RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.3yvpeW/RM_2698588.MonApr211255572025 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: 1745265356 Database = /dev/shm/rModeler.3yvpeW/GCA_965202585.1_ktThaDemo2.hap1.1 - Sequences = 1833 - Bases = 801813394 - N50 = 101358551 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 109117753-116911807 | [ 1 ] 101323699-109117752 | [ 2 ] 93529645-101323698 | [ ] 85735591-93529644 | [ ] 77941538-85735591 | [ 2 ] 70147484-77941537 | [ ] 62353430-70147483 | [ 2 ] 54559376-62353429 | [ 1 ] 46765322-54559375 | [ ] 38971269-46765322 | [ 1 ] 31177215-38971268 | [ ] 23383161-31177214 | [ ] 15589107-23383160 | [ ] 7795053-15589106 | [ ] 1000-7795053 |************************************************** [ 1824 ] Storage Throughput = excellent ( 1650.20 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40013868 bp ( 40011813 non ambiguous ) - Num Contigs Represented = 153 - Sequence extraction : 00:00:48 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:42 (hh:mm:ss) Elapsed Time Round Time: 00:18:41 (hh:mm:ss) Elapsed Time : 513 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9591 repeats masked totaling 2681716 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10020410 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10019610 bp After Masking: 6802830 bp Masked: 32.10 % -- Input Database Coverage: 10020410 bp out of 801813394 bp ( 1.25 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33153 Comparison Time: 00:06:00 (hh:mm:ss) Elapsed Time, 3087 HSPs Collected Number of families returned by RECON: 603 Round Time: 00:07:20 (hh:mm:ss) Elapsed Time : 4 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 31933 repeats masked totaling 8456676 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30033458 bp Num Contigs Represented = 117 Non ambiguous bp: Initial: 30032203 bp After Masking: 20624727 bp Masked: 31.32 % -- Input Database Coverage: 40053868 bp out of 801813394 bp ( 5.00 % ) Sampling Time: 00:03:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 311655 Comparison Time: 00:37:47 (hh:mm:ss) Elapsed Time, 26800 HSPs Collected Number of families returned by RECON: 2523 Round Time: 00:42:13 (hh:mm:ss) Elapsed Time : 40 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 94413 repeats masked totaling 25046729 bp(s). - TE Masking time 00:03:53 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039428 bp Num Contigs Represented = 306 Non ambiguous bp: Initial: 90033528 bp After Masking: 61525031 bp Masked: 31.66 % -- Input Database Coverage: 130093296 bp out of 801813394 bp ( 16.22 % ) Sampling Time: 00:11:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2753031 Comparison Time: 04:35:04 (hh:mm:ss) Elapsed Time, 246780 HSPs Collected Number of families returned by RECON: 9914 Round Time: 04:48:57 (hh:mm:ss) Elapsed Time : 207 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 317113 repeats masked totaling 87837699 bp(s). - TE Masking time 00:18:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021943 bp Num Contigs Represented = 799 Non ambiguous bp: Initial: 270006298 bp After Masking: 172452740 bp Masked: 36.13 % -- Input Database Coverage: 400115239 bp out of 801813394 bp ( 49.90 % ) Sampling Time: 00:42:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 24847725 Comparison Time: 34:47:57 (hh:mm:ss) Elapsed Time, 891662 HSPs Collected Number of families returned by RECON: 31989 Round Time: 35:56:23 (hh:mm:ss) Elapsed Time : 617 families discovered. RepeatScout/RECON discovery complete: 1381 families found Classification Time: 01:19:41 (hh:mm:ss) Elapsed Time Program Time: 43:13:15 (hh:mm:ss) Elapsed Time