RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.a3mNWj/RM_404655.WedMar130800572024 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: 1710342056 Database = /dev/shm/rModeler.a3mNWj/GCA_035084135.1_sHepPer1.hap2 - Sequences = 1194 - Bases = 3059754027 - N50 = 73952655 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 184213738-197371158 | [ 1 ] 171056318-184213737 | [ 1 ] 157898899-171056318 | [ ] 144741479-157898898 | [ ] 131584060-144741479 | [ 3 ] 118426640-131584059 | [ ] 105269221-118426640 | [ 1 ] 92111801-105269220 | [ 2 ] 78954382-92111801 | [ 3 ] 65796962-78954381 | [ 3 ] 52639543-65796962 | [ 4 ] 39482123-52639542 | [ 9 ] 26324704-39482123 | [ 6 ] 13167284-26324703 | [ 13 ] 9865-13167284 |************************************************** [ 1148 ] Storage Throughput = excellent ( 1111.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40043070 bp ( 40038070 non ambiguous ) - Num Contigs Represented = 137 - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:53 (hh:mm:ss) Elapsed Time Round Time: 00:27:26 (hh:mm:ss) Elapsed Time : 376 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:26 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14153 repeats masked totaling 4600456 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10006257 bp Num Contigs Represented = 67 Non ambiguous bp: Initial: 10004657 bp After Masking: 3971593 bp Masked: 60.30 % -- Input Database Coverage: 10006257 bp out of 3059754027 bp ( 0.33 % ) Sampling Time: 00:05:06 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:04:23 (hh:mm:ss) Elapsed Time, 6084 HSPs Collected Number of families returned by RECON: 987 Round Time: 00:09:45 (hh:mm:ss) Elapsed Time : 20 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 00:12:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 45704 repeats masked totaling 14766385 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036806 bp Num Contigs Represented = 123 Non ambiguous bp: Initial: 30033406 bp After Masking: 11093173 bp Masked: 63.06 % -- Input Database Coverage: 40043063 bp out of 3059754027 bp ( 1.31 % ) Sampling Time: 00:14:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 288420 Comparison Time: 00:19:12 (hh:mm:ss) Elapsed Time, 35261 HSPs Collected Number of families returned by RECON: 3117 Round Time: 00:35:01 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:42:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 148587 repeats masked totaling 45967918 bp(s). - TE Masking time 00:01:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90013965 bp Num Contigs Represented = 206 Non ambiguous bp: Initial: 90004150 bp After Masking: 32096662 bp Masked: 64.34 % -- Input Database Coverage: 130057028 bp out of 3059754027 bp ( 4.25 % ) Sampling Time: 00:48:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 01:46:25 (hh:mm:ss) Elapsed Time, 144073 HSPs Collected Number of families returned by RECON: 8833 Round Time: 02:39:54 (hh:mm:ss) Elapsed Time : 325 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:13 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:17:00 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 500474 repeats masked totaling 146991369 bp(s). - TE Masking time 00:07:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270041830 bp Num Contigs Represented = 398 Non ambiguous bp: Initial: 270011925 bp After Masking: 85264299 bp Masked: 68.42 % -- Input Database Coverage: 400098858 bp out of 3059754027 bp ( 13.08 % ) Sampling Time: 02:36:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23130201 Comparison Time: 10:41:25 (hh:mm:ss) Elapsed Time, 348647 HSPs Collected Number of families returned by RECON: 23180 Round Time: 13:36:34 (hh:mm:ss) Elapsed Time : 732 families discovered. RepeatScout/RECON discovery complete: 1541 families found Classification Time: 00:57:23 (hh:mm:ss) Elapsed Time Program Time: 18:26:03 (hh:mm:ss) Elapsed Time