RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.IRy3Ql/RM_2409759.SatMay272053202023 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: 1685246000 Database = /dev/shm/rModeler.IRy3Ql/GCF_023864275.1_iqSchCanc2.1 - Sequences = 1108 - Bases = 8536893415 - N50 = 963605626 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1202924151-1288847234 | [ 1 ] 1117001069-1202924151 | [ 1 ] 1031077987-1117001069 | [ ] 945154904-1031077986 | [ 1 ] 859231822-945154904 | [ 1 ] 773308740-859231822 | [ 1 ] 687385658-773308740 | [ 1 ] 601462575-687385657 | [ 2 ] 515539493-601462575 | [ 1 ] 429616411-515539493 | [ ] 343693329-429616411 | [ ] 257770246-343693328 | [ ] 171847164-257770246 | [ 2 ] 85924082-171847164 | [ 1 ] 1000-85924082 |************************************************* [ 1096 ] Storage Throughput = good ( 778.93 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40030723 bp ( 40029223 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:17:42 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:14 (hh:mm:ss) Elapsed Time Round Time: 00:37:57 (hh:mm:ss) Elapsed Time : 793 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:03:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14710 repeats masked totaling 5113253 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10039620 bp Num Contigs Represented = 19 Non ambiguous bp: Initial: 10039620 bp After Masking: 4556506 bp Masked: 54.61 % -- Input Database Coverage: 10039620 bp out of 8536893415 bp ( 0.12 % ) Sampling Time: 00:04:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:58 (hh:mm:ss) Elapsed Time, 13345 HSPs Collected Number of families returned by RECON: 1474 Round Time: 00:10:53 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:11:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43846 repeats masked totaling 15287245 bp(s). - TE Masking time 00:00:43 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30031023 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 30029523 bp After Masking: 13466621 bp Masked: 55.16 % -- Input Database Coverage: 40070643 bp out of 8536893415 bp ( 0.47 % ) Sampling Time: 00:13:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:24:45 (hh:mm:ss) Elapsed Time, 57985 HSPs Collected Number of families returned by RECON: 4954 Round Time: 00:39:41 (hh:mm:ss) Elapsed Time : 116 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:34:31 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:13 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 143315 repeats masked totaling 48971362 bp(s). - TE Masking time 00:02:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90029146 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 90028146 bp After Masking: 37229334 bp Masked: 58.65 % -- Input Database Coverage: 130099789 bp out of 8536893415 bp ( 1.52 % ) Sampling Time: 00:40:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 02:02:43 (hh:mm:ss) Elapsed Time, 316774 HSPs Collected Number of families returned by RECON: 13625 Round Time: 02:54:12 (hh:mm:ss) Elapsed Time : 640 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:43:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 497661 repeats masked totaling 166913603 bp(s). - TE Masking time 00:12:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270012716 bp Num Contigs Represented = 121 Non ambiguous bp: Initial: 270007716 bp After Masking: 92601720 bp Masked: 65.70 % -- Input Database Coverage: 400112505 bp out of 8536893415 bp ( 4.69 % ) Sampling Time: 02:05:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22885995 Comparison Time: 11:21:45 (hh:mm:ss) Elapsed Time, 927485 HSPs Collected Number of families returned by RECON: 30951 Round Time: 14:19:30 (hh:mm:ss) Elapsed Time : 1787 families discovered. RepeatScout/RECON discovery complete: 3354 families found Classification Time: 02:38:49 (hh:mm:ss) Elapsed Time Program Time: 21:21:02 (hh:mm:ss) Elapsed Time