RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.XgqsXt/RM_3536416.MonJun241444212024 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: 1719265461 Database = /dev/shm/rModeler.XgqsXt/GCF_963662255.1_bCinCin1.1 - Sequences = 277 - Bases = 1170837027 - N50 = 74413991 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 142206966-152364536 | [ 1 ] 132049397-142206966 | [ ] 121891828-132049397 | [ ] 111734259-121891828 | [ 2 ] 101576690-111734259 | [ ] 91419121-101576690 | [ ] 81261552-91419121 | [ 1 ] 71103983-81261552 | [ 2 ] 60946414-71103983 | [ 1 ] 50788845-60946414 | [ ] 40631276-50788845 | [ ] 30473707-40631276 | [ 2 ] 20316138-30473707 |* [ 7 ] 10158569-20316138 |* [ 7 ] 1000-10158569 |************************************************** [ 254 ] Storage Throughput = excellent ( 1363.17 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009970 bp ( 40005170 non ambiguous ) - Num Contigs Represented = 81 - Sequence extraction : 00:01:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:26 (hh:mm:ss) Elapsed Time Round Time: 00:23:10 (hh:mm:ss) Elapsed Time : 98 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2573 repeats masked totaling 632663 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10007477 bp Num Contigs Represented = 48 Non ambiguous bp: Initial: 10006477 bp After Masking: 8519520 bp Masked: 14.86 % -- Input Database Coverage: 10007477 bp out of 1170837027 bp ( 0.85 % ) Sampling Time: 00:02:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:32 (hh:mm:ss) Elapsed Time, 1035 HSPs Collected Number of families returned by RECON: 260 Round Time: 00:08:35 (hh:mm:ss) Elapsed Time : 0 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6655 repeats masked totaling 1764852 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30043903 bp Num Contigs Represented = 69 Non ambiguous bp: Initial: 30040103 bp After Masking: 25701083 bp Masked: 14.44 % -- Input Database Coverage: 40051380 bp out of 1170837027 bp ( 3.42 % ) Sampling Time: 00:04:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:31:03 (hh:mm:ss) Elapsed Time, 9587 HSPs Collected Number of families returned by RECON: 1363 Round Time: 00:36:14 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:40 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:11:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22615 repeats masked totaling 5862953 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90026557 bp Num Contigs Represented = 118 Non ambiguous bp: Initial: 90015357 bp After Masking: 77573975 bp Masked: 13.82 % -- Input Database Coverage: 130077937 bp out of 1170837027 bp ( 11.11 % ) Sampling Time: 00:16:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 03:48:25 (hh:mm:ss) Elapsed Time, 76688 HSPs Collected Number of families returned by RECON: 9210 Round Time: 04:08:01 (hh:mm:ss) Elapsed Time : 83 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:09:23 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:37:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 73104 repeats masked totaling 20131809 bp(s). - TE Masking time 00:04:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031966 bp Num Contigs Represented = 181 Non ambiguous bp: Initial: 270001856 bp After Masking: 227648416 bp Masked: 15.69 % -- Input Database Coverage: 400109903 bp out of 1170837027 bp ( 34.17 % ) Sampling Time: 00:51:46 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23041866 Comparison Time: 30:27:02 (hh:mm:ss) Elapsed Time, 1268359 HSPs Collected Number of families returned by RECON: 62810 Round Time: 32:12:00 (hh:mm:ss) Elapsed Time : 221 families discovered. RepeatScout/RECON discovery complete: 415 families found Classification Time: 00:44:35 (hh:mm:ss) Elapsed Time Program Time: 38:12:35 (hh:mm:ss) Elapsed Time