RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.Qqw8Ig/RM_982636.TueMar111243342025 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: 1741722214 Database = /dev/shm/rModeler.Qqw8Ig/GCA_048129065.1_fEpiMut1.hap2.cur.20240206 - Sequences = 199 - Bases = 1018963042 - N50 = 42470193 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 46519299-49840761 | [ 3 ] 43197837-46519298 |** [ 7 ] 39876375-43197836 |** [ 8 ] 36554914-39876375 | [ 2 ] 33233452-36554913 | [ 3 ] 29911990-33233451 | [ ] 26590528-29911989 | [ ] 23269067-26590528 | [ ] 19947605-23269066 | [ 1 ] 16626143-19947604 | [ ] 13304681-16626142 | [ ] 9983220-13304681 | [ ] 6661758-9983219 | [ ] 3340296-6661757 | [ ] 18835-3340296 |************************************************** [ 175 ] Storage Throughput = excellent ( 1771.10 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008329 bp ( 40008129 non ambiguous ) - Num Contigs Represented = 56 - Sequence extraction : 00:00:18 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:01 (hh:mm:ss) Elapsed Time Round Time: 00:10:05 (hh:mm:ss) Elapsed Time : 910 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14996 repeats masked totaling 2132992 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018062 bp Num Contigs Represented = 35 Non ambiguous bp: Initial: 10017862 bp After Masking: 7340878 bp Masked: 26.72 % -- Input Database Coverage: 10018062 bp out of 1018963042 bp ( 0.98 % ) Sampling Time: 00:00:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:02:53 (hh:mm:ss) Elapsed Time, 11551 HSPs Collected Number of families returned by RECON: 2005 Round Time: 00:03:52 (hh:mm:ss) Elapsed Time : 21 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:45 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 47816 repeats masked totaling 6769227 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030187 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 30030187 bp After Masking: 21852095 bp Masked: 27.23 % -- Input Database Coverage: 40048249 bp out of 1018963042 bp ( 3.93 % ) Sampling Time: 00:02:15 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:13:05 (hh:mm:ss) Elapsed Time, 97363 HSPs Collected Number of families returned by RECON: 6662 Round Time: 00:16:55 (hh:mm:ss) Elapsed Time : 237 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 165301 repeats masked totaling 24503769 bp(s). - TE Masking time 00:00:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90036431 bp Num Contigs Represented = 74 Non ambiguous bp: Initial: 90035431 bp After Masking: 61879506 bp Masked: 31.27 % -- Input Database Coverage: 130084680 bp out of 1018963042 bp ( 12.77 % ) Sampling Time: 00:05:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 01:14:38 (hh:mm:ss) Elapsed Time, 435226 HSPs Collected Number of families returned by RECON: 18970 Round Time: 01:27:55 (hh:mm:ss) Elapsed Time : 796 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 606350 repeats masked totaling 93317621 bp(s). - TE Masking time 00:05:01 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270014399 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 270012999 bp After Masking: 166275706 bp Masked: 38.42 % -- Input Database Coverage: 400099079 bp out of 1018963042 bp ( 39.27 % ) Sampling Time: 00:18:48 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 07:59:43 (hh:mm:ss) Elapsed Time, 1233325 HSPs Collected Number of families returned by RECON: 58448 Round Time: 09:00:33 (hh:mm:ss) Elapsed Time : 1635 families discovered. RepeatScout/RECON discovery complete: 3599 families found Classification Time: 01:01:56 (hh:mm:ss) Elapsed Time Program Time: 12:01:16 (hh:mm:ss) Elapsed Time