RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.69W1k7/RM_1378021.FriMar292248072024 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: 1711777687 Database = /dev/shm/rModeler.69W1k7/GCA_963924665.1_mMicMin1.1 - Sequences = 894 - Bases = 2651787409 - N50 = 61790571 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 243897568-261318752 | [ 1 ] 226476385-243897568 | [ ] 209055201-226476384 | [ ] 191634018-209055201 | [ ] 174212834-191634017 | [ ] 156791651-174212834 | [ ] 139370467-156791650 | [ ] 121949284-139370467 | [ 1 ] 104528100-121949283 | [ 1 ] 87106917-104528100 | [ 3 ] 69685733-87106916 | [ 3 ] 52264550-69685733 | [ 13 ] 34843366-52264549 | [ 8 ] 17422183-34843366 | [ 4 ] 1000-17422183 |************************************************** [ 860 ] Storage Throughput = excellent ( 1178.43 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40015599 bp ( 40012199 non ambiguous ) - Num Contigs Represented = 148 - Sequence extraction : 00:01:29 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:22:18 (hh:mm:ss) Elapsed Time Round Time: 00:36:55 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8262 repeats masked totaling 2092321 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004513 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 10003913 bp After Masking: 6248890 bp Masked: 37.54 % -- Input Database Coverage: 10004513 bp out of 2651787409 bp ( 0.38 % ) Sampling Time: 00:04:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:27 (hh:mm:ss) Elapsed Time, 7142 HSPs Collected Number of families returned by RECON: 737 Round Time: 00:10:52 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 28033 repeats masked totaling 6856488 bp(s). - TE Masking time 00:00:19 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30011082 bp Num Contigs Represented = 130 Non ambiguous bp: Initial: 30008282 bp After Masking: 17186703 bp Masked: 42.73 % -- Input Database Coverage: 40015595 bp out of 2651787409 bp ( 1.51 % ) Sampling Time: 00:19:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 01:20:21 (hh:mm:ss) Elapsed Time, 15609 HSPs Collected Number of families returned by RECON: 1786 Round Time: 01:41:35 (hh:mm:ss) Elapsed Time : 46 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:46:25 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 89844 repeats masked totaling 21839294 bp(s). - TE Masking time 00:00:54 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044423 bp Num Contigs Represented = 234 Non ambiguous bp: Initial: 90030069 bp After Masking: 52305133 bp Masked: 41.90 % -- Input Database Coverage: 130060018 bp out of 2651787409 bp ( 4.90 % ) Sampling Time: 00:50:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 02:32:29 (hh:mm:ss) Elapsed Time, 93108 HSPs Collected Number of families returned by RECON: 7464 Round Time: 03:26:34 (hh:mm:ss) Elapsed Time : 143 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:46 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:12:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 308641 repeats masked totaling 72582490 bp(s). - TE Masking time 00:03:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270077819 bp Num Contigs Represented = 407 Non ambiguous bp: Initial: 270035419 bp After Masking: 151333856 bp Masked: 43.96 % -- Input Database Coverage: 400137837 bp out of 2651787409 bp ( 15.09 % ) Sampling Time: 02:26:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23123400 Comparison Time: 18:55:53 (hh:mm:ss) Elapsed Time, 195049 HSPs Collected Number of families returned by RECON: 31044 Round Time: 21:38:03 (hh:mm:ss) Elapsed Time : 339 families discovered. RepeatScout/RECON discovery complete: 725 families found Classification Time: 00:27:38 (hh:mm:ss) Elapsed Time Program Time: 28:01:37 (hh:mm:ss) Elapsed Time