RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.4Ixgbw/RM_3092881.MonMar251310552024 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: 1711397455 Database = /dev/shm/rModeler.4Ixgbw/GCA_947650265.1_fSymMel2.1 - Sequences = 395 - Bases = 636368453 - N50 = 27804104 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 53160956-56958096 | [ 1 ] 49363816-53160955 | [ ] 45566676-49363815 | [ ] 41769537-45566676 | [ ] 37972397-41769536 | [ ] 34175257-37972396 | [ ] 30378117-34175256 | [ 3 ] 26580978-30378117 | [ 6 ] 22783838-26580977 |* [ 8 ] 18986698-22783837 | [ 4 ] 15189558-18986697 | [ ] 11392419-15189558 | [ 1 ] 7595279-11392418 | [ ] 3798139-7595278 | [ ] 1000-3798139 |************************************************** [ 372 ] Storage Throughput = good ( 976.52 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40031952 bp ( 40013698 non ambiguous ) - Num Contigs Represented = 51 - Sequence extraction : 00:00:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:32 (hh:mm:ss) Elapsed Time Round Time: 00:31:22 (hh:mm:ss) Elapsed Time : 294 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:37 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 4622 repeats masked totaling 793179 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10043372 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10038118 bp After Masking: 8580564 bp Masked: 14.52 % -- Input Database Coverage: 10043372 bp out of 636368453 bp ( 1.58 % ) Sampling Time: 00:01:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:06:36 (hh:mm:ss) Elapsed Time, 9983 HSPs Collected Number of families returned by RECON: 1190 Round Time: 00:08:52 (hh:mm:ss) Elapsed Time : 14 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:12:23 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15109 repeats masked totaling 2905154 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30028446 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 30015446 bp After Masking: 24988353 bp Masked: 16.75 % -- Input Database Coverage: 40071818 bp out of 636368453 bp ( 6.30 % ) Sampling Time: 00:13:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:33:08 (hh:mm:ss) Elapsed Time, 54626 HSPs Collected Number of families returned by RECON: 4465 Round Time: 00:48:12 (hh:mm:ss) Elapsed Time : 100 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:25:47 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 56137 repeats masked totaling 9935889 bp(s). - TE Masking time 00:01:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90067344 bp Num Contigs Represented = 92 Non ambiguous bp: Initial: 90026753 bp After Masking: 73235552 bp Masked: 18.65 % -- Input Database Coverage: 130139162 bp out of 636368453 bp ( 20.45 % ) Sampling Time: 00:28:40 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2609470 Comparison Time: 03:36:10 (hh:mm:ss) Elapsed Time, 212827 HSPs Collected Number of families returned by RECON: 16832 Round Time: 04:13:47 (hh:mm:ss) Elapsed Time : 378 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:28 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 02:06:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 221400 repeats masked totaling 40420428 bp(s). - TE Masking time 00:07:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270117305 bp Num Contigs Represented = 206 Non ambiguous bp: Initial: 270002959 bp After Masking: 208312507 bp Masked: 22.85 % -- Input Database Coverage: 400256467 bp out of 636368453 bp ( 62.90 % ) Sampling Time: 02:17:17 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23471526 Comparison Time: 26:26:33 (hh:mm:ss) Elapsed Time, 931889 HSPs Collected Number of families returned by RECON: 67466 Round Time: 30:05:32 (hh:mm:ss) Elapsed Time : 969 families discovered. RepeatScout/RECON discovery complete: 1755 families found Classification Time: 01:37:14 (hh:mm:ss) Elapsed Time Program Time: 37:24:59 (hh:mm:ss) Elapsed Time