build_badges
Gervaise Henry
1Running with gitlab-runner 12.9.0 (4c96e5ad)2 on Runner_GUDMAP.RBK zQsjNk-Q4Using Shell executor...6Running on Nucleus009...8Fetching changes...9Initialized empty Git repository in /project/BICF/BICF_Core/shared/gudmap/runner/zQsjNk-Q/rna-seq/11214/148890/.git/10Created fresh repository.12 * [new ref] f9ecbb83c686046f1a688f74eb63dffec8b19527 -> refs/pipelines/1121413 * [new branch] develop -> origin/develop14 * [new branch] master -> origin/master15 * [new tag] 0.0.2 -> 0.0.216 * [new tag] 0.0.3 -> 0.0.317 * [new tag] 0.0.4_indev -> 0.0.4_indev18 * [new tag] 0.1.0 -> 0.1.019 * [new tag] aws -> aws20 * [new tag] v0.0.1 -> v0.0.121 * [new tag] v1.0.0 -> v1.0.022 * [new tag] v1.0.1 -> v1.0.123 * [new tag] v1.0.2 -> v1.0.224 * [new tag] v2.0.0 -> v2.0.025 * [new tag] v2.0.0rc01 -> v2.0.0rc0126 * [new tag] v2.0.0rc02 -> v2.0.0rc0227 * [new tag] v2.0.1 -> v2.0.128Checking out f9ecbb83 as master...29Removing .tmp/30Skipping Git submodules setup33Downloading artifacts for collect (148889)...37$ module load singularity/3.5.338$ chmod +x ./workflow/scripts/get_updated_badge_info.sh39$ echo "Building badges"40Building badges41$ baseImg=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep gudmap-rbk_base | cut -d"/" -f2 | cut -d":" -f1)42$ baseVar=$(cat nextflow.config | grep -oP "container = \K.*" | tr -d "'" | sort | uniq | grep gudmap-rbk_base | cut -d"/" -f2 | cut -d":" -f2)43$ echo ${dir}${baseImg}_${baseVar}.sif44/project/BICF/BICF_Core/shared/gudmap/singularity_cache/gudmap-rbk_base_1.0.1.sif45$ singularity run ${dir}${baseImg}_${baseVar}.sif bash ./workflow/scripts/get_updated_badge_info.sh46collecting stats for badges47collecting tool version for badges48collecting badges49 % Total % Received % Xferd Average Speed Time Time Time Current50 Dload Upload Total Spent Left Speed51100 1175 0 1175 0 0 4936 0 --:--:-- --:--:-- --:--:-- 493652 % Total % Received % Xferd Average Speed Time Time Time Current53 Dload Upload Total Spent Left Speed54100 1183 0 1183 0 0 5974 0 --:--:-- --:--:-- --:--:-- 597455 % Total % Received % Xferd Average Speed Time Time Time Current56 Dload Upload Total Spent Left Speed57 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 058 % Total % Received % Xferd Average Speed Time Time Time Current59 Dload Upload Total Spent Left Speed60100 1183 0 1183 0 0 17924 0 --:--:-- --:--:-- --:--:-- 1792461 % Total % Received % Xferd Average Speed Time Time Time Current62 Dload Upload Total Spent Left Speed63 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 064 % Total % Received % Xferd Average Speed Time Time Time Current65 Dload Upload Total Spent Left Speed66100 1183 0 1183 0 0 25170 0 --:--:-- --:--:-- --:--:-- 2571767 % Total % Received % Xferd Average Speed Time Time Time Current68 Dload Upload Total Spent Left Speed69 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 070 % Total % Received % Xferd Average Speed Time Time Time Current71 Dload Upload Total Spent Left Speed72100 1178 0 1178 0 0 7455 0 --:--:-- --:--:-- --:--:-- 745573 % Total % Received % Xferd Average Speed Time Time Time Current74 Dload Upload Total Spent Left Speed75100 1178 0 1178 0 0 6731 0 --:--:-- --:--:-- --:--:-- 673176 % Total % Received % Xferd Average Speed Time Time Time Current77 Dload Upload Total Spent Left Speed78100 1174 0 1174 0 0 6051 0 --:--:-- --:--:-- --:--:-- 602079 % Total % Received % Xferd Average Speed Time Time Time Current80 Dload Upload Total Spent Left Speed81100 1202 0 1202 0 0 5414 0 --:--:-- --:--:-- --:--:-- 541482 % Total % Received % Xferd Average Speed Time Time Time Current83 Dload Upload Total Spent Left Speed84100 1178 0 1178 0 0 7649 0 --:--:-- --:--:-- --:--:-- 764985 % Total % Received % Xferd Average Speed Time Time Time Current86 Dload Upload Total Spent Left Speed87100 1184 0 1184 0 0 7841 0 --:--:-- --:--:-- --:--:-- 784188 % Total % Received % Xferd Average Speed Time Time Time Current89 Dload Upload Total Spent Left Speed90100 1182 0 1182 