RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.cuuMPq/RM_1611.MonDec40152392023 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: 1701683558 Database = /dev/shm/rModeler.cuuMPq/GCA_030867145.1_bOpiHoa1.hap1 - Sequences = 415 - Bases = 1482459898 - N50 = 88572250 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 147019314-157519659 | [ 1 ] 136518970-147019314 | [ ] 126018626-136518970 | [ 1 ] 115518282-126018626 | [ ] 105017938-115518282 | [ 1 ] 94517594-105017938 | [ 1 ] 84017250-94517594 | [ 2 ] 73516906-84017250 | [ 3 ] 63016562-73516906 | [ ] 52516218-63016562 | [ ] 42015874-52516218 | [ 2 ] 31515530-42015874 | [ 1 ] 21015186-31515530 | [ 7 ] 10514842-21015186 |* [ 9 ] 14498-10514842 |************************************************** [ 387 ] Storage Throughput = excellent ( 1104.25 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019424 bp ( 40018824 non ambiguous ) - Num Contigs Represented = 68 - Sequence extraction : 00:01:37 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:25:12 (hh:mm:ss) Elapsed Time Round Time: 00:33:19 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1868 repeats masked totaling 890386 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005833 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10005633 bp After Masking: 8146327 bp Masked: 18.58 % -- Input Database Coverage: 10005833 bp out of 1482459898 bp ( 0.67 % ) Sampling Time: 00:01:25 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:46 (hh:mm:ss) Elapsed Time, 842 HSPs Collected Number of families returned by RECON: 179 Round Time: 00:07:50 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6461 repeats masked totaling 2989019 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013511 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30013111 bp After Masking: 23369575 bp Masked: 22.14 % -- Input Database Coverage: 40019344 bp out of 1482459898 bp ( 2.70 % ) Sampling Time: 00:03:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:30:27 (hh:mm:ss) Elapsed Time, 7233 HSPs Collected Number of families returned by RECON: 1081 Round Time: 00:34:37 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21670 repeats masked totaling 9537219 bp(s). - TE Masking time 00:00:50 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90022023 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 90018023 bp After Masking: 70144052 bp Masked: 22.08 % -- Input Database Coverage: 130041367 bp out of 1482459898 bp ( 8.77 % ) Sampling Time: 00:13:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 03:40:39 (hh:mm:ss) Elapsed Time, 64989 HSPs Collected Number of families returned by RECON: 5939 Round Time: 03:59:14 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:10:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 76933 repeats masked totaling 35319924 bp(s). - TE Masking time 00:04:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021843 bp Num Contigs Represented = 204 Non ambiguous bp: Initial: 270013349 bp After Masking: 203531650 bp Masked: 24.62 % -- Input Database Coverage: 400063210 bp out of 1482459898 bp ( 26.99 % ) Sampling Time: 00:42:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22987590 Comparison Time: 28:34:26 (hh:mm:ss) Elapsed Time, 190374 HSPs Collected Number of families returned by RECON: 37134 Round Time: 29:43:03 (hh:mm:ss) Elapsed Time : 231 families discovered. RepeatScout/RECON discovery complete: 379 families found Classification Time: 00:36:18 (hh:mm:ss) Elapsed Time Program Time: 35:34:21 (hh:mm:ss) Elapsed Time