RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.41SosP/RM_23721.TueJan100040292023 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: 1673340028 Database = /dev/shm/rModeler.41SosP/GCA_011004875.1_bBalReg1.pri - Sequences = 105 - Bases = 1221051782 - N50 = 126494509 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 204650125-219267915 | [ 1 ] 190032335-204650124 | [ ] 175414545-190032334 | [ ] 160796755-175414544 | [ 1 ] 146178966-160796755 | [ ] 131561176-146178965 | [ ] 116943386-131561175 | [ 1 ] 102325596-116943385 | [ ] 87707806-102325595 | [ ] 73090017-87707806 |* [ 2 ] 58472227-73090016 | [ 1 ] 43854437-58472226 | [ ] 29236647-43854436 |** [ 5 ] 14618857-29236646 |**** [ 8 ] 1068-14618857 |************************************************** [ 86 ] Storage Throughput = excellent ( 1159.79 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40132949 bp ( 40019551 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:02:12 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:21:41 (hh:mm:ss) Elapsed Time Round Time: 00:27:27 (hh:mm:ss) Elapsed Time : 51 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1564 repeats masked totaling 773588 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000748 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10000648 bp After Masking: 9171148 bp Masked: 8.29 % -- Input Database Coverage: 10000748 bp out of 1221051782 bp ( 0.82 % ) Sampling Time: 00:00:56 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:07:07 (hh:mm:ss) Elapsed Time, 488 HSPs Collected Number of families returned by RECON: 250 Round Time: 00:08:05 (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 : 00:01:38 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:48 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4922 repeats masked totaling 2228906 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30132121 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30018823 bp After Masking: 27636153 bp Masked: 7.94 % -- Input Database Coverage: 40132869 bp out of 1221051782 bp ( 3.29 % ) Sampling Time: 00:02:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:39:49 (hh:mm:ss) Elapsed Time, 8280 HSPs Collected Number of families returned by RECON: 1449 Round Time: 00:42:55 (hh:mm:ss) Elapsed Time : 13 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:57 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15827 repeats masked totaling 6401194 bp(s). - TE Masking time 00:00:38 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90496203 bp Num Contigs Represented = 47 Non ambiguous bp: Initial: 90010474 bp After Masking: 83181176 bp Masked: 7.59 % -- Input Database Coverage: 130629072 bp out of 1221051782 bp ( 10.70 % ) Sampling Time: 00:08:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2566245 Comparison Time: 04:55:57 (hh:mm:ss) Elapsed Time, 41049 HSPs Collected Number of families returned by RECON: 9181 Round Time: 05:06:09 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:30 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 60664 repeats masked totaling 23092584 bp(s). - TE Masking time 00:02:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270921715 bp Num Contigs Represented = 63 Non ambiguous bp: Initial: 270030059 bp After Masking: 245416260 bp Masked: 9.12 % -- Input Database Coverage: 401550787 bp out of 1221051782 bp ( 32.89 % ) Sampling Time: 00:24:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23001153 Comparison Time: 39:54:40 (hh:mm:ss) Elapsed Time, 330161 HSPs Collected Number of families returned by RECON: 57449 Round Time: 41:07:06 (hh:mm:ss) Elapsed Time : 203 families discovered. RepeatScout/RECON discovery complete: 321 families found Classification Time: 00:19:30 (hh:mm:ss) Elapsed Time Program Time: 47:51:12 (hh:mm:ss) Elapsed Time