RepeatModeler Version 2.0.4 =========================== Using output directory = /scratch/tmp/rModeler.UndZAl/RM_1123841.SunNov170632462024 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: 1731853966 Database = /scratch/tmp/rModeler.UndZAl/GCA_011762505.2_mArvNil1.pat.X - Sequences = 1596 - Bases = 2496777707 - N50 = 86386494 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 155975538-167116563 | [ 1 ] 144834513-155975537 | [ 1 ] 133693489-144834513 | [ 2 ] 122552464-133693488 | [ 1 ] 111411440-122552464 | [ ] 100270415-111411439 | [ 2 ] 89129390-100270414 | [ 1 ] 77988366-89129390 | [ 6 ] 66847341-77988365 | [ 3 ] 55706317-66847341 | [ 1 ] 44565292-55706316 | [ 7 ] 33424267-44565291 | [ 2 ] 22283243-33424267 | [ 4 ] 11142218-22283242 | [ 1 ] 1194-11142218 |************************************************** [ 1564 ] Storage Throughput = excellent ( 1481.68 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40309840 bp ( 40005344 non ambiguous ) - Num Contigs Represented = 97 - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:29 (hh:mm:ss) Elapsed Time Round Time: 00:13:26 (hh:mm:ss) Elapsed Time : 366 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13795 repeats masked totaling 2688388 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10113019 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 10003091 bp After Masking: 6848355 bp Masked: 31.54 % -- Input Database Coverage: 10113019 bp out of 2496777707 bp ( 0.41 % ) Sampling Time: 00:03:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:05:51 (hh:mm:ss) Elapsed Time, 76959 HSPs Collected Number of families returned by RECON: 832 Round Time: 00:09:10 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:42 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42552 repeats masked totaling 8060474 bp(s). - TE Masking time 00:00:11 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30196810 bp Num Contigs Represented = 82 Non ambiguous bp: Initial: 30002242 bp After Masking: 20681808 bp Masked: 31.07 % -- Input Database Coverage: 40309829 bp out of 2496777707 bp ( 1.61 % ) Sampling Time: 00:03:32 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 297606 Comparison Time: 00:14:53 (hh:mm:ss) Elapsed Time, 126279 HSPs Collected Number of families returned by RECON: 2686 Round Time: 00:18:49 (hh:mm:ss) Elapsed Time : 49 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 133142 repeats masked totaling 25285696 bp(s). - TE Masking time 00:00:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90988663 bp Num Contigs Represented = 144 Non ambiguous bp: Initial: 90010333 bp After Masking: 61028435 bp Masked: 32.20 % -- Input Database Coverage: 131298492 bp out of 2496777707 bp ( 5.26 % ) Sampling Time: 00:09:03 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2639253 Comparison Time: 01:35:08 (hh:mm:ss) Elapsed Time, 1363669 HSPs Collected Number of families returned by RECON: 9679 Round Time: 01:46:48 (hh:mm:ss) Elapsed Time : 195 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:30:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 449762 repeats masked totaling 83377243 bp(s). - TE Masking time 00:02:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 272204169 bp Num Contigs Represented = 343 Non ambiguous bp: Initial: 270016379 bp After Masking: 175324488 bp Masked: 35.07 % -- Input Database Coverage: 403502661 bp out of 2496777707 bp ( 16.16 % ) Sampling Time: 00:39:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23739495 Comparison Time: 11:36:00 (hh:mm:ss) Elapsed Time, 17570135 HSPs Collected Number of families returned by RECON: 38511 Round Time: 12:32:05 (hh:mm:ss) Elapsed Time : 417 families discovered. RepeatScout/RECON discovery complete: 1039 families found Classification Time: 00:21:22 (hh:mm:ss) Elapsed Time Program Time: 15:21:40 (hh:mm:ss) Elapsed Time