RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WaaJQS/RM_2046572.SunJul201554142025 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: 1753052053 Database = /dev/shm/rModeler.WaaJQS/GCA_965194725.1_mBalBor1.hap2.1 - Sequences = 1851 - Bases = 2988821750 - N50 = 107749909 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 176132886-188713735 | [ 2 ] 163552037-176132886 | [ 1 ] 150971188-163552037 | [ ] 138390339-150971188 | [ 2 ] 125809490-138390339 | [ 1 ] 113228641-125809490 | [ 2 ] 100647792-113228641 | [ 4 ] 88066943-100647792 | [ 4 ] 75486094-88066943 | [ 3 ] 62905245-75486094 | [ ] 50324396-62905245 | [ 2 ] 37743547-50324396 | [ ] 25162698-37743547 | [ 1 ] 12581849-25162698 | [ ] 1000-12581849 |************************************************** [ 1829 ] Storage Throughput = excellent ( 1747.67 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40029133 bp ( 40025333 non ambiguous ) - Num Contigs Represented = 222 - Sequence extraction : 00:00:59 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:40 (hh:mm:ss) Elapsed Time Round Time: 00:16:30 (hh:mm:ss) Elapsed Time : 200 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10244 repeats masked totaling 3619061 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10018843 bp Num Contigs Represented = 79 Non ambiguous bp: Initial: 10017643 bp After Masking: 5987517 bp Masked: 40.23 % -- Input Database Coverage: 10018843 bp out of 2988821750 bp ( 0.34 % ) Sampling Time: 00:00:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:06:18 (hh:mm:ss) Elapsed Time, 40104 HSPs Collected Number of families returned by RECON: 635 Round Time: 00:07:38 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 32158 repeats masked totaling 12287120 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30010210 bp Num Contigs Represented = 177 Non ambiguous bp: Initial: 30007610 bp After Masking: 16677311 bp Masked: 44.42 % -- Input Database Coverage: 40029053 bp out of 2988821750 bp ( 1.34 % ) Sampling Time: 00:04:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:10:32 (hh:mm:ss) Elapsed Time, 25843 HSPs Collected Number of families returned by RECON: 1911 Round Time: 00:15:47 (hh:mm:ss) Elapsed Time : 62 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 105074 repeats masked totaling 36657812 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027620 bp Num Contigs Represented = 379 Non ambiguous bp: Initial: 90020820 bp After Masking: 49517865 bp Masked: 44.99 % -- Input Database Coverage: 130056673 bp out of 2988821750 bp ( 4.35 % ) Sampling Time: 00:08:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 01:09:14 (hh:mm:ss) Elapsed Time, 141881 HSPs Collected Number of families returned by RECON: 6962 Round Time: 01:18:23 (hh:mm:ss) Elapsed Time : 157 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 357854 repeats masked totaling 120879391 bp(s). - TE Masking time 00:02:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270055125 bp Num Contigs Represented = 793 Non ambiguous bp: Initial: 270034440 bp After Masking: 139747265 bp Masked: 48.25 % -- Input Database Coverage: 400111798 bp out of 2988821750 bp ( 13.39 % ) Sampling Time: 00:19:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23300551 Comparison Time: 06:40:26 (hh:mm:ss) Elapsed Time, 799659 HSPs Collected Number of families returned by RECON: 27897 Round Time: 07:08:45 (hh:mm:ss) Elapsed Time : 326 families discovered. RepeatScout/RECON discovery complete: 758 families found Classification Time: 00:18:04 (hh:mm:ss) Elapsed Time Program Time: 09:25:07 (hh:mm:ss) Elapsed Time