RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.7YXtww/RM_1771044.FriMar220649102024 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: 1711115350 Database = /dev/shm/rModeler.7YXtww/GCA_036417845.1_bAptMan1.hap1 - Sequences = 409 - Bases = 1504415252 - N50 = 88548715 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 208065238-222926480 | [ 1 ] 193203997-208065238 | [ ] 178342756-193203997 | [ ] 163481515-178342756 | [ 1 ] 148620274-163481515 | [ ] 133759033-148620274 | [ 1 ] 118897792-133759033 | [ ] 104036550-118897791 | [ ] 89175309-104036550 | [ 1 ] 74314068-89175309 | [ 2 ] 59452827-74314068 | [ ] 44591586-59452827 | [ 2 ] 29730345-44591586 | [ 3 ] 14869104-29730345 |* [ 13 ] 7863-14869104 |************************************************** [ 385 ] Storage Throughput = excellent ( 1025.54 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40010864 bp ( 40010464 non ambiguous ) - Num Contigs Represented = 93 - Sequence extraction : 00:01:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:19 (hh:mm:ss) Elapsed Time Round Time: 00:36:38 (hh:mm:ss) Elapsed Time : 105 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:32 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1646 repeats masked totaling 974002 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10014642 bp Num Contigs Represented = 43 Non ambiguous bp: Initial: 10014642 bp After Masking: 8723740 bp Masked: 12.89 % -- Input Database Coverage: 10014642 bp out of 1504415252 bp ( 0.67 % ) Sampling Time: 00:01:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32131 Comparison Time: 00:06:27 (hh:mm:ss) Elapsed Time, 1214 HSPs Collected Number of families returned by RECON: 339 Round Time: 00:07:55 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5399 repeats masked totaling 3202242 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30036142 bp Num Contigs Represented = 83 Non ambiguous bp: Initial: 30035742 bp After Masking: 25458954 bp Masked: 15.24 % -- Input Database Coverage: 40050784 bp out of 1504415252 bp ( 2.66 % ) Sampling Time: 00:04:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:33:30 (hh:mm:ss) Elapsed Time, 12244 HSPs Collected Number of families returned by RECON: 1630 Round Time: 00:41:06 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:08:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 21892 repeats masked totaling 11249069 bp(s). - TE Masking time 00:01:24 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90018391 bp Num Contigs Represented = 135 Non ambiguous bp: Initial: 90016591 bp After Masking: 74929069 bp Masked: 16.76 % -- Input Database Coverage: 130069175 bp out of 1504415252 bp ( 8.65 % ) Sampling Time: 00:13:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 03:43:29 (hh:mm:ss) Elapsed Time, 95351 HSPs Collected Number of families returned by RECON: 8076 Round Time: 04:28:22 (hh:mm:ss) Elapsed Time : 110 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:53 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:26:50 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 86305 repeats masked totaling 42602312 bp(s). - TE Masking time 00:08:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270028928 bp Num Contigs Represented = 221 Non ambiguous bp: Initial: 270022728 bp After Masking: 215482776 bp Masked: 20.20 % -- Input Database Coverage: 400098103 bp out of 1504415252 bp ( 26.59 % ) Sampling Time: 00:48:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23055445 Comparison Time: 27:15:24 (hh:mm:ss) Elapsed Time, 312528 HSPs Collected Number of families returned by RECON: 46775 Round Time: 28:36:02 (hh:mm:ss) Elapsed Time : 311 families discovered. RepeatScout/RECON discovery complete: 552 families found Classification Time: 01:11:17 (hh:mm:ss) Elapsed Time Program Time: 35:41:20 (hh:mm:ss) Elapsed Time