(s) remaining
Completed 1.0 MiB/1.0 MiB (2.0 MiB/s) with 1 file(s) remaining
upload: test_data/fastq/xsmall/Q-Y5F6_10K.R1.fastq.gz to s3://bicf-nf-output/ci-env/input/Q-Y5F6_10K.R1.fastq.gz
[32;1m$ id=$(aws batch submit-job\ # collapsed multi-line command[0;m
[32;1m$ status=$(aws batch describe-jobs --jobs ${id} | grep -oP "status\": \K.*" | tr -d '"' | tr -d ',' | tr -d " " ) && until [[ "${status}" == "SUCCEEDED" || "${status}" == "FAILED" ]]; do # collapsed multi-line command[0;m
SUBMITTED
RUNNABLE
RUNNABLE
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RUNNING
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SUCCEEDED
[32;1m$ if [ "${status}" == "SUCCEEDED" ]; then # collapsed multi-line command[0;m
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1208 0 1208 0 0 6169 0 --:--:-- --:--:-- --:--:-- 6226
section_end:1634276045:build_script
[0Ksection_start:1634276045:after_script
[0K[0K[36;1mRunning after_script[0;m
[0;m[32;1mRunning after script...[0;m
[32;1m$ module load awscli/1.11.139[0;m
[32;1m$ export AWS_ACCESS_KEY_ID=${aws_accesskeyid}[0;m
[32;1m$ export AWS_SECRET_ACCESS_KEY=${aws_secretaccesskey}[0;m
[32;1m$ aws configure set region ${aws_region}[0;m
[32;1m$ aws s3 rm s3://bicf-nf-output/ci-env/auth/ --recursive[0;m
delete: s3://bicf-nf-output/ci-env/auth/cookies.txt
Completed 1 file(s) with 1 file(s) remaining
delete: s3://bicf-nf-output/ci-env/auth/credential.json
[32;1m$ aws s3 rm s3://bicf-nf-output/ci-env/input/ --recursive[0;m
delete: s3://bicf-nf-output/ci-env/input/Q-Y5F6_10K.R1.fastq.gz
Completed 1 file(s) with 1 file(s) remaining
delete: s3://bicf-nf-output/ci-env/input/Q-Y5F6_10K.R2.fastq.gz
section_end:1634276049:after_script
[0Ksection_start:1634276049:archive_cache
[0K[0K[36;1mSaving cache[0;m
[0;msection_end:1634276049:archive_cache
[0Ksection_start:1634276049:upload_artifacts_on_success
[0K[0K[36;1mUploading artifacts for successful job[0;m
[0;m[32;1mUploading artifacts...[0;m
Runtime platform [0;m arch[0;m=amd64 os[0;m=linux pid[0;m=41311 revision[0;m=4c96e5ad version[0;m=12.9.0
badges/: found 3 matching files [0;m
Uploading artifacts to coordinator... ok [0;m id[0;m=148910 responseStatus[0;m=201 Created token[0;m=QNUCi8AG
section_end:1634276050:upload_artifacts_on_success
[0K[32;1mJob succeeded
[0;m