RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.WyTphT/RM_2814529.ThuMar281754092024 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: 1711673649 Database = /dev/shm/rModeler.WyTphT/GCA_963924245.1_bChrRid1.1 - Sequences = 729 - Bases = 1417571123 - N50 = 95717064 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 206184293-220911672 | [ 1 ] 191456915-206184293 | [ ] 176729537-191456915 | [ ] 162002159-176729537 | [ 1 ] 147274781-162002159 | [ ] 132547403-147274781 | [ ] 117820025-132547403 | [ 1 ] 103092646-117820024 | [ ] 88365268-103092646 | [ 1 ] 73637890-88365268 | [ 3 ] 58910512-73637890 | [ 1 ] 44183134-58910512 | [ 2 ] 29455756-44183134 | [ ] 14728378-29455756 | [ 5 ] 1000-14728378 |************************************************** [ 714 ] Storage Throughput = excellent ( 1317.73 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40009658 bp ( 40007258 non ambiguous ) - Num Contigs Represented = 125 - Sequence extraction : 00:01:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:20:04 (hh:mm:ss) Elapsed Time Round Time: 00:26:13 (hh:mm:ss) Elapsed Time : 56 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 00:00:31 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3690 repeats masked totaling 1060891 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10001984 bp Num Contigs Represented = 52 Non ambiguous bp: Initial: 10000984 bp After Masking: 8068035 bp Masked: 19.33 % -- Input Database Coverage: 10001984 bp out of 1417571123 bp ( 0.71 % ) Sampling Time: 00:01:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:09 (hh:mm:ss) Elapsed Time, 574 HSPs Collected Number of families returned by RECON: 152 Round Time: 00:07:24 (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 : 00:01:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12846 repeats masked totaling 3423929 bp(s). - TE Masking time 00:00:13 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30007594 bp Num Contigs Represented = 109 Non ambiguous bp: Initial: 30006194 bp After Masking: 23882040 bp Masked: 20.41 % -- Input Database Coverage: 40009578 bp out of 1417571123 bp ( 2.82 % ) Sampling Time: 00:03:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286146 Comparison Time: 00:30:38 (hh:mm:ss) Elapsed Time, 8451 HSPs Collected Number of families returned by RECON: 1105 Round Time: 00:34:18 (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 : 00:04:54 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:59 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36037 repeats masked totaling 9744063 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90012673 bp Num Contigs Represented = 228 Non ambiguous bp: Initial: 90006273 bp After Masking: 72119246 bp Masked: 19.87 % -- Input Database Coverage: 130022251 bp out of 1417571123 bp ( 9.17 % ) Sampling Time: 00:10:34 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2584401 Comparison Time: 03:16:41 (hh:mm:ss) Elapsed Time, 60944 HSPs Collected Number of families returned by RECON: 6667 Round Time: 03:29:07 (hh:mm:ss) Elapsed Time : 67 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:12:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 127883 repeats masked totaling 32847898 bp(s). - TE Masking time 00:02:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044919 bp Num Contigs Represented = 398 Non ambiguous bp: Initial: 270025919 bp After Masking: 211359342 bp Masked: 21.73 % -- Input Database Coverage: 400067170 bp out of 1417571123 bp ( 28.22 % ) Sampling Time: 00:31:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23314206 Comparison Time: 26:52:34 (hh:mm:ss) Elapsed Time, 145779 HSPs Collected Number of families returned by RECON: 39993 Round Time: 27:54:25 (hh:mm:ss) Elapsed Time : 177 families discovered. RepeatScout/RECON discovery complete: 314 families found Classification Time: 00:30:41 (hh:mm:ss) Elapsed Time Program Time: 33:02:08 (hh:mm:ss) Elapsed Time