------------------------------------------------- phylotaR: Implementation of PhyLoTa in R [v1.0.0] ------------------------------------------------- Checking for valid NCBI BLAST+ Tools ... Found: [/home/evolecolab/Software/ncbi-blast-2.9.0+-x64-linux/ncbi-blast-2.9.0+/bin/makeblastdb] Found: [/home/evolecolab/Software/ncbi-blast-2.9.0+-x64-linux/ncbi-blast-2.9.0+/bin/blastn] Setting up pipeline with the following parameters: . blstn [/home/evolecolab/Software/ncbi-blast-2.9.0+-x64-linux/ncbi-blast-2.9.0+/bin/blastn] . btchsz [100] . date [2019-06-25] . mdlthrs [3000] . mkblstdb [/home/evolecolab/Software/ncbi-blast-2.9.0+-x64-linux/ncbi-blast-2.9.0+/bin/makeblastdb] . mncvrg [51] . mnsql [250] . mxevl [1e-10] . mxnds [1e+05] . mxrtry [100] . mxsql [2000] . mxsqs [50000] . ncps [1] . txid [9443] . v [FALSE] . wd [/home/evolecolab/Escritorio/PhylotaRtest] ------------------------------------------------- --------------------------------------------------- Running pipeline on [unix] at [2019-06-25 00:08:51] --------------------------------------------------- Running stages: taxise, download, cluster, cluster2 -------------------------------------------- Starting stage TAXISE: [2019-06-25 00:08:51] -------------------------------------------- Searching taxonomic IDs ... Downloading taxonomic records ... . [1-100] . [101-200] . [201-300] . [301-400] . [401-500] . [501-600] . [601-700] . [701-800] . [801-900] . [901-929] Generating taxonomic dictionary ... --------------------------------------------- Completed stage TAXISE: [2019-06-25 00:09:28] --------------------------------------------- ---------------------------------------------- Starting stage DOWNLOAD: [2019-06-25 00:09:28] ---------------------------------------------- Identifying suitable clades ... . [2787000 sqs] and [929 nds] for clade [id 9443] - searching descendants instead ... . [2043000 sqs] and [681 nds] for clade [id 376913] - searching descendants instead ... . [1983000 sqs] and [661 nds] for clade [id 314293] - searching descendants instead ... . [1128000 sqs] and [376 nds] for clade [id 9526] - searching descendants instead ... . [586444 sqs] and [284 nds] for clade [id 9479] - searching descendants instead ... . [243000 sqs] and [81 nds] for clade [id 314295] - searching descendants instead ... . [882000 sqs] and [294 nds] for clade [id 314294] - searching descendants instead ... . [381000 sqs] and [127 nds] for clade [id 9498] - searching descendants instead ... . [96000 sqs] and [32 nds] for clade [id 9604] - searching descendants instead ... . [879000 sqs] and [293 nds] for clade [id 9527] - searching descendants instead ... . [213000 sqs] and [71 nds] for clade [id 9480] - searching descendants instead ... . [69000 sqs] and [23 nds] for clade [id 207598] - searching descendants instead ... . [540000 sqs] and [180 nds] for clade [id 9528] - searching descendants instead ... . [78000 sqs] and [26 nds] for clade [id 9481] - searching descendants instead ... . [54000 sqs] and [18 nds] for clade [id 392815] - searching descendants instead ... . [66000 sqs] and [22 nds] for clade [id 9554] - searching descendants instead ... . [129000 sqs] and [43 nds] for clade [id 9539] - searching descendants instead ... Identified [89] suitable clades. Downloading hierarchically ... Working on parent [id 376911]: [1/89] ... . + direct ... . + by child ... . . Working on child [id 376917] . . + whole subtree ... . . . Getting [1700 sqs] ... . . . . [1-100] . . . . [101-200] . . . . [201-300] . . . . [301-400] . . . . [401-500] . . . . [501-600] . . . . [601-700] . . . . [701-800] . . . . [801-900] . . . . [901-1000] . . . . [1001-1100] . . . . [1101-1200] . . . . [1201-1300] . . . . [1301-1400] . . . . [1401-1500] . . . . [1501-1600] . . . . [1601-1700] . . . Working on child [id 376916] . . . + whole subtree ... . . . . Getting [200 sqs] ... . . . . . [1-100] . . . . . [101-200] . . . . Working on child [id 376915] . . . . + direct ... . . . . + by child ... . . . . . Working on child [id 1513476] . . . . . + whole subtree ... . . . . . . Getting [2 sqs] ... . . . . . . . [1-2] . . . . . . Working on child [id 30615] . . . . . . + direct ... . . . . . . + by child ... . . . . . . . Working on child [id 261733] . . . . . . . + whole subtree ... . . . . . . . . Getting [43 sqs] ... . . . . . . . . . [1-43] . . . . . . . . Working on child [id 122247] . . . . . . . . + whole subtree ... . . . . . . . . . Getting [58 sqs] ... . . . . . . . . . . [1-58] . . . . . . . . . Working on child [id 83691] . . . . . . . . . + whole subtree ... . . . . . . . . . . Getting [100 sqs] ... . . . . . . . . . . . [1-100] . . . . . . . . . . Working on child [id 13149] . . . . . . . . . . + direct ... . . . . . . . . . . + by child ... . . . . . . . . . . . Working on child [id 2483760] . