RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.YQXwBD/RM_463544.MonJan221206392024 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: 1705953999 Database = /dev/shm/rModeler.YQXwBD/GCF_949987515.1_mDelDel1.1 - Sequences = 630 - Bases = 2663516986 - N50 = 110534049 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 172543118-184867555 | [ 3 ] 160218681-172543118 | [ ] 147894244-160218681 | [ ] 135569807-147894244 | [ 2 ] 123245370-135569807 | [ 1 ] 110920933-123245370 | [ 2 ] 98596496-110920933 | [ 4 ] 86272059-98596496 | [ 4 ] 73947622-86272059 | [ 3 ] 61623185-73947622 | [ ] 49298748-61623185 | [ 2 ] 36974311-49298748 | [ ] 24649874-36974311 | [ 1 ] 12325437-24649874 | [ ] 1000-12325437 |************************************************** [ 608 ] Storage Throughput = fair ( 609.38 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40040209 bp ( 40036209 non ambiguous ) - Num Contigs Represented = 103 - Sequence extraction : 00:02:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:31 (hh:mm:ss) Elapsed Time Round Time: 00:35:31 (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 : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10384 repeats masked totaling 3206303 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10003891 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 10003291 bp After Masking: 6391399 bp Masked: 36.11 % -- Input Database Coverage: 10003891 bp out of 2663516986 bp ( 0.38 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:20 (hh:mm:ss) Elapsed Time, 296458 HSPs Collected Number of families returned by RECON: 910 Round Time: 00:13:12 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36876 repeats masked totaling 10486041 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036238 bp Num Contigs Represented = 86 Non ambiguous bp: Initial: 30032838 bp After Masking: 18900341 bp Masked: 37.07 % -- Input Database Coverage: 40040129 bp out of 2663516986 bp ( 1.50 % ) Sampling Time: 00:04:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:25:34 (hh:mm:ss) Elapsed Time, 31656 HSPs Collected Number of families returned by RECON: 2345 Round Time: 00:31:41 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 123871 repeats masked totaling 34237584 bp(s). - TE Masking time 00:01:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90038359 bp Num Contigs Represented = 180 Non ambiguous bp: Initial: 90031159 bp After Masking: 53247136 bp Masked: 40.86 % -- Input Database Coverage: 130078488 bp out of 2663516986 bp ( 4.88 % ) Sampling Time: 00:15:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 04:53:41 (hh:mm:ss) Elapsed Time, 95833 HSPs Collected Number of families returned by RECON: 8200 Round Time: 05:15:52 (hh:mm:ss) Elapsed Time : 189 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 415044 repeats masked totaling 111304732 bp(s). - TE Masking time 00:04:41 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270035778 bp Num Contigs Represented = 328 Non ambiguous bp: Initial: 270016318 bp After Masking: 152390930 bp Masked: 43.56 % -- Input Database Coverage: 400114266 bp out of 2663516986 bp ( 15.02 % ) Sampling Time: 00:35:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22980810 Comparison Time: 19:42:50 (hh:mm:ss) Elapsed Time, 262742 HSPs Collected Number of families returned by RECON: 30011 Round Time: 20:35:31 (hh:mm:ss) Elapsed Time : 340 families discovered. RepeatScout/RECON discovery complete: 803 families found Classification Time: 00:27:36 (hh:mm:ss) Elapsed Time Program Time: 27:39:23 (hh:mm:ss) Elapsed Time