RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.82qHCj/RM_13638.FriDec11706462023 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: 1701479204 Database = /dev/shm/rModeler.82qHCj/GCA_030020955.1_mDugDug1.hap2 - Sequences = 167 - Bases = 3154453075 - N50 = 176986036 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 214921237-230272189 | [ 1 ] 199570285-214921236 | [ 1 ] 184219333-199570284 |* [ 4 ] 168868381-184219332 | [ 1 ] 153517430-168868381 | [ ] 138166478-153517429 | [ 1 ] 122815526-138166477 |* [ 4 ] 107464574-122815525 |* [ 3 ] 92113622-107464573 | [ 1 ] 76762671-92113622 |* [ 5 ] 61411719-76762670 | [ 2 ] 46060767-61411718 | [ 1 ] 30709815-46060766 | [ ] 15358863-30709814 | [ ] 7912-15358863 |************************************************** [ 143 ] Storage Throughput = excellent ( 1159.09 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038841 bp ( 40038441 non ambiguous ) - Num Contigs Represented = 30 - Sequence extraction : 00:03:05 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:50 (hh:mm:ss) Elapsed Time Round Time: 00:39:19 (hh:mm:ss) Elapsed Time : 252 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14365 repeats masked totaling 4589055 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001558 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10001558 bp After Masking: 5369701 bp Masked: 46.31 % -- Input Database Coverage: 10001558 bp out of 3154453075 bp ( 0.32 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:00 (hh:mm:ss) Elapsed Time, 5471 HSPs Collected Number of families returned by RECON: 708 Round Time: 00:06:39 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 44642 repeats masked totaling 13820152 bp(s). - TE Masking time 00:00:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30037203 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 30036803 bp After Masking: 16067436 bp Masked: 46.51 % -- Input Database Coverage: 40038761 bp out of 3154453075 bp ( 1.27 % ) Sampling Time: 00:04:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:29:03 (hh:mm:ss) Elapsed Time, 22485 HSPs Collected Number of families returned by RECON: 2115 Round Time: 00:33:56 (hh:mm:ss) Elapsed Time : 60 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:07:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 144080 repeats masked totaling 44159316 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026831 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 90026431 bp After Masking: 45472419 bp Masked: 49.49 % -- Input Database Coverage: 130065592 bp out of 3154453075 bp ( 4.12 % ) Sampling Time: 00:11:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2539131 Comparison Time: 02:33:58 (hh:mm:ss) Elapsed Time, 236744 HSPs Collected Number of families returned by RECON: 7230 Round Time: 02:54:52 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 478088 repeats masked totaling 139878730 bp(s). - TE Masking time 00:07:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021876 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 270019276 bp After Masking: 128771542 bp Masked: 52.31 % -- Input Database Coverage: 400087468 bp out of 3154453075 bp ( 12.68 % ) Sampling Time: 00:39:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22879230 Comparison Time: 19:05:18 (hh:mm:ss) Elapsed Time, 204868 HSPs Collected Number of families returned by RECON: 25868 Round Time: 20:04:37 (hh:mm:ss) Elapsed Time : 352 families discovered. RepeatScout/RECON discovery complete: 844 families found Classification Time: 00:35:22 (hh:mm:ss) Elapsed Time Program Time: 24:54:45 (hh:mm:ss) Elapsed Time