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . Working on child [id 1310125] . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . Getting [49 sqs] ... . . . . . . . . . . . . . . [1-49] . . . . . . . . . . . . . Working on child [id 1310124] . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . Getting [29 sqs] ... . . . . . . . . . . . . . . . [1-29] . . . . . . . . . . . . . . Working on child [id 1310123] . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . Getting [87 sqs] ... . . . . . . . . . . . . . . . . [1-87] . . . . . . . . . . . . . . . Working on child [id 1131379] . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . Getting [17 sqs] ... . . . . . . . . . . . . . . . . . [1-17] . . . . . . . . . . . . . . . . Working on child [id 864581] . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . Getting [8 sqs] ... . . . . . . . . . . . . . . . . . . [1-8] . . . . . . . . . . . . . . . . . Working on child [id 864580] . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . Getting [8 sqs] ... . . . . . . . . . . . . . . . . . . . [1-8] . . . . . . . . . . . . . . . . . . Working on child [id 764313] . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . Working on child [id 548482] . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . Getting [2 sqs] ... . . . . . . . . . . . . . . . . . . . . . [1-2] . . . . . . . . . . . . . . . . . . . . Working on child [id 548481] . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . Getting [9 sqs] ... . . . . . . . . . . . . . . . . . . . . . . [1-9] . . . . . . . . . . . . . . . . . . . . . Working on child [id 418100] . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . Getting [33 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . [1-33] . . . . . . . . . . . . . . . . . . . . . . Working on child [id 415757] . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . Getting [18 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . [1-18] . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412761] . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . Getting [16 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . [1-16] . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412760] . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . Getting [4 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . [1-4] . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412759] . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [1 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-1] . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412758] . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [7 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-7] . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412752] . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [8 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-8] . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412751] . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [33 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-33] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412750] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [19 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-19] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 388736] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [7 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-7] Retrying in [1s] for [fetch] Retrying in [3s] for [fetch] Retrying in [6s] for [fetch] Retrying in [10s] for [fetch] Retrying in [60s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 343908] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [94 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-94] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 270675] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [7 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-7] Retrying in [1s] for [fetch] Retrying in [3s] for [fetch] Retrying in [6s] for [fetch] Retrying in [10s] for [fetch] Retrying in [60s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] ----------------------------------------- The following parameters have been reset: . btchz [300] ----------------------------------------- ------------------------------------------------------ Restarting pipeline on [unix] at [2019-06-25 15:11:17] ------------------------------------------------------ Running stages: download, cluster, cluster2 ---------------------------------------------- Starting stage DOWNLOAD: [2019-06-25 15:11:17] ---------------------------------------------- Identifying suitable clades ... . [2787000 sqs] and [929 nds] for