RepeatModeler Version 2.0.7 =========================== Using output directory = /dev/shm/rModeler.Vm3oae/RM_600104.ThuOct91211182025 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: 1760037077 Database = /dev/shm/rModeler.Vm3oae/GCA_028023455.1_ASM2802345v1 - Sequences = 18588 - Bases = 5601407764 - N50 = 5355636 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 33114421-35479710 | [ 6 ] 30749133-33114421 | [ 1 ] 28383845-30749133 | [ ] 26018556-28383844 | [ 3 ] 23653268-26018556 | [ 2 ] 21287980-23653268 | [ 3 ] 18922691-21287979 | [ 8 ] 16557403-18922691 | [ 12 ] 14192115-16557403 | [ 10 ] 11826826-14192114 | [ 23 ] 9461538-11826826 | [ 44 ] 7096250-9461538 | [ 73 ] 4730961-7096249 | [ 115 ] 2365673-4730961 | [ 274 ] 385-2365673 |************************************************** [ 18014 ] Storage Throughput = excellent ( 1171.42 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40051516 bp ( 40032381 non ambiguous ) - Num Contigs Represented = 738 - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: Running build_lmer_table ( l = 14, min = 10 ).. - RepeatScout: Running RepeatScout.. : 688 raw families identified - RepeatScout: Running filtering stage.. 604 families remaining - RepeatScout: 00:06:30 (hh:mm:ss) Elapsed Time - Collecting repeat instances... - Refining 589 families... 00:02:53 (hh:mm:ss) Elapsed Time - Redundant Families and Large Satellite Filtering.. : 1 satellite(s), 243 contained, found in 00:00:11 (hh:mm:ss) Elapsed Time Family Refinement: 00:00:12 (hh:mm:ss) Elapsed Time Round Time: 00:09:56 (hh:mm:ss) Elapsed Time : 345 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12308 repeats masked totaling 4189043 bp(s). - TE Masking time 00:01:37 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10016910 bp Num Contigs Represented = 249 Non ambiguous bp: Initial: 10012382 bp After Masking: 5693390 bp Masked: 43.14 % -- Input Database Coverage: 10016910 bp out of 5601407764 bp ( 0.18 % ) Sampling Time: 00:02:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 38503 Comparison Time: 00:08:21 (hh:mm:ss) Elapsed Time, 35004 HSPs Collected Number of families returned by RECON: 1916 Round Time: 00:11:49 (hh:mm:ss) Elapsed Time : 32 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:09 (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... 40490 repeats masked totaling 13505262 bp(s). - TE Masking time 00:05:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30034559 bp Num Contigs Represented = 597 Non ambiguous bp: Initial: 30019952 bp After Masking: 16159177 bp Masked: 46.17 % -- Input Database Coverage: 40051469 bp out of 5601407764 bp ( 0.72 % ) Sampling Time: 00:07:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 334153 Comparison Time: 00:52:58 (hh:mm:ss) Elapsed Time, 111559 HSPs Collected Number of families returned by RECON: 5311 Round Time: 01:04:46 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140980 repeats masked totaling 46824942 bp(s). - TE Masking time 00:22:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90041877 bp Num Contigs Represented = 1267 Non ambiguous bp: Initial: 90006108 bp After Masking: 41999090 bp Masked: 53.34 % -- Input Database Coverage: 130093346 bp out of 5601407764 bp ( 2.32 % ) Sampling Time: 00:28:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2970703 Comparison Time: 05:56:03 (hh:mm:ss) Elapsed Time, 435203 HSPs Collected Number of families returned by RECON: 11473 Round Time: 06:42:14 (hh:mm:ss) Elapsed Time : 487 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 533007 repeats masked totaling 178934088 bp(s). - TE Masking time 02:52:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270140769 bp Num Contigs Represented = 2549 Non ambiguous bp: Initial: 270009607 bp After Masking: 87493747 bp Masked: 67.60 % -- Input Database Coverage: 400234115 bp out of 5601407764 bp ( 7.15 % ) Sampling Time: 03:16:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 26868115 Comparison Time: 31:56:15 (hh:mm:ss) Elapsed Time, 743236 HSPs Collected Number of families returned by RECON: 21437 Round Time: 35:55:48 (hh:mm:ss) Elapsed Time : 1040 families discovered. RepeatScout/RECON discovery complete: 2002 families found # # RepeatClassifier # # Version 2.0.7 # Threads: 32 # Current Working Directory: /dev/shm/rModeler.Vm3oae/RM_600104.ThuOct91211182025 # 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: 00:19:54 (hh:mm:ss) Elapsed Time Program Time: 44:24:27 (hh:mm:ss) Elapsed Time