RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.5d3gSx/RM_14003.ThuNov300746002023 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: 1701359159 Database = /dev/shm/rModeler.5d3gSx/GCA_029633855.1_fHopMal1.hap1 - Sequences = 597 - Bases = 1115418468 - N50 = 56848262 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 85606581-91721194 | [ 3 ] 79491968-85606580 | [ 1 ] 73377355-79491967 | [ 1 ] 67262742-73377354 | [ ] 61148129-67262741 | [ 1 ] 55033516-61148128 | [ 1 ] 48918903-55033515 | [ ] 42804290-48918902 | [ 4 ] 36689677-42804289 | [ 6 ] 30575064-36689676 | [ 2 ] 24460451-30575063 | [ ] 18345838-24460450 | [ ] 12231225-18345837 | [ ] 6116612-12231224 | [ ] 2000-6116612 |************************************************** [ 578 ] Storage Throughput = excellent ( 1156.45 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 42803580 bp ( 40034016 non ambiguous ) - Num Contigs Represented = 76 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:27:21 (hh:mm:ss) Elapsed Time Round Time: 00:46:21 (hh:mm:ss) Elapsed Time : 534 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13032 repeats masked totaling 2295059 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10820486 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10023299 bp After Masking: 6702666 bp Masked: 33.13 % -- Input Database Coverage: 10820486 bp out of 1115418468 bp ( 0.97 % ) Sampling Time: 00:01:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 37401 Comparison Time: 00:06:39 (hh:mm:ss) Elapsed Time, 11388 HSPs Collected Number of families returned by RECON: 1329 Round Time: 00:09:09 (hh:mm:ss) Elapsed Time : 22 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 41943 repeats masked totaling 7222093 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 31983086 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 30010709 bp After Masking: 19648376 bp Masked: 34.53 % -- Input Database Coverage: 42803572 bp out of 1115418468 bp ( 3.84 % ) Sampling Time: 00:06:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 324415 Comparison Time: 00:35:11 (hh:mm:ss) Elapsed Time, 164983 HSPs Collected Number of families returned by RECON: 4643 Round Time: 00:43:39 (hh:mm:ss) Elapsed Time : 120 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:32 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 139659 repeats masked totaling 23386600 bp(s). - TE Masking time 00:02:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 96017821 bp Num Contigs Represented = 122 Non ambiguous bp: Initial: 90017756 bp After Masking: 56862830 bp Masked: 36.83 % -- Input Database Coverage: 138821393 bp out of 1115418468 bp ( 12.45 % ) Sampling Time: 00:19:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2924571 Comparison Time: 03:44:36 (hh:mm:ss) Elapsed Time, 1183600 HSPs Collected Number of families returned by RECON: 15276 Round Time: 04:17:44 (hh:mm:ss) Elapsed Time : 457 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:01 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 496192 repeats masked totaling 85819528 bp(s). - TE Masking time 00:12:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 290947538 bp Num Contigs Represented = 299 Non ambiguous bp: Initial: 270028499 bp After Masking: 156558456 bp Masked: 42.02 % -- Input Database Coverage: 429768931 bp out of 1115418468 bp ( 38.53 % ) Sampling Time: 01:04:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 27110566 Comparison Time: 28:24:49 (hh:mm:ss) Elapsed Time, 8246514 HSPs Collected Number of families returned by RECON: 50673 Round Time: 31:04:24 (hh:mm:ss) Elapsed Time : 1008 families discovered. RepeatScout/RECON discovery complete: 2141 families found Classification Time: 01:40:54 (hh:mm:ss) Elapsed Time Program Time: 38:42:11 (hh:mm:ss) Elapsed Time