RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.FIHvJF/RM_121524.WedJan112006132023 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: 1673496372 Database = /dev/shm/rModeler.FIHvJF/GCA_013368605.1_bNycGra1.pri - Sequences = 191 - Bases = 1256414880 - N50 = 99981954 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 124846559-133763977 | [ 2 ] 115929142-124846559 | [ ] 107011724-115929141 | [ 1 ] 98094307-107011724 | [ 2 ] 89176890-98094307 | [ 1 ] 80259472-89176889 | [ 1 ] 71342055-80259472 | [ ] 62424637-71342054 | [ ] 53507220-62424637 | [ 1 ] 44589803-53507220 | [ 1 ] 35672385-44589802 | [ 1 ] 26754968-35672385 | [ 3 ] 17837550-26754967 | [ 2 ] 8920133-17837550 |** [ 9 ] 2716-8920133 |************************************************** [ 167 ] Storage Throughput = good ( 987.63 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40244740 bp ( 40026320 non ambiguous ) - Num Contigs Represented = 46 - Sequence extraction : 00:02:19 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:34 (hh:mm:ss) Elapsed Time Round Time: 00:28:21 (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 : 00:00:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1814 repeats masked totaling 1010416 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10064273 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 10024073 bp After Masking: 8938990 bp Masked: 10.82 % -- Input Database Coverage: 10064273 bp out of 1256414880 bp ( 0.80 % ) Sampling Time: 00:01:09 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:07:37 (hh:mm:ss) Elapsed Time, 418 HSPs Collected Number of families returned by RECON: 217 Round Time: 00:08:48 (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 : 00:01:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:15 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5508 repeats masked totaling 3150708 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30180387 bp Num Contigs Represented = 45 Non ambiguous bp: Initial: 30002167 bp After Masking: 26613386 bp Masked: 11.30 % -- Input Database Coverage: 40244660 bp out of 1256414880 bp ( 3.20 % ) Sampling Time: 00:03:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:39:03 (hh:mm:ss) Elapsed Time, 5966 HSPs Collected Number of families returned by RECON: 1504 Round Time: 00:42:44 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 18607 repeats masked totaling 10429476 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90404910 bp Num Contigs Represented = 60 Non ambiguous bp: Initial: 90021408 bp After Masking: 78995548 bp Masked: 12.25 % -- Input Database Coverage: 130649570 bp out of 1256414880 bp ( 10.40 % ) Sampling Time: 00:08:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 04:15:11 (hh:mm:ss) Elapsed Time, 36946 HSPs Collected Number of families returned by RECON: 8103 Round Time: 04:25:36 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:10:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 69937 repeats masked totaling 35650687 bp(s). - TE Masking time 00:02:52 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271452404 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 270010019 bp After Masking: 232557067 bp Masked: 13.87 % -- Input Database Coverage: 402101974 bp out of 1256414880 bp ( 32.00 % ) Sampling Time: 00:25:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23184645 Comparison Time: 30:18:47 (hh:mm:ss) Elapsed Time, 182610 HSPs Collected Number of families returned by RECON: 51511 Round Time: 31:31:07 (hh:mm:ss) Elapsed Time : 245 families discovered. RepeatScout/RECON discovery complete: 382 families found Classification Time: 00:28:46 (hh:mm:ss) Elapsed Time Program Time: 37:45:22 (hh:mm:ss) Elapsed Time