RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.1BXAgw/RM_3447923.SatApr120158552025 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: 1744448333 Database = /dev/shm/rModeler.1BXAgw/GCA_964339955.1_mPipHan1.1 - Sequences = 141 - Bases = 1892221984 - N50 = 102958539 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 196725041-210776044 | [ 2 ] 182674038-196725040 | [ 1 ] 168623035-182674037 | [ ] 154572032-168623034 | [ ] 140521029-154572031 | [ ] 126470026-140521028 | [ ] 112419023-126470025 | [ ] 98368020-112419022 |* [ 3 ] 84317017-98368019 |* [ 3 ] 70266014-84317016 |* [ 4 ] 56215011-70266013 | [ 1 ] 42164008-56215010 |* [ 4 ] 28113005-42164007 | [ 1 ] 14062002-28113004 | [ 2 ] 11000-14062002 |************************************************** [ 120 ] Storage Throughput = excellent ( 1821.00 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40014439 bp ( 40013739 non ambiguous ) - Num Contigs Represented = 37 - Sequence extraction : 00:01:08 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:07:07 (hh:mm:ss) Elapsed Time Round Time: 00:13:02 (hh:mm:ss) Elapsed Time : 319 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:17 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14016 repeats masked totaling 2360587 bp(s). - TE Masking time 00:00:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000973 bp Num Contigs Represented = 26 Non ambiguous bp: Initial: 10000873 bp After Masking: 7247795 bp Masked: 27.53 % -- Input Database Coverage: 10000973 bp out of 1892221984 bp ( 0.53 % ) Sampling Time: 00:00:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:03:04 (hh:mm:ss) Elapsed Time, 8689 HSPs Collected Number of families returned by RECON: 827 Round Time: 00:03:47 (hh:mm:ss) Elapsed Time : 16 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 42519 repeats masked totaling 7193895 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30013386 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 30012786 bp After Masking: 20748457 bp Masked: 30.87 % -- Input Database Coverage: 40014359 bp out of 1892221984 bp ( 2.11 % ) Sampling Time: 00:01:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 281625 Comparison Time: 00:13:30 (hh:mm:ss) Elapsed Time, 78453 HSPs Collected Number of families returned by RECON: 2329 Round Time: 00:15:44 (hh:mm:ss) Elapsed Time : 59 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:02:35 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:39 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 135210 repeats masked totaling 22839407 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90034739 bp Num Contigs Represented = 54 Non ambiguous bp: Initial: 90032339 bp After Masking: 60958754 bp Masked: 32.29 % -- Input Database Coverage: 130049098 bp out of 1892221984 bp ( 6.87 % ) Sampling Time: 00:05:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2536878 Comparison Time: 01:13:16 (hh:mm:ss) Elapsed Time, 175254 HSPs Collected Number of families returned by RECON: 8907 Round Time: 01:21:11 (hh:mm:ss) Elapsed Time : 202 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:07:43 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 461500 repeats masked totaling 78243097 bp(s). - TE Masking time 00:02:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270021547 bp Num Contigs Represented = 76 Non ambiguous bp: Initial: 270016247 bp After Masking: 173943289 bp Masked: 35.58 % -- Input Database Coverage: 400070645 bp out of 1892221984 bp ( 21.14 % ) Sampling Time: 00:17:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22858941 Comparison Time: 08:32:39 (hh:mm:ss) Elapsed Time, 622887 HSPs Collected Number of families returned by RECON: 35704 Round Time: 09:01:02 (hh:mm:ss) Elapsed Time : 462 families discovered. RepeatScout/RECON discovery complete: 1058 families found Classification Time: 00:17:06 (hh:mm:ss) Elapsed Time Program Time: 11:11:52 (hh:mm:ss) Elapsed Time