RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.Y2ZhpN/RM_4012920.TueApr221215432025 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: 1745349342 Database = /data/tmp/rModeler.Y2ZhpN/GCA_041903045.1_ASM4190304v1 - Sequences = 176 - Bases = 1089387278 - N50 = 46035659 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 50113327-53692833 | [ 3 ] 46533821-50113326 |** [ 7 ] 42954316-46533821 |** [ 8 ] 39374810-42954315 |* [ 4 ] 35795304-39374809 | [ 1 ] 32215799-35795304 | [ ] 28636293-32215798 | [ ] 25056787-28636292 | [ 1 ] 21477282-25056787 | [ ] 17897776-21477281 | [ ] 14318270-17897775 | [ ] 10738765-14318270 | [ ] 7159259-10738764 | [ ] 3579753-7159258 | [ ] 248-3579753 |************************************************** [ 152 ] Storage Throughput = excellent ( 1037.85 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013572 bp ( 40013572 non ambiguous ) - Num Contigs Represented = 36 - Sequence extraction : 00:00:31 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:03 (hh:mm:ss) Elapsed Time Round Time: 00:21:05 (hh:mm:ss) Elapsed Time : 1016 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16499 repeats masked totaling 2906418 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011326 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10011326 bp After Masking: 6680282 bp Masked: 33.27 % -- Input Database Coverage: 10011326 bp out of 1089387278 bp ( 0.92 % ) Sampling Time: 00:01:05 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:11 (hh:mm:ss) Elapsed Time, 9465 HSPs Collected Number of families returned by RECON: 1948 Round Time: 00:07:56 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 50175 repeats masked totaling 8507060 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002166 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 30002166 bp After Masking: 20471846 bp Masked: 31.77 % -- Input Database Coverage: 40013492 bp out of 1089387278 bp ( 3.67 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:25:41 (hh:mm:ss) Elapsed Time, 79200 HSPs Collected Number of families returned by RECON: 6058 Round Time: 00:37:19 (hh:mm:ss) Elapsed Time : 218 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 168422 repeats masked totaling 28605152 bp(s). - TE Masking time 00:02:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90028670 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 90028670 bp After Masking: 58341162 bp Masked: 35.20 % -- Input Database Coverage: 130042162 bp out of 1089387278 bp ( 11.94 % ) Sampling Time: 00:10:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 02:58:07 (hh:mm:ss) Elapsed Time, 398176 HSPs Collected Number of families returned by RECON: 17742 Round Time: 04:05:37 (hh:mm:ss) Elapsed Time : 768 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 603266 repeats masked totaling 106223619 bp(s). - TE Masking time 00:11:47 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270017089 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 270016089 bp After Masking: 154442130 bp Masked: 42.80 % -- Input Database Coverage: 400059251 bp out of 1089387278 bp ( 36.72 % ) Sampling Time: 00:33:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22946925 Comparison Time: 18:34:17 (hh:mm:ss) Elapsed Time, 917080 HSPs Collected Number of families returned by RECON: 53429 Round Time: 22:41:22 (hh:mm:ss) Elapsed Time : 1557 families discovered. RepeatScout/RECON discovery complete: 3569 families found Classification Time: 02:17:21 (hh:mm:ss) Elapsed Time Program Time: 30:10:40 (hh:mm:ss) Elapsed Time