RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.qMYNF4/RM_1363790.FriApr111258102025 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: 1744401490 Database = /dev/shm/rModeler.qMYNF4/GCA_964656225.1_mPipNat1.hap1.1 - Sequences = 1062 - Bases = 1916223105 - N50 = 99813412 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 197994341-212136723 | [ 1 ] 183851959-197994340 | [ 2 ] 169709578-183851959 | [ ] 155567196-169709577 | [ ] 141424815-155567196 | [ ] 127282433-141424814 | [ ] 113140052-127282433 | [ ] 98997670-113140051 | [ 3 ] 84855289-98997670 | [ 2 ] 70712907-84855288 | [ 4 ] 56570526-70712907 | [ 1 ] 42428144-56570525 | [ 6 ] 28285763-42428144 | [ ] 14143381-28285762 | [ 2 ] 1000-14143381 |************************************************** [ 1041 ] Storage Throughput = excellent ( 1762.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40008862 bp ( 40001262 non ambiguous ) - Num Contigs Represented = 82 - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:17 (hh:mm:ss) Elapsed Time Round Time: 00:12:50 (hh:mm:ss) Elapsed Time : 312 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14710 repeats masked totaling 2329055 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10040493 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10038493 bp After Masking: 7150038 bp Masked: 28.77 % -- Input Database Coverage: 10040493 bp out of 1916223105 bp ( 0.52 % ) Sampling Time: 00:00:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:02:55 (hh:mm:ss) Elapsed Time, 4887 HSPs Collected Number of families returned by RECON: 814 Round Time: 00:03:43 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42519 repeats masked totaling 7287577 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30008284 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30002484 bp After Masking: 20510309 bp Masked: 31.64 % -- Input Database Coverage: 40048777 bp out of 1916223105 bp ( 2.09 % ) Sampling Time: 00:02:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:12:31 (hh:mm:ss) Elapsed Time, 26477 HSPs Collected Number of families returned by RECON: 2474 Round Time: 00:14:54 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 140177 repeats masked totaling 23817604 bp(s). - TE Masking time 00:00:31 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90053424 bp Num Contigs Represented = 139 Non ambiguous bp: Initial: 90036447 bp After Masking: 60199403 bp Masked: 33.14 % -- Input Database Coverage: 130102201 bp out of 1916223105 bp ( 6.79 % ) Sampling Time: 00:05:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2602621 Comparison Time: 01:13:08 (hh:mm:ss) Elapsed Time, 89595 HSPs Collected Number of families returned by RECON: 8455 Round Time: 01:20:19 (hh:mm:ss) Elapsed Time : 212 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 457114 repeats masked totaling 78443128 bp(s). - TE Masking time 00:02:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270083889 bp Num Contigs Represented = 288 Non ambiguous bp: Initial: 270035486 bp After Masking: 170965649 bp Masked: 36.69 % -- Input Database Coverage: 400186090 bp out of 1916223105 bp ( 20.88 % ) Sampling Time: 00:19:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23245971 Comparison Time: 08:32:00 (hh:mm:ss) Elapsed Time, 228779 HSPs Collected Number of families returned by RECON: 34038 Round Time: 09:02:02 (hh:mm:ss) Elapsed Time : 404 families discovered. RepeatScout/RECON discovery complete: 1010 families found Classification Time: 00:17:21 (hh:mm:ss) Elapsed Time Program Time: 11:11:09 (hh:mm:ss) Elapsed Time