RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.9j6alC/RM_411424.FriJan61808102023 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: 1673057290 Database = /dev/shm/rModeler.9j6alC/GCA_009769605.1_bBucAby1.pri - Sequences = 112 - Bases = 1132597561 - N50 = 41247383 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 127355723-136452362 | [ 1 ] 118259085-127355723 | [ ] 109162447-118259085 | [ ] 100065809-109162447 | [ ] 90969171-100065809 | [ ] 81872533-90969171 | [ 1 ] 72775895-81872533 | [ 1 ] 63679256-72775894 | [ ] 54582618-63679256 | [ 1 ] 45485980-54582618 | [ 1 ] 36389342-45485980 |*** [ 5 ] 27292704-36389342 |* [ 2 ] 18196066-27292704 |***** [ 9 ] 9099428-18196066 |********* [ 14 ] 2790-9099428 |************************************************** [ 77 ] Storage Throughput = excellent ( 1268.97 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40525359 bp ( 40027730 non ambiguous ) - Num Contigs Represented = 44 - Sequence extraction : 00:00:47 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:12:13 (hh:mm:ss) Elapsed Time Round Time: 00:14:39 (hh:mm:ss) Elapsed Time : 81 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1650 repeats masked totaling 632117 bp(s). - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10202276 bp Num Contigs Represented = 38 Non ambiguous bp: Initial: 10029209 bp After Masking: 9351958 bp Masked: 6.75 % -- Input Database Coverage: 10202276 bp out of 1132597561 bp ( 0.90 % ) Sampling Time: 00:00:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:14 (hh:mm:ss) Elapsed Time, 584 HSPs Collected Number of families returned by RECON: 240 Round Time: 00:06:46 (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 : 00:00:48 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5026 repeats masked totaling 1850823 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30363020 bp Num Contigs Represented = 44 Non ambiguous bp: Initial: 30038458 bp After Masking: 28024270 bp Masked: 6.71 % -- Input Database Coverage: 40565296 bp out of 1132597561 bp ( 3.58 % ) Sampling Time: 00:01:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:27:05 (hh:mm:ss) Elapsed Time, 4855 HSPs Collected Number of families returned by RECON: 1412 Round Time: 00:29:08 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15726 repeats masked totaling 5738620 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90580205 bp Num Contigs Represented = 58 Non ambiguous bp: Initial: 90033721 bp After Masking: 83833445 bp Masked: 6.89 % -- Input Database Coverage: 131145501 bp out of 1132597561 bp ( 11.58 % ) Sampling Time: 00:04:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2575315 Comparison Time: 02:30:48 (hh:mm:ss) Elapsed Time, 36875 HSPs Collected Number of families returned by RECON: 8944 Round Time: 02:36:38 (hh:mm:ss) Elapsed Time : 71 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:05:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56829 repeats masked totaling 19343379 bp(s). - TE Masking time 00:00:58 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271878510 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 270009552 bp After Masking: 249536211 bp Masked: 7.58 % -- Input Database Coverage: 403024011 bp out of 1132597561 bp ( 35.58 % ) Sampling Time: 00:12:12 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23198266 Comparison Time: 18:11:20 (hh:mm:ss) Elapsed Time, 141640 HSPs Collected Number of families returned by RECON: 57540 Round Time: 18:45:48 (hh:mm:ss) Elapsed Time : 159 families discovered. RepeatScout/RECON discovery complete: 322 families found Classification Time: 00:12:10 (hh:mm:ss) Elapsed Time Program Time: 22:25:09 (hh:mm:ss) Elapsed Time