RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.KdJtn5/RM_4054861.TueApr222310572025 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: 1745388657 Database = /dev/shm/rModeler.KdJtn5/GCA_964195595.2_bCalBor7.hap1.2 - Sequences = 355 - Bases = 1366205003 - N50 = 87715099 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206368189-221108703 | [ 1 ] 191627675-206368188 | [ ] 176887162-191627675 | [ ] 162146648-176887161 | [ 1 ] 147406135-162146648 | [ ] 132665621-147406134 | [ ] 117925108-132665621 | [ 1 ] 103184594-117925107 | [ ] 88444081-103184594 | [ ] 73703567-88444080 | [ 2 ] 58963054-73703567 | [ ] 44222540-58963053 | [ 4 ] 29482027-44222540 | [ 2 ] 14741513-29482026 |* [ 11 ] 1000-14741513 |************************************************** [ 333 ] Storage Throughput = excellent ( 1673.89 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40038531 bp ( 40035931 non ambiguous ) - Num Contigs Represented = 78 - Sequence extraction : 00:00:57 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:59 (hh:mm:ss) Elapsed Time Round Time: 00:16:54 (hh:mm:ss) Elapsed Time : 93 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 2525 repeats masked totaling 1037849 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10034329 bp Num Contigs Represented = 49 Non ambiguous bp: Initial: 10033729 bp After Masking: 8536753 bp Masked: 14.92 % -- Input Database Coverage: 10034329 bp out of 1366205003 bp ( 0.73 % ) Sampling Time: 00:00:57 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:02:58 (hh:mm:ss) Elapsed Time, 1217 HSPs Collected Number of families returned by RECON: 279 Round Time: 00:03:56 (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 : 00:00:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5221 repeats masked totaling 2753134 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30004200 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30002200 bp After Masking: 26074748 bp Masked: 13.09 % -- Input Database Coverage: 40038529 bp out of 1366205003 bp ( 2.93 % ) Sampling Time: 00:02:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:14:03 (hh:mm:ss) Elapsed Time, 6474 HSPs Collected Number of families returned by RECON: 1386 Round Time: 00:16:41 (hh:mm:ss) Elapsed Time : 18 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19048 repeats masked totaling 8857898 bp(s). - TE Masking time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90044156 bp Num Contigs Represented = 128 Non ambiguous bp: Initial: 90038756 bp After Masking: 77547991 bp Masked: 13.87 % -- Input Database Coverage: 130082685 bp out of 1366205003 bp ( 9.52 % ) Sampling Time: 00:07:43 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2561716 Comparison Time: 01:27:38 (hh:mm:ss) Elapsed Time, 53494 HSPs Collected Number of families returned by RECON: 7610 Round Time: 01:36:42 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:06:21 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:21 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 67998 repeats masked totaling 30416195 bp(s). - TE Masking time 00:01:33 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270025380 bp Num Contigs Represented = 196 Non ambiguous bp: Initial: 270002780 bp After Masking: 228421041 bp Masked: 15.40 % -- Input Database Coverage: 400108065 bp out of 1366205003 bp ( 29.29 % ) Sampling Time: 00:23:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23062236 Comparison Time: 10:54:00 (hh:mm:ss) Elapsed Time, 188020 HSPs Collected Number of families returned by RECON: 46713 Round Time: 11:28:27 (hh:mm:ss) Elapsed Time : 243 families discovered. RepeatScout/RECON discovery complete: 424 families found Classification Time: 00:15:36 (hh:mm:ss) Elapsed Time Program Time: 13:58:16 (hh:mm:ss) Elapsed Time