clade [id 9443] - searching descendants instead ... . [2043000 sqs] and [681 nds] for clade [id 376913] - searching descendants instead ... . [1983000 sqs] and [661 nds] for clade [id 314293] - searching descendants instead ... . [1128000 sqs] and [376 nds] for clade [id 9526] - searching descendants instead ... . [586444 sqs] and [284 nds] for clade [id 9479] - searching descendants instead ... . [243000 sqs] and [81 nds] for clade [id 314295] - searching descendants instead ... . [882000 sqs] and [294 nds] for clade [id 314294] - searching descendants instead ... . [381000 sqs] and [127 nds] for clade [id 9498] - searching descendants instead ... . [96000 sqs] and [32 nds] for clade [id 9604] - searching descendants instead ... . [879000 sqs] and [293 nds] for clade [id 9527] - searching descendants instead ... . [213000 sqs] and [71 nds] for clade [id 9480] - searching descendants instead ... . [69000 sqs] and [23 nds] for clade [id 207598] - searching descendants instead ... . [540000 sqs] and [180 nds] for clade [id 9528] - searching descendants instead ... . [78000 sqs] and [26 nds] for clade [id 9481] - searching descendants instead ... . [54000 sqs] and [18 nds] for clade [id 392815] - searching descendants instead ... . [66000 sqs] and [22 nds] for clade [id 9554] - searching descendants instead ... . [129000 sqs] and [43 nds] for clade [id 9539] - searching descendants instead ... Identified [89] suitable clades. Downloading hierarchically ... Working on parent [id 376911]: [1/89] ... . + direct ... . + by child ... . . Working on child [id 376917] . . + whole subtree ... . . . Getting [1700 sqs] ... . . . . [1-100] . . . . [101-200] . . . . [201-300] . . . . [301-400] . . . . [401-500] . . . . [501-600] . . . . [601-700] . . . . [701-800] . . . . [801-900] . . . . [901-1000] . . . . [1001-1100] . . . . [1101-1200] . . . . [1201-1300] . . . . [1301-1400] . . . . [1401-1500] . . . . [1501-1600] . . . . [1601-1700] . . . Working on child [id 376916] . . . + whole subtree ... . . . . Getting [200 sqs] ... . . . . . [1-100] . . . . . [101-200] . . . . Working on child [id 376915] . . . . + direct ... . . . . + by child ... . . . . . Working on child [id 1513476] . . . . . + whole subtree ... . . . . . . Getting [2 sqs] ... . . . . . . . [1-2] . . . . . . Working on child [id 30615] . . . . . . + direct ... . . . . . . + by child ... . . . . . . . Working on child [id 261733] . . . . . . . + whole subtree ... . . . . . . . . Getting [43 sqs] ... . . . . . . . . . [1-43] . . . . . . . . Working on child [id 122247] . . . . . . . . + whole subtree ... . . . . . . . . . Getting [58 sqs] ... . . . . . . . . . . [1-58] . . . . . . . . . Working on child [id 83691] . . . . . . . . . + whole subtree ... . . . . . . . . . . Getting [100 sqs] ... . . . . . . . . . . . [1-100] . . . . . . . . . . Working on child [id 13149] . . . . . . . . . . + direct ... . . . . . . . . . . + by child ... . . . . . . . . . . . Working on child [id 2483760] . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . Working on child [id 1310125] . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . Getting [49 sqs] ... . . . . . . . . . . . . . . [1-49] . . . . . . . . . . . . . Working on child [id 1310124] . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . Getting [29 sqs] ... . . . . . . . . . . . . . . . [1-29] . . . . . . . . . . . . . . Working on child [id 1310123] . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . Getting [87 sqs] ... . . . . . . . . . . . . . . . . [1-87] . . . . . . . . . . . . . . . Working on child [id 1131379] . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . Getting [17 sqs] ... . . . . . . . . . . . . . . . . . [1-17] . . . . . . . . . . . . . . . . Working on child [id 864581] . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . Getting [8 sqs] ... . . . . . . . . . . . . . . . . . . [1-8] . . . . . . . . . . . . . . . . . Working on child [id 864580] . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . Getting [8 sqs] ... . . . . . . . . . . . . . . . . . . . [1-8] . . . . . . . . . . . . . . . . . . Working on child [id 764313] . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . Working on child [id 548482] . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . Getting [2 sqs] ... . . . . . . . . . . . . . . . . . . . . . [1-2] . . . . . . . . . . . . . . . . . . . . Working on child [id 548481] . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . Getting [9 sqs] ... . . . . . . . . . . . . . . . . . . . . . . [1-9] . . . . . . . . . . . . . . . . . . . . . Working on child [id 418100] . