RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ki2TxS/RM_12783.ThuJul110520532024 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: 1720700452 Database = /dev/shm/rModeler.ki2TxS/GCF_002234675.1_ASM223467v1 - Sequences = 25 - Bases = 734057086 Storage Throughput = excellent ( 1028.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40028956 bp ( 40004289 non ambiguous ) - Num Contigs Represented = 24 - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:18 (hh:mm:ss) Elapsed Time Round Time: 00:32:30 (hh:mm:ss) Elapsed Time : 621 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13960 repeats masked totaling 2795568 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10041610 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10033610 bp After Masking: 7044992 bp Masked: 29.79 % -- Input Database Coverage: 10041610 bp out of 734057086 bp ( 1.37 % ) Sampling Time: 00:00:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:18 (hh:mm:ss) Elapsed Time, 4415 HSPs Collected Number of families returned by RECON: 913 Round Time: 00:07:31 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43168 repeats masked totaling 8704869 bp(s). - TE Masking time 00:00:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30027338 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 30010671 bp After Masking: 20692597 bp Masked: 31.05 % -- Input Database Coverage: 40068948 bp out of 734057086 bp ( 5.46 % ) Sampling Time: 00:03:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:35:13 (hh:mm:ss) Elapsed Time, 34466 HSPs Collected Number of families returned by RECON: 3202 Round Time: 00:39:47 (hh:mm:ss) Elapsed Time : 86 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 135855 repeats masked totaling 27728317 bp(s). - TE Masking time 00:02:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90091714 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 90034627 bp After Masking: 60197203 bp Masked: 33.14 % -- Input Database Coverage: 130160662 bp out of 734057086 bp ( 17.73 % ) Sampling Time: 00:11:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 04:43:26 (hh:mm:ss) Elapsed Time, 190676 HSPs Collected Number of families returned by RECON: 11087 Round Time: 05:03:04 (hh:mm:ss) Elapsed Time : 367 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 456905 repeats masked totaling 94758039 bp(s). - TE Masking time 00:12:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270217066 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 270029653 bp After Masking: 169504663 bp Masked: 37.23 % -- Input Database Coverage: 400377728 bp out of 734057086 bp ( 54.54 % ) Sampling Time: 00:34:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 28:18:53 (hh:mm:ss) Elapsed Time, 564198 HSPs Collected Number of families returned by RECON: 43553 Round Time: 29:55:03 (hh:mm:ss) Elapsed Time : 903 families discovered. RepeatScout/RECON discovery complete: 1988 families found Classification Time: 01:49:45 (hh:mm:ss) Elapsed Time Program Time: 38:07:40 (hh:mm:ss) Elapsed Time