RepeatModeler Version 2.0.4 =========================== Using output directory = /data/tmp/rModeler.ApvxCq/RM_259903.WedDec181112252024 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: 1734549144 Database = /data/tmp/rModeler.ApvxCq/GCA_040807015.1_bStrCam1.hap2 - Sequences = 250 - Bases = 1383056266 - N50 = 86633230 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 209681393-224657354 | [ 1 ] 194705432-209681392 | [ ] 179729472-194705432 | [ ] 164753511-179729471 | [ 1 ] 149777550-164753510 | [ ] 134801590-149777550 | [ 1 ] 119825629-134801589 | [ ] 104849668-119825628 | [ ] 89873708-104849668 | [ ] 74897747-89873707 | [ 1 ] 59921786-74897746 | [ 1 ] 44945826-59921786 | [ 2 ] 29969865-44945825 | [ 4 ] 14993904-29969864 |** [ 10 ] 17944-14993904 |************************************************** [ 229 ] Storage Throughput = fair ( 622.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40020938 bp ( 40020538 non ambiguous ) - Num Contigs Represented = 81 - Sequence extraction : 00:01:26 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:14:04 (hh:mm:ss) Elapsed Time Round Time: 00:42:28 (hh:mm:ss) Elapsed Time : 66 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1055 repeats masked totaling 829684 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10004426 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10004226 bp After Masking: 8114079 bp Masked: 18.89 % -- Input Database Coverage: 10004426 bp out of 1383056266 bp ( 0.72 % ) Sampling Time: 00:01:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:14 (hh:mm:ss) Elapsed Time, 1149 HSPs Collected Number of families returned by RECON: 251 Round Time: 00:07:09 (hh:mm:ss) Elapsed Time : 2 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3104 repeats masked totaling 2157419 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016498 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 30016298 bp After Masking: 25742980 bp Masked: 14.24 % -- Input Database Coverage: 40020924 bp out of 1383056266 bp ( 2.89 % ) Sampling Time: 00:04:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:24:13 (hh:mm:ss) Elapsed Time, 12777 HSPs Collected Number of families returned by RECON: 1558 Round Time: 00:32:02 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13111 repeats masked totaling 7950731 bp(s). - TE Masking time 00:00:39 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90035176 bp Num Contigs Represented = 111 Non ambiguous bp: Initial: 90034176 bp After Masking: 73397547 bp Masked: 18.48 % -- Input Database Coverage: 130056100 bp out of 1383056266 bp ( 9.40 % ) Sampling Time: 00:13:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 02:12:27 (hh:mm:ss) Elapsed Time, 85531 HSPs Collected Number of families returned by RECON: 7610 Round Time: 02:42:41 (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 : 00:09:06 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:27:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 52310 repeats masked totaling 29491264 bp(s). - TE Masking time 00:03:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270031567 bp Num Contigs Represented = 154 Non ambiguous bp: Initial: 270029567 bp After Masking: 216865636 bp Masked: 19.69 % -- Input Database Coverage: 400087667 bp out of 1383056266 bp ( 28.93 % ) Sampling Time: 00:40:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22933378 Comparison Time: 16:06:30 (hh:mm:ss) Elapsed Time, 623462 HSPs Collected Number of families returned by RECON: 45134 Round Time: 17:23:36 (hh:mm:ss) Elapsed Time : 280 families discovered. RepeatScout/RECON discovery complete: 461 families found Classification Time: 00:34:15 (hh:mm:ss) Elapsed Time Program Time: 22:02:11 (hh:mm:ss) Elapsed Time