RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qDCaaA/RM_25316.MonAug122010502024 Search Engine = rmblast 2.13.0+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.4 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1723518649 Database = /dev/shm/rModeler.qDCaaA/GCA_001599035.1_JCM_9410_assembly_v001 - Sequences = 23 - Bases = 37316984 Storage Throughput = excellent ( 1044.03 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 37316879 bp ( 36954135 non ambiguous ) - Num Contigs Represented = 23 - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:27 (hh:mm:ss) Elapsed Time Round Time: 00:16:41 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 262 repeats masked totaling 30372 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10100218 bp Num Contigs Represented = 12 Non ambiguous bp: Initial: 10039732 bp After Masking: 9972316 bp Masked: 0.67 % -- Input Database Coverage: 10100218 bp out of 37316984 bp ( 27.07 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:17:38 (hh:mm:ss) Elapsed Time, 1522 HSPs Collected Number of families returned by RECON: 574 Round Time: 00:25:19 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 717 repeats masked totaling 84009 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 27216587 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 26914329 bp After Masking: 26734330 bp Masked: 0.67 % -- Input Database Coverage: 37316805 bp out of 37316984 bp ( 100.00 % ) Sampling Time: 00:01:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 241165 Comparison Time: 01:12:52 (hh:mm:ss) Elapsed Time, 12082 HSPs Collected Number of families returned by RECON: 2728 Round Time: 06:33:03 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatScout/RECON discovery complete: 28 families found Classification Time: 00:03:16 (hh:mm:ss) Elapsed Time Program Time: 07:18:19 (hh:mm:ss) Elapsed Time