0 0 7528 0 --:--:-- --:--:-- --:--:-- 752891 % Total % Received % Xferd Average Speed Time Time Time Current92 Dload Upload Total Spent Left Speed93100 1210 0 1210 0 0 6797 0 --:--:-- --:--:-- --:--:-- 679794 % Total % Received % Xferd Average Speed Time Time Time Current95 Dload Upload Total Spent Left Speed96100 1194 0 1194 0 0 7509 0 --:--:-- --:--:-- --:--:-- 746297 % Total % Received % Xferd Average Speed Time Time Time Current98 Dload Upload Total Spent Left Speed99100 1186 0 1186 0 0 7854 0 --:--:-- --:--:-- --:--:-- 7854100 % Total % Received % Xferd Average Speed Time Time Time Current101 Dload Upload Total Spent Left Speed102100 1156 0 1156 0 0 5958 0 --:--:-- --:--:-- --:--:-- 5958103 % Total % Received % Xferd Average Speed Time Time Time Current104 Dload Upload Total Spent Left Speed105100 1182 0 1182 0 0 7528 0 --:--:-- --:--:-- --:--:-- 7528106 % Total % Received % Xferd Average Speed Time Time Time Current107 Dload Upload Total Spent Left Speed108100 1200 0 1200 0 0 7692 0 --:--:-- --:--:-- --:--:-- 7692109 % Total % Received % Xferd Average Speed Time Time Time Current110 Dload Upload Total Spent Left Speed111100 1174 0 1174 0 0 7072 0 --:--:-- --:--:-- --:--:-- 7029112 % Total % Received % Xferd Average Speed Time Time Time Current113 Dload Upload Total Spent Left Speed114100 1178 0 1178 0 0 11009 0 --:--:-- --:--:-- --:--:-- 11009115creating blank env badges if not tested116 % Total % Received % Xferd Average Speed Time Time Time Current117 Dload Upload Total Spent Left Speed118100 1219 0 1219 0 0 7087 0 --:--:-- --:--:-- --:--:-- 7087119 % Total % Received % Xferd Average Speed Time Time Time Current120 Dload Upload Total Spent Left Speed121100 1199 0 1199 0 0 7888 0 --:--:-- --:--:-- --:--:-- 7888122 % Total % Received % Xferd Average Speed Time Time Time Current123 Dload Upload Total Spent Left Speed124100 1207 0 1207 0 0 12978 0 --:--:-- --:--:-- --:--:-- 12978125 % Total % Received % Xferd Average Speed Time Time Time Current126 Dload Upload Total Spent Left Speed127100 1197 0 1197 0 0 7298 0 --:--:-- --:--:-- --:--:-- 7298128$ singularity run ${dir}${baseImg}_${baseVar}.sif bash ./workflow/scripts/get_updated_rep_count.sh129collecting stats for badges130Major pipeline version for search: v2.131collecting workflow RIDs from servers132collecting unique replicates with successful execution runs133collecting badges134 % Total % Received % Xferd Average Speed Time Time Time Current135 Dload Upload Total Spent Left Speed136100 1257 0 1257 0 0 7572 0 --:--:-- --:--:-- --:--:-- 7526137 % Total % Received % Xferd Average Speed Time Time Time Current138 Dload Upload Total Spent Left Speed139100 1257 0 1257 0 0 10303 0 --:--:-- --:--:-- --:--:-- 10303140 % Total % Received % Xferd Average Speed Time Time Time Current141 Dload Upload Total Spent Left Speed142100 1243 0 1243 0 0 12555 0 --:--:-- --:--:-- --:--:-- 12555143 % Total % Received % Xferd Average Speed Time Time Time Current144 Dload Upload Total Spent Left Speed145100 1239 0 1239 0 0 8486 0 --:--:-- --:--:-- --:--:-- 8486146 % Total % Received % Xferd Average Speed Time Time Time Current147 Dload Upload Total Spent Left Speed148100 1255 0 1255 0 0 7843 0 --:--:-- --:--:-- --:--:-- 7843149 % Total % Received % Xferd Average Speed Time Time Time Current150 Dload Upload Total Spent Left Speed151100 1243 0 1243 0 0 7269 0 --:--:-- --:--:-- --:--:-- 7269152 % Total % Received % Xferd Average Speed Time Time Time Current153 Dload Upload Total Spent Left Speed154100 1215 0 1215 0 0 7546 0 --:--:-- --:--:-- --:--:-- 7546155 % Total % Received % Xferd Average Speed Time Time Time Current156 Dload Upload Total Spent Left Speed157100 1203 0 1203 0 0 7035 0 --:--:-- --:--:-- --:--:-- 7035158 % Total % Received % Xferd Average Speed Time Time Time Current159 Dload Upload Total Spent Left Speed160100 1215 0 1215 0 0 7275 0 --:--:-- --:--:-- --:--:-- 7275162Running after script...163$ unset SINGULARITY_CACHEDIR166Uploading artifacts...170Job succeeded