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . Getting [33 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . [1-33] . . . . . . . . . . . . . . . . . . . . . . Working on child [id 415757] . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . Getting [18 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . [1-18] . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412761] . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . Getting [16 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . [1-16] . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412760] . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . Getting [4 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . [1-4] . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412759] . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [1 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-1] . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412758] . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [7 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-7] . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412752] . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [8 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-8] . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412751] . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [33 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-33] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412750] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [19 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-19] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 388736] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [7 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-7] Retrying in [1s] for [fetch] Retrying in [3s] for [fetch] Retrying in [6s] for [fetch] Retrying in [10s] for [fetch] Retrying in [60s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] Retrying in [300s] for [fetch] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 343908] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [94 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-94] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 270675] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [7 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-7] Unexpected Error in gzfile(file, "rb") : argumento 'description' inválido Occurred [2019-06-25 23:09:58] Contact package maintainer for help. ------------------------------------------------------ Restarting pipeline on [unix] at [2019-06-25 23:36:52] ------------------------------------------------------ Running stages: download, cluster, cluster2 ---------------------------------------------- Starting stage DOWNLOAD: [2019-06-25 23:36:52] ---------------------------------------------- Identifying suitable clades ... . [2787000 sqs] and [929 nds] for clade [id 9443] - searching descendants instead ... . [2043000 sqs] and [681 nds] for clade [id 376913] - searching descendants instead ... . [1983000 sqs] and [661 nds] for clade [id 314293] - searching descendants instead ... . [1128000 sqs] and [376 nds] for clade [id 9526] - searching descendants instead ... . [586444 sqs] and [284 nds] for clade [id 9479] - searching descendants instead ... . [243000 sqs] and [81 nds] for clade [id 314295] - searching descendants instead ... . [882000 sqs] and [294 nds] for clade [id 314294] - searching descendants instead ... . [381000 sqs] and [127 nds] for clade [id 9498] - searching descendants instead ... . [96000 sqs] and [32 nds] for clade [id 9604] - searching descendants instead ... . [879000 sqs] and [293 nds] for clade [id 9527] - searching descendants instead ... . [213000 sqs] and [71 nds] for clade [id 9480] - searching descendants instead ... . [69000 sqs] and [23 nds] for clade [id 207598] - searching descendants instead ... . [540000 sqs] and [180 nds] for clade [id 9528] - searching descendants instead ... . [78000 sqs] and [26 nds] for clade [id 9481] - searching descendants instead ... . [54000 sqs] and [18 nds] for clade [id 392815] - searching descendants instead ... . [66000 sqs] and [22 nds] for clade [id 9554] - searching descendants instead ... . [129000 sqs] and [43 nds] for clade [id 9539] - searching descendants instead ... Identified [89] suitable clades. Downloading hierarchically ... Working on parent [id 376911]: [1/89] ... . + direct ... . + by child ... . . Working on child [id 376917] . . + whole subtree ... . . . Getting [1700 sqs] ... . . . . [1-100] . . . . [101-200] . . . . [201-300] . . . . [301-400] . . . . [401-500] . . . . [501-600] . . . . [601-700] . . . . [701-800] . . . . [801-900] . . . . [901-1000] . . . . [1001-1100] . . . . [1101-1200] . . . . [1201-1300] . . . . [1301-1400] . . . . [1401-1500] . . . . [1501-1600] . . . . [1601-1700] . . . Working