RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.82jXjG/RM_158639.TueJan101831452023 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: 1673404303 Database = /dev/shm/rModeler.82jXjG/GCA_009819775.1_bPhoRub2.pri - Sequences = 90 - Bases = 1246226932 Storage Throughput = excellent ( 1286.51 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40254556 bp ( 40014008 non ambiguous ) - Num Contigs Represented = 38 - Sequence extraction : 00:01:35 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:03 (hh:mm:ss) Elapsed Time Round Time: 00:16:08 (hh:mm:ss) Elapsed Time : 44 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1731 repeats masked totaling 847683 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10042589 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10002288 bp After Masking: 9116347 bp Masked: 8.86 % -- Input Database Coverage: 10042589 bp out of 1246226932 bp ( 0.81 % ) Sampling Time: 00:00:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 811 HSPs Collected Number of families returned by RECON: 255 Round Time: 00:07:02 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4681 repeats masked totaling 2190483 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30211887 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30011640 bp After Masking: 27731343 bp Masked: 7.60 % -- Input Database Coverage: 40254476 bp out of 1246226932 bp ( 3.23 % ) Sampling Time: 00:01:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:27:00 (hh:mm:ss) Elapsed Time, 5627 HSPs Collected Number of families returned by RECON: 1450 Round Time: 00:29:13 (hh:mm:ss) Elapsed Time : 9 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14928 repeats masked totaling 6532539 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90847707 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 90035894 bp After Masking: 83127468 bp Masked: 7.67 % -- Input Database Coverage: 131102183 bp out of 1246226932 bp ( 10.52 % ) Sampling Time: 00:07:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2588950 Comparison Time: 02:32:52 (hh:mm:ss) Elapsed Time, 39567 HSPs Collected Number of families returned by RECON: 8769 Round Time: 02:41:46 (hh:mm:ss) Elapsed Time : 79 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 59954 repeats masked totaling 22884985 bp(s). - TE Masking time 00:01:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271774118 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 270015879 bp After Masking: 246102098 bp Masked: 8.86 % -- Input Database Coverage: 402876301 bp out of 1246226932 bp ( 32.33 % ) Sampling Time: 00:18:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23150610 Comparison Time: 19:27:54 (hh:mm:ss) Elapsed Time, 150003 HSPs Collected Number of families returned by RECON: 52641 Round Time: 20:07:03 (hh:mm:ss) Elapsed Time : 190 families discovered. RepeatScout/RECON discovery complete: 324 families found Classification Time: 00:11:26 (hh:mm:ss) Elapsed Time Program Time: 23:52:38 (hh:mm:ss) Elapsed Time