RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4gIAr0/RM_10250.FriDec11746462023 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: 1701481605 Database = /dev/shm/rModeler.4gIAr0/GCA_030028035.1_mHipAmp2.hap1 - Sequences = 545 - Bases = 2533318371 - N50 = 141325653 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 223285423-239233223 | [ 1 ] 207337624-223285423 | [ 1 ] 191389825-207337624 | [ ] 175442026-191389825 | [ 1 ] 159494227-175442026 | [ 1 ] 143546428-159494227 | [ 2 ] 127598629-143546428 | [ 3 ] 111650830-127598629 | [ 1 ] 95703031-111650830 | [ 3 ] 79755232-95703031 | [ 3 ] 63807433-79755232 | [ 2 ] 47859634-63807433 | [ 1 ] 31911835-47859634 | [ 1 ] 15964036-31911835 | [ ] 16237-15964036 |************************************************** [ 525 ] Storage Throughput = excellent ( 1113.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40023105 bp ( 40022505 non ambiguous ) - Num Contigs Represented = 57 - Sequence extraction : 00:02:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:56 (hh:mm:ss) Elapsed Time Round Time: 00:38:10 (hh:mm:ss) Elapsed Time : 211 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:45 (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... 8873 repeats masked totaling 2366194 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10031968 bp Num Contigs Represented = 29 Non ambiguous bp: Initial: 10031568 bp After Masking: 7607338 bp Masked: 24.17 % -- Input Database Coverage: 10031968 bp out of 2533318371 bp ( 0.40 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:56 (hh:mm:ss) Elapsed Time, 14877 HSPs Collected Number of families returned by RECON: 1006 Round Time: 00:07:39 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:10 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 29025 repeats masked totaling 8090560 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031136 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 30030936 bp After Masking: 21812629 bp Masked: 27.37 % -- Input Database Coverage: 40063104 bp out of 2533318371 bp ( 1.58 % ) Sampling Time: 00:03:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:37:46 (hh:mm:ss) Elapsed Time, 111762 HSPs Collected Number of families returned by RECON: 2524 Round Time: 00:42:35 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 100722 repeats masked totaling 27359598 bp(s). - TE Masking time 00:01:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90033216 bp Num Contigs Represented = 94 Non ambiguous bp: Initial: 90032816 bp After Masking: 62250124 bp Masked: 30.86 % -- Input Database Coverage: 130096320 bp out of 2533318371 bp ( 5.14 % ) Sampling Time: 00:10:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 04:16:01 (hh:mm:ss) Elapsed Time, 1117218 HSPs Collected Number of families returned by RECON: 9235 Round Time: 04:58:10 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:16 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 354017 repeats masked totaling 90482443 bp(s). - TE Masking time 00:07:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035763 bp Num Contigs Represented = 199 Non ambiguous bp: Initial: 270034363 bp After Masking: 178219829 bp Masked: 34.00 % -- Input Database Coverage: 400132083 bp out of 2533318371 bp ( 15.79 % ) Sampling Time: 00:35:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 32:34:03 (hh:mm:ss) Elapsed Time, 10178512 HSPs Collected Number of families returned by RECON: 36990 Round Time: 33:45:41 (hh:mm:ss) Elapsed Time : 368 families discovered. RepeatScout/RECON discovery complete: 843 families found Classification Time: 00:43:18 (hh:mm:ss) Elapsed Time Program Time: 40:55:33 (hh:mm:ss) Elapsed Time