RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.r1p7fy/RM_5417.ThuDec70731532023 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: 1701963111 Database = /dev/shm/rModeler.r1p7fy/GCA_949752795.1_mHypAmp2.1 - Sequences = 757 - Bases = 2828760712 - N50 = 117531870 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 215086425-230449670 | [ 1 ] 199723180-215086424 | [ 1 ] 184359936-199723180 | [ ] 168996691-184359935 | [ 2 ] 153633446-168996690 | [ ] 138270202-153633446 | [ 2 ] 122906957-138270201 | [ 1 ] 107543712-122906956 | [ 3 ] 92180468-107543712 | [ 2 ] 76817223-92180467 | [ 6 ] 61453978-76817222 | [ 1 ] 46090734-61453978 | [ 1 ] 30727489-46090733 | [ 1 ] 15364244-30727488 | [ 2 ] 1000-15364244 |************************************************** [ 734 ] Storage Throughput = excellent ( 1219.37 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40012885 bp ( 40008885 non ambiguous ) - Num Contigs Represented = 119 - Sequence extraction : 00:02:28 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:27:26 (hh:mm:ss) Elapsed Time Round Time: 00:45:50 (hh:mm:ss) Elapsed Time : 201 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 9057 repeats masked totaling 2821789 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005981 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 10004781 bp After Masking: 6801334 bp Masked: 32.02 % -- Input Database Coverage: 10005981 bp out of 2828760712 bp ( 0.35 % ) Sampling Time: 00:01:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:07:14 (hh:mm:ss) Elapsed Time, 418451 HSPs Collected Number of families returned by RECON: 783 Round Time: 00:21:58 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:52 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33030 repeats masked totaling 10956958 bp(s). - TE Masking time 00:00:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30006903 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 30004103 bp After Masking: 18161939 bp Masked: 39.47 % -- Input Database Coverage: 40012884 bp out of 2828760712 bp ( 1.41 % ) Sampling Time: 00:04:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:26:34 (hh:mm:ss) Elapsed Time, 33777 HSPs Collected Number of families returned by RECON: 2228 Round Time: 00:32:46 (hh:mm:ss) Elapsed Time : 65 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 109700 repeats masked totaling 34531050 bp(s). - TE Masking time 00:01:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90039389 bp Num Contigs Represented = 208 Non ambiguous bp: Initial: 90033589 bp After Masking: 51257795 bp Masked: 43.07 % -- Input Database Coverage: 130052273 bp out of 2828760712 bp ( 4.60 % ) Sampling Time: 00:13:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2554930 Comparison Time: 02:54:13 (hh:mm:ss) Elapsed Time, 115113 HSPs Collected Number of families returned by RECON: 7827 Round Time: 03:12:09 (hh:mm:ss) Elapsed Time : 149 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:16:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:18:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 365933 repeats masked totaling 111804339 bp(s). - TE Masking time 00:05:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270056082 bp Num Contigs Represented = 381 Non ambiguous bp: Initial: 270029007 bp After Masking: 147050405 bp Masked: 45.54 % -- Input Database Coverage: 400108355 bp out of 2828760712 bp ( 14.14 % ) Sampling Time: 00:40:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23075821 Comparison Time: 21:03:58 (hh:mm:ss) Elapsed Time, 340292 HSPs Collected Number of families returned by RECON: 29899 Round Time: 22:10:29 (hh:mm:ss) Elapsed Time : 342 families discovered. RepeatScout/RECON discovery complete: 775 families found Classification Time: 00:32:49 (hh:mm:ss) Elapsed Time Program Time: 27:36:01 (hh:mm:ss) Elapsed Time