RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.uSsgFL/RM_98647.SunMar300216122025 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: 1743326172 Database = /dev/shm/rModeler.uSsgFL/GCA_048565335.1_aManAur1.hap2 - Sequences = 2611 - Bases = 3319283846 - N50 = 378957233 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 465775839-499045298 | [ 1 ] 432506380-465775838 | [ ] 399236921-432506379 | [ 1 ] 365967462-399236920 | [ 2 ] 332698003-365967461 | [ ] 299428544-332698002 | [ 1 ] 266159085-299428543 | [ ] 232889626-266159084 | [ ] 199620167-232889625 | [ ] 166350708-199620166 | [ 3 ] 133081249-166350707 | [ 2 ] 99811790-133081248 | [ 3 ] 66542331-99811789 | [ ] 33272872-66542330 | [ ] 3414-33272872 |************************************************** [ 2598 ] Storage Throughput = excellent ( 1769.33 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40019619 bp ( 40009019 non ambiguous ) - Num Contigs Represented = 76 - Sequence extraction : 00:03:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:09:26 (hh:mm:ss) Elapsed Time Round Time: 00:16:37 (hh:mm:ss) Elapsed Time : 738 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 19341 repeats masked totaling 4144747 bp(s). - TE Masking time 00:00:05 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028653 bp Num Contigs Represented = 32 Non ambiguous bp: Initial: 10025453 bp After Masking: 4435838 bp Masked: 55.75 % -- Input Database Coverage: 10028653 bp out of 3319283846 bp ( 0.30 % ) Sampling Time: 00:03:13 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 32385 Comparison Time: 00:03:01 (hh:mm:ss) Elapsed Time, 20386 HSPs Collected Number of families returned by RECON: 1342 Round Time: 00:06:39 (hh:mm:ss) Elapsed Time : 25 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:18 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:19 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 62077 repeats masked totaling 12794089 bp(s). - TE Masking time 00:00:15 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30030965 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 30023565 bp After Masking: 12830278 bp Masked: 57.27 % -- Input Database Coverage: 40059618 bp out of 3319283846 bp ( 1.21 % ) Sampling Time: 00:07:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 286903 Comparison Time: 00:11:27 (hh:mm:ss) Elapsed Time, 48747 HSPs Collected Number of families returned by RECON: 4665 Round Time: 00:20:03 (hh:mm:ss) Elapsed Time : 128 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 199307 repeats masked totaling 40495759 bp(s). - TE Masking time 00:00:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032764 bp Num Contigs Represented = 165 Non ambiguous bp: Initial: 90009364 bp After Masking: 37136834 bp Masked: 58.74 % -- Input Database Coverage: 130092382 bp out of 3319283846 bp ( 3.92 % ) Sampling Time: 00:23:31 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2618616 Comparison Time: 00:56:17 (hh:mm:ss) Elapsed Time, 307767 HSPs Collected Number of families returned by RECON: 12058 Round Time: 01:24:14 (hh:mm:ss) Elapsed Time : 536 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:20:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:45:16 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 681950 repeats masked totaling 138482773 bp(s). - TE Masking time 00:03:55 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270059004 bp Num Contigs Represented = 429 Non ambiguous bp: Initial: 270002033 bp After Masking: 95663819 bp Masked: 64.57 % -- Input Database Coverage: 400151386 bp out of 3319283846 bp ( 12.06 % ) Sampling Time: 01:09:53 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23396220 Comparison Time: 05:23:31 (hh:mm:ss) Elapsed Time, 1217987 HSPs Collected Number of families returned by RECON: 31214 Round Time: 06:52:17 (hh:mm:ss) Elapsed Time : 1295 families discovered. RepeatScout/RECON discovery complete: 2722 families found Classification Time: 00:47:01 (hh:mm:ss) Elapsed Time Program Time: 09:46:51 (hh:mm:ss) Elapsed Time