RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.LmvMp0/RM_2552789.WedJan100917352024 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: 1704907053 Database = /dev/shm/rModeler.LmvMp0/GCA_002915635.3_AmbMex60DD - Sequences = 9053 - Bases = 10002547957 - N50 = 1382406544 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1518548906-1627016608 | [ 1 ] 1410081204-1518548905 | [ 1 ] 1301613503-1410081204 | [ 1 ] 1193145801-1301613502 | [ 1 ] 1084678100-1193145801 | [ ] 976210398-1084678099 | [ 1 ] 867742697-976210398 | [ 1 ] 759274995-867742696 | [ 1 ] 650807294-759274995 | [ ] 542339592-650807293 | [ ] 433871891-542339592 | [ 1 ] 325404189-433871890 | [ ] 216936488-325404189 | [ 1 ] 108468786-216936487 | [ 1 ] 1085-108468786 |************************************************* [ 9043 ] Storage Throughput = excellent ( 1173.47 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40035736 bp ( 40030496 non ambiguous ) - Num Contigs Represented = 84 - Sequence extraction : 00:20:52 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:08:35 (hh:mm:ss) Elapsed Time Round Time: 00:40:20 (hh:mm:ss) Elapsed Time : 832 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:05:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11482 repeats masked totaling 4882203 bp(s). - TE Masking time 00:00:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10022866 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10021546 bp After Masking: 4770870 bp Masked: 52.39 % -- Input Database Coverage: 10022866 bp out of 10002547957 bp ( 0.10 % ) Sampling Time: 00:06:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32640 Comparison Time: 00:05:19 (hh:mm:ss) Elapsed Time, 7774 HSPs Collected Number of families returned by RECON: 1400 Round Time: 00:12:09 (hh:mm:ss) Elapsed Time : 7 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:15:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 33987 repeats masked totaling 14723580 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30012790 bp Num Contigs Represented = 61 Non ambiguous bp: Initial: 30008870 bp After Masking: 14082899 bp Masked: 53.07 % -- Input Database Coverage: 40035656 bp out of 10002547957 bp ( 0.40 % ) Sampling Time: 00:17:49 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 292995 Comparison Time: 00:22:37 (hh:mm:ss) Elapsed Time, 61341 HSPs Collected Number of families returned by RECON: 4485 Round Time: 00:42:00 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:47:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 108634 repeats masked totaling 47923155 bp(s). - TE Masking time 00:02:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90014557 bp Num Contigs Represented = 141 Non ambiguous bp: Initial: 90002397 bp After Masking: 38975504 bp Masked: 56.70 % -- Input Database Coverage: 130050213 bp out of 10002547957 bp ( 1.30 % ) Sampling Time: 00:54:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2620905 Comparison Time: 01:58:38 (hh:mm:ss) Elapsed Time, 345994 HSPs Collected Number of families returned by RECON: 12838 Round Time: 03:02:15 (hh:mm:ss) Elapsed Time : 430 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 02:19:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:13:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 379656 repeats masked totaling 165601925 bp(s). - TE Masking time 00:10:59 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270063660 bp Num Contigs Represented = 460 Non ambiguous bp: Initial: 270028702 bp After Masking: 94848509 bp Masked: 64.87 % -- Input Database Coverage: 400113873 bp out of 10002547957 bp ( 4.00 % ) Sampling Time: 02:44:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23650003 Comparison Time: 10:33:18 (hh:mm:ss) Elapsed Time, 1122112 HSPs Collected Number of families returned by RECON: 33357 Round Time: 14:10:56 (hh:mm:ss) Elapsed Time : 1155 families discovered. RepeatScout/RECON discovery complete: 2517 families found Classification Time: 02:05:10 (hh:mm:ss) Elapsed Time Program Time: 20:52:50 (hh:mm:ss) Elapsed Time