on child [id 376916] . . . + whole subtree ... . . . . Getting [200 sqs] ... . . . . . [1-100] . . . . . [101-200] . . . . Working on child [id 376915] . . . . + direct ... . . . . + by child ... . . . . . Working on child [id 1513476] . . . . . + whole subtree ... . . . . . . Getting [2 sqs] ... . . . . . . . [1-2] . . . . . . Working on child [id 30615] . . . . . . + direct ... . . . . . . + by child ... . . . . . . . Working on child [id 261733] . . . . . . . + whole subtree ... . . . . . . . . Getting [43 sqs] ... . . . . . . . . . [1-43] . . . . . . . . Working on child [id 122247] . . . . . . . . + whole subtree ... . . . . . . . . . Getting [58 sqs] ... . . . . . . . . . . [1-58] . . . . . . . . . Working on child [id 83691] . . . . . . . . . + whole subtree ... . . . . . . . . . . Getting [100 sqs] ... . . . . . . . . . . . [1-100] . . . . . . . . . . Working on child [id 13149] . . . . . . . . . . + direct ... . . . . . . . . . . + by child ... . . . . . . . . . . . Working on child [id 2483760] . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . Working on child [id 1310125] . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . Getting [49 sqs] ... . . . . . . . . . . . . . . [1-49] . . . . . . . . . . . . . Working on child [id 1310124] . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . Getting [29 sqs] ... . . . . . . . . . . . . . . . [1-29] . . . . . . . . . . . . . . Working on child [id 1310123] . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . Getting [87 sqs] ... . . . . . . . . . . . . . . . . [1-87] . . . . . . . . . . . . . . . Working on child [id 1131379] . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . Getting [17 sqs] ... . . . . . . . . . . . . . . . . . [1-17] . . . . . . . . . . . . . . . . Working on child [id 864581] . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . Getting [8 sqs] ... . . . . . . . . . . . . . . . . . . [1-8] . . . . . . . . . . . . . . . . . Working on child [id 864580] . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . Getting [8 sqs] ... . . . . . . . . . . . . . . . . . . . [1-8] . . . . . . . . . . . . . . . . . . Working on child [id 764313] . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . Working on child [id 548482] . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . Getting [2 sqs] ... . . . . . . . . . . . . . . . . . . . . . [1-2] . . . . . . . . . . . . . . . . . . . . Working on child [id 548481] . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . Getting [9 sqs] ... . . . . . . . . . . . . . . . . . . . . . . [1-9] . . . . . . . . . . . . . . . . . . . . . Working on child [id 418100] . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . Getting [33 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . [1-33] . . . . . . . . . . . . . . . . . . . . . . Working on child [id 415757] . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . Getting [18 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . [1-18] . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412761] . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . Getting [16 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . [1-16] . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412760] . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . Getting [4 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . [1-4] . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412759] . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [1 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-1] . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412758] . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [7 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-7] . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412752] . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [8 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-8] . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412751] . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [33 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-33] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 412750] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [19 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-19] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Working on child [id 388736] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . + whole subtree ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Getting [7 sqs] ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . [1-7] Unexpected Error in gzfile(file, "rb") : argumento 'description' inválido Occurred [2019-06-25 23:38:03] Contact package maintainer for help.