RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.gIoAHs/RM_751052.FriApr182307352025 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: 1745042853 Database = /dev/shm/rModeler.gIoAHs/GCF_035609145.1_aEleCoq1.hap1 - Sequences = 956 - Bases = 3371297528 - N50 = 304122739 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 502246707-538120716 | [ 1 ] 466372698-502246706 | [ ] 430498689-466372697 | [ ] 394624681-430498689 | [ ] 358750672-394624680 | [ ] 322876663-358750671 | [ 1 ] 287002654-322876662 | [ 2 ] 251128646-287002654 | [ 1 ] 215254637-251128645 | [ 2 ] 179380628-215254636 | [ 1 ] 143506619-179380627 | [ 2 ] 107632611-143506619 | [ 3 ] 71758602-107632610 | [ ] 35884593-71758601 | [ ] 10585-35884593 |************************************************** [ 943 ] Storage Throughput = excellent ( 1797.92 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010653 bp ( 40009253 non ambiguous ) - Num Contigs Represented = 64 - Sequence extraction : 00:02:49 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:17 (hh:mm:ss) Elapsed Time Round Time: 00:16:13 (hh:mm:ss) Elapsed Time : 992 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21757 repeats masked totaling 4748463 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10032765 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10032165 bp After Masking: 4220805 bp Masked: 57.93 % -- Input Database Coverage: 10032765 bp out of 3371297528 bp ( 0.30 % ) Sampling Time: 00:01:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:44 (hh:mm:ss) Elapsed Time, 13355 HSPs Collected Number of families returned by RECON: 1596 Round Time: 00:04:26 (hh:mm:ss) Elapsed Time : 33 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 66755 repeats masked totaling 14737638 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30018687 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 30017887 bp After Masking: 11899314 bp Masked: 60.36 % -- Input Database Coverage: 40051452 bp out of 3371297528 bp ( 1.19 % ) Sampling Time: 00:04:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:10:16 (hh:mm:ss) Elapsed Time, 85413 HSPs Collected Number of families returned by RECON: 4569 Round Time: 00:15:50 (hh:mm:ss) Elapsed Time : 144 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 208181 repeats masked totaling 45900767 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038171 bp Num Contigs Represented = 124 Non ambiguous bp: Initial: 90033171 bp After Masking: 32955176 bp Masked: 63.40 % -- Input Database Coverage: 130089623 bp out of 3371297528 bp ( 3.86 % ) Sampling Time: 00:15:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2552670 Comparison Time: 00:47:42 (hh:mm:ss) Elapsed Time, 311932 HSPs Collected Number of families returned by RECON: 12075 Round Time: 01:07:51 (hh:mm:ss) Elapsed Time : 562 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 707053 repeats masked totaling 154876123 bp(s). - TE Masking time 00:04:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028832 bp Num Contigs Represented = 250 Non ambiguous bp: Initial: 270020432 bp After Masking: 83551751 bp Masked: 69.06 % -- Input Database Coverage: 400118455 bp out of 3371297528 bp ( 11.87 % ) Sampling Time: 00:49:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 04:29:42 (hh:mm:ss) Elapsed Time, 871638 HSPs Collected Number of families returned by RECON: 30022 Round Time: 05:37:51 (hh:mm:ss) Elapsed Time : 1304 families discovered. RepeatScout/RECON discovery complete: 3035 families found Classification Time: 00:50:10 (hh:mm:ss) Elapsed Time Program Time: 08:12:21 (hh:mm:ss) Elapsed Time