RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.2J3LPQ/RM_3536094.MonJun241444042024 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: 1719265443 Database = /dev/shm/rModeler.2J3LPQ/GCF_963854185.1_fSarPil1.1 - Sequences = 240 - Bases = 869396467 - N50 = 34697421 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 48585582-52055910 | [ 1 ] 45115255-48585582 | [ 1 ] 41644928-45115255 | [ ] 38174600-41644927 | [ 2 ] 34704273-38174600 |* [ 6 ] 31233946-34704273 |** [ 11 ] 27763618-31233945 | [ 3 ] 24293291-27763618 | [ ] 20822964-24293291 | [ ] 17352636-20822963 | [ ] 13882309-17352636 | [ ] 10411982-13882309 | [ ] 6941654-10411981 | [ ] 3471327-6941654 | [ ] 1000-3471327 |************************************************** [ 216 ] Storage Throughput = excellent ( 1112.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40027887 bp ( 40013487 non ambiguous ) - Num Contigs Represented = 40 - Sequence extraction : 00:00:38 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:18:06 (hh:mm:ss) Elapsed Time Round Time: 00:35:07 (hh:mm:ss) Elapsed Time : 535 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:12 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 6431 repeats masked totaling 1261921 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10011496 bp Num Contigs Represented = 28 Non ambiguous bp: Initial: 10007696 bp After Masking: 7498265 bp Masked: 25.08 % -- Input Database Coverage: 10011496 bp out of 869396467 bp ( 1.15 % ) Sampling Time: 00:02:42 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:25 (hh:mm:ss) Elapsed Time, 10052 HSPs Collected Number of families returned by RECON: 1209 Round Time: 00:09:23 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:07 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 22096 repeats masked totaling 4496883 bp(s). - TE Masking time 00:00:44 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016383 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 30005783 bp After Masking: 22102674 bp Masked: 26.34 % -- Input Database Coverage: 40027879 bp out of 869396467 bp ( 4.60 % ) Sampling Time: 00:07:28 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:31:26 (hh:mm:ss) Elapsed Time, 42485 HSPs Collected Number of families returned by RECON: 4864 Round Time: 00:40:04 (hh:mm:ss) Elapsed Time : 82 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 72755 repeats masked totaling 14387616 bp(s). - TE Masking time 00:02:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90072253 bp Num Contigs Represented = 77 Non ambiguous bp: Initial: 90035053 bp After Masking: 65194274 bp Masked: 27.59 % -- Input Database Coverage: 130100132 bp out of 869396467 bp ( 14.96 % ) Sampling Time: 00:23:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2579856 Comparison Time: 03:28:44 (hh:mm:ss) Elapsed Time, 344279 HSPs Collected Number of families returned by RECON: 17413 Round Time: 04:18:59 (hh:mm:ss) Elapsed Time : 535 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:04:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:55:49 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 284993 repeats masked totaling 58938253 bp(s). - TE Masking time 00:14:27 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270129525 bp Num Contigs Represented = 133 Non ambiguous bp: Initial: 270030125 bp After Masking: 178437645 bp Masked: 33.92 % -- Input Database Coverage: 400229657 bp out of 869396467 bp ( 46.04 % ) Sampling Time: 01:14:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23007936 Comparison Time: 25:39:25 (hh:mm:ss) Elapsed Time, 1098542 HSPs Collected Number of families returned by RECON: 59724 Round Time: 28:19:40 (hh:mm:ss) Elapsed Time : 1202 families discovered. RepeatScout/RECON discovery complete: 2359 families found Classification Time: 02:00:00 (hh:mm:ss) Elapsed Time Program Time: 36:03:13 (hh:mm:ss) Elapsed Time