RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.h5CXyA/RM_7337.SatDec21806182023 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: 1701569177 Database = /dev/shm/rModeler.h5CXyA/GCA_030412085.1_rCycPin1.hap2 - Sequences = 33 - Bases = 1955392031 Storage Throughput = excellent ( 1182.75 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40491742 bp ( 40011715 non ambiguous ) - Num Contigs Represented = 21 - Sequence extraction : 00:05:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:32 (hh:mm:ss) Elapsed Time Round Time: 00:36:00 (hh:mm:ss) Elapsed Time : 424 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:01:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15571 repeats masked totaling 3133954 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10160510 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10000510 bp After Masking: 6788093 bp Masked: 32.12 % -- Input Database Coverage: 10160510 bp out of 1955392031 bp ( 0.52 % ) Sampling Time: 00:02:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:05:40 (hh:mm:ss) Elapsed Time, 12947 HSPs Collected Number of families returned by RECON: 1435 Round Time: 00:08:12 (hh:mm:ss) Elapsed Time : 45 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:04:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50812 repeats masked totaling 10436335 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30331152 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 30011125 bp After Masking: 19367214 bp Masked: 35.47 % -- Input Database Coverage: 40491662 bp out of 1955392031 bp ( 2.07 % ) Sampling Time: 00:05:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:28:19 (hh:mm:ss) Elapsed Time, 50176 HSPs Collected Number of families returned by RECON: 3865 Round Time: 00:35:39 (hh:mm:ss) Elapsed Time : 101 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:12:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 169282 repeats masked totaling 34301091 bp(s). - TE Masking time 00:01:57 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90844394 bp Num Contigs Represented = 20 Non ambiguous bp: Initial: 90025492 bp After Masking: 54955588 bp Masked: 38.96 % -- Input Database Coverage: 131336056 bp out of 1955392031 bp ( 6.72 % ) Sampling Time: 00:17:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2577585 Comparison Time: 03:06:50 (hh:mm:ss) Elapsed Time, 160210 HSPs Collected Number of families returned by RECON: 12038 Round Time: 03:33:07 (hh:mm:ss) Elapsed Time : 339 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:37:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:05 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 555129 repeats masked totaling 113706389 bp(s). - TE Masking time 00:09:21 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272755169 bp Num Contigs Represented = 22 Non ambiguous bp: Initial: 270031377 bp After Masking: 154573287 bp Masked: 42.76 % -- Input Database Coverage: 404091225 bp out of 1955392031 bp ( 20.67 % ) Sampling Time: 00:54:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23259610 Comparison Time: 23:29:29 (hh:mm:ss) Elapsed Time, 446670 HSPs Collected Number of families returned by RECON: 44274 Round Time: 25:39:22 (hh:mm:ss) Elapsed Time : 789 families discovered. RepeatScout/RECON discovery complete: 1698 families found Classification Time: 01:08:39 (hh:mm:ss) Elapsed Time Program Time: 31:40:59 (hh:mm:ss) Elapsed Time