RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.F6OMTm/RM_3708563.FriFeb142046172025 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: 1739594775 Database = /dev/shm/rModeler.F6OMTm/GCA_905221635.1_Slin_CCMP2456 - Sequences = 37772 - Bases = 694902460 - N50 = 58086 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 430017-460662 | [ 1 ] 399373-430017 | [ 2 ] 368729-399373 | [ 3 ] 338085-368729 | [ 8 ] 307441-338085 | [ 10 ] 276797-307441 | [ 16 ] 246153-276797 | [ 34 ] 215508-246152 | [ 47 ] 184864-215508 | [ 97 ] 154220-184864 | [ 170 ] 123576-154220 | [ 354 ] 92932-123576 |* [ 749 ] 62288-92932 |** [ 1571 ] 31644-62288 |***** [ 3619 ] 1000-31644 |************************************************* [ 31091 ] Storage Throughput = excellent ( 1845.41 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40567399 bp ( 40017586 non ambiguous ) - Num Contigs Represented = 2646 - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:13 (hh:mm:ss) Elapsed Time Round Time: 00:07:10 (hh:mm:ss) Elapsed Time : 134 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:20 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10148 repeats masked totaling 930240 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10140150 bp Num Contigs Represented = 654 Non ambiguous bp: Initial: 10002683 bp After Masking: 8247772 bp Masked: 17.54 % -- Input Database Coverage: 10140150 bp out of 694902460 bp ( 1.46 % ) Sampling Time: 00:00:24 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 214840 Comparison Time: 00:04:21 (hh:mm:ss) Elapsed Time, 43155 HSPs Collected Number of families returned by RECON: 1937 Round Time: 00:05:28 (hh:mm:ss) Elapsed Time : 23 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:03 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 40320 repeats masked totaling 4098707 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30427180 bp Num Contigs Represented = 2011 Non ambiguous bp: Initial: 30014834 bp After Masking: 23482686 bp Masked: 21.76 % -- Input Database Coverage: 40567330 bp out of 694902460 bp ( 5.84 % ) Sampling Time: 00:01:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2067561 Comparison Time: 00:16:21 (hh:mm:ss) Elapsed Time, 27362 HSPs Collected Number of families returned by RECON: 5443 Round Time: 00:18:00 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 122973 repeats masked totaling 12666402 bp(s). - TE Masking time 00:00:30 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91226661 bp Num Contigs Represented = 5669 Non ambiguous bp: Initial: 90007126 bp After Masking: 70297875 bp Masked: 21.90 % -- Input Database Coverage: 131793991 bp out of 694902460 bp ( 18.97 % ) Sampling Time: 00:03:38 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 17520240 Comparison Time: 01:25:46 (hh:mm:ss) Elapsed Time, 173623 HSPs Collected Number of families returned by RECON: 23564 Round Time: 01:34:38 (hh:mm:ss) Elapsed Time : 181 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:11 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 418345 repeats masked totaling 44243382 bp(s). - TE Masking time 00:02:20 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273704388 bp Num Contigs Represented = 16779 Non ambiguous bp: Initial: 270014427 bp After Masking: 204569597 bp Masked: 24.24 % -- Input Database Coverage: 405498379 bp out of 694902460 bp ( 58.35 % ) Sampling Time: 00:11:45 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 172728991 Comparison Time: 09:30:20 (hh:mm:ss) Elapsed Time, 878751 HSPs Collected Number of families returned by RECON: 94373 Round Time: 10:50:22 (hh:mm:ss) Elapsed Time : 689 families discovered. RepeatScout/RECON discovery complete: 1056 families found Classification Time: 00:26:38 (hh:mm:ss) Elapsed Time Program Time: 13:22:16 (hh:mm:ss) Elapsed Time