RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.CZiJ2A/RM_2691423.ThuNov62348282025 Search Engine = rmblast 2.14.1+ Threads = 32 Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7 LTR Structural Analysis: Disabled [use -LTRStruct to enable] Random Number Seed: 1762501706 Database = /dev/shm/rModeler.CZiJ2A/GCA_019843795.1_ASM1984379v1 - Sequences = 320461 - Bases = 2485459324 - N50 = 16557 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 333262-356996 | [ 1 ] 309529-333262 | [ ] 285796-309529 | [ 1 ] 262063-285796 | [ ] 238330-262063 | [ ] 214597-238330 | [ 1 ] 190864-214597 | [ 2 ] 167131-190864 | [ ] 143398-167131 | [ 4 ] 119665-143398 | [ 2 ] 95932-119665 | [ 22 ] 72199-95932 | [ 450 ] 48466-72199 | [ 2953 ] 24733-48466 |*** [ 19555 ] 1000-24733 |************************************************** [ 297470 ] Storage Throughput = excellent ( 1891.15 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40394674 bp ( 40011254 non ambiguous ) - Num Contigs Represented = 5451 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 287 raw families identified - RepeatScout: Running filtering stage.. 259 families remaining - RepeatScout: 00:01:28 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 256 families... 00:01:04 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 0 satellite(s), 91 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time Round Time: 00:02:37 (hh:mm:ss) Elapsed Time : 165 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12294 repeats masked totaling 2496386 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10086267 bp Num Contigs Represented = 1341 Non ambiguous bp: Initial: 10004337 bp After Masking: 7309363 bp Masked: 26.94 % -- Input Database Coverage: 10086267 bp out of 2485459324 bp ( 0.41 % ) Sampling Time: 00:00:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 898470 Comparison Time: 00:06:52 (hh:mm:ss) Elapsed Time, 23560 HSPs Collected Number of families returned by RECON: 1092 Round Time: 00:07:28 (hh:mm:ss) Elapsed Time : 28 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46114 repeats masked totaling 9115554 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30308373 bp Num Contigs Represented = 4111 Non ambiguous bp: Initial: 30006883 bp After Masking: 20284388 bp Masked: 32.40 % -- Input Database Coverage: 40394640 bp out of 2485459324 bp ( 1.63 % ) Sampling Time: 00:00:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 8452216 Comparison Time: 00:25:13 (hh:mm:ss) Elapsed Time, 26943 HSPs Collected Number of families returned by RECON: 2131 Round Time: 00:26:32 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 149814 repeats masked totaling 29404899 bp(s). - TE Masking time 00:00:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90905681 bp Num Contigs Represented = 12045 Non ambiguous bp: Initial: 90012231 bp After Masking: 58729196 bp Masked: 34.75 % -- Input Database Coverage: 131300321 bp out of 2485459324 bp ( 5.28 % ) Sampling Time: 00:02:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 72691653 Comparison Time: 01:59:16 (hh:mm:ss) Elapsed Time, 92329 HSPs Collected Number of families returned by RECON: 7516 Round Time: 02:03:43 (hh:mm:ss) Elapsed Time : 174 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 514990 repeats masked totaling 98151601 bp(s). - TE Masking time 00:03:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272544485 bp Num Contigs Represented = 35402 Non ambiguous bp: Initial: 270006990 bp After Masking: 166302407 bp Masked: 38.41 % -- Input Database Coverage: 403844806 bp out of 2485459324 bp ( 16.25 % ) Sampling Time: 00:09:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 630462295 Comparison Time: 11:39:55 (hh:mm:ss) Elapsed Time, 222579 HSPs Collected Number of families returned by RECON: 29562 Round Time: 11:58:01 (hh:mm:ss) Elapsed Time : 362 families discovered. RepeatScout/RECON discovery complete: 788 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.CZiJ2A/RM_2691423.ThuNov62348282025 # Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib # - 18011 proteins # Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib # - 26292 consensus sequences - Looking for simple/tandem and low complexity sequences.. - Looking for similarity to known repeat proteins.. - Looking for similarity to known repeat consensi.. Classification Time: 00:01:35 (hh:mm:ss) Elapsed Time Program Time: 14:39:56 (hh:mm:ss) Elapsed Time