RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.pIRi1I/RM_11143.SatDec311117492022 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: 1672514268 Database = /dev/shm/rModeler.pIRi1I/GCF_017976325.1_fCheRos1.pri - Sequences = 29 - Bases = 644208431 Storage Throughput = excellent ( 1108.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030056 bp ( 40029856 non ambiguous ) - Num Contigs Represented = 25 - Sequence extraction : 00:00:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:29 (hh:mm:ss) Elapsed Time Round Time: 00:25:31 (hh:mm:ss) Elapsed Time : 313 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5888 repeats masked totaling 817549 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001822 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10001722 bp After Masking: 9059767 bp Masked: 9.42 % -- Input Database Coverage: 10001822 bp out of 644208431 bp ( 1.55 % ) Sampling Time: 00:00:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:33 (hh:mm:ss) Elapsed Time, 7420 HSPs Collected Number of families returned by RECON: 1665 Round Time: 00:07:29 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19977 repeats masked totaling 2748582 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028154 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 30028054 bp After Masking: 26809256 bp Masked: 10.72 % -- Input Database Coverage: 40029976 bp out of 644208431 bp ( 6.21 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:36:23 (hh:mm:ss) Elapsed Time, 57776 HSPs Collected Number of families returned by RECON: 6669 Round Time: 00:40:58 (hh:mm:ss) Elapsed Time : 125 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 75153 repeats masked totaling 10433961 bp(s). - TE Masking time 00:01:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90006125 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 90005225 bp After Masking: 78275906 bp Masked: 13.03 % -- Input Database Coverage: 130036101 bp out of 644208431 bp ( 20.19 % ) Sampling Time: 00:06:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 04:18:15 (hh:mm:ss) Elapsed Time, 267280 HSPs Collected Number of families returned by RECON: 23893 Round Time: 04:43:08 (hh:mm:ss) Elapsed Time : 454 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 291952 repeats masked totaling 42919448 bp(s). - TE Masking time 00:08:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270016666 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 270011586 bp After Masking: 223164652 bp Masked: 17.35 % -- Input Database Coverage: 400052767 bp out of 644208431 bp ( 62.10 % ) Sampling Time: 00:22:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22845420 Comparison Time: 33:25:06 (hh:mm:ss) Elapsed Time, 928870 HSPs Collected Number of families returned by RECON: 90589 Round Time: 37:11:58 (hh:mm:ss) Elapsed Time : 1121 families discovered. RepeatScout/RECON discovery complete: 2029 families found Classification Time: 01:31:57 (hh:mm:ss) Elapsed Time Program Time: 44:41:01 (hh:mm:ss) Elapsed Time