RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.8pyD6U/RM_26559.FriJan131043022023 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: 1673635381 Database = /dev/shm/rModeler.8pyD6U/GCA_023634155.1_bFalPer1.pri - Sequences = 124 - Bases = 1311580791 - N50 = 115608600 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 122060882-130779382 |* [ 4 ] 113342383-122060882 | [ 1 ] 104623883-113342382 | [ ] 95905384-104623883 | [ ] 87186884-95905383 | [ 2 ] 78468385-87186884 | [ 1 ] 69749885-78468384 | [ ] 61031386-69749885 | [ 1 ] 52312886-61031385 | [ ] 43594387-52312886 | [ ] 34875887-43594386 | [ 2 ] 26157388-34875887 |* [ 3 ] 17438888-26157387 | [ 2 ] 8720389-17438888 | [ 1 ] 1890-8720389 |************************************************** [ 107 ] Storage Throughput = excellent ( 1176.59 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40176334 bp ( 40036018 non ambiguous ) - Num Contigs Represented = 60 - Sequence extraction : 00:01:50 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:26:53 (hh:mm:ss) Elapsed Time Round Time: 00:33:02 (hh:mm:ss) Elapsed Time : 56 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:27 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1231 repeats masked totaling 401926 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10029595 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10026820 bp After Masking: 8777205 bp Masked: 12.46 % -- Input Database Coverage: 10029595 bp out of 1311580791 bp ( 0.76 % ) Sampling Time: 00:04:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:07:08 (hh:mm:ss) Elapsed Time, 1232 HSPs Collected Number of families returned by RECON: 233 Round Time: 00:11:21 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3592 repeats masked totaling 1217997 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30146659 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 30009118 bp After Masking: 26066688 bp Masked: 13.14 % -- Input Database Coverage: 40176254 bp out of 1311580791 bp ( 3.06 % ) Sampling Time: 00:11:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:37:23 (hh:mm:ss) Elapsed Time, 4226 HSPs Collected Number of families returned by RECON: 1386 Round Time: 00:49:41 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12325 repeats masked totaling 3922367 bp(s). - TE Masking time 00:00:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90327071 bp Num Contigs Represented = 80 Non ambiguous bp: Initial: 90024623 bp After Masking: 79000687 bp Masked: 12.25 % -- Input Database Coverage: 130503325 bp out of 1311580791 bp ( 9.95 % ) Sampling Time: 00:32:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 04:32:55 (hh:mm:ss) Elapsed Time, 51770 HSPs Collected Number of families returned by RECON: 8725 Round Time: 05:12:29 (hh:mm:ss) Elapsed Time : 96 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 01:22:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 53915 repeats masked totaling 17376845 bp(s). - TE Masking time 00:03:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270620709 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 270001527 bp After Masking: 232180458 bp Masked: 14.01 % -- Input Database Coverage: 401124034 bp out of 1311580791 bp ( 30.58 % ) Sampling Time: 01:39:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22953700 Comparison Time: 36:36:23 (hh:mm:ss) Elapsed Time, 176942 HSPs Collected Number of families returned by RECON: 55140 Round Time: 39:49:54 (hh:mm:ss) Elapsed Time : 183 families discovered. RepeatScout/RECON discovery complete: 341 families found Classification Time: 00:45:54 (hh:mm:ss) Elapsed Time Program Time: 47:22:21 (hh:mm:ss) Elapsed Time