RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.BHCSak/RM_1774.FriMay122258172023 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: 1683957495 Database = /dev/shm/rModeler.BHCSak/GCA_900324485.3_fMasArm1.3 - Sequences = 123 - Bases = 591951591 - N50 = 25822229 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 27182527-29124071 |*** [ 6 ] 25240984-27182527 |** [ 4 ] 23299441-25240984 |** [ 4 ] 21357898-23299441 |* [ 3 ] 19416355-21357898 |** [ 5 ] 17474812-19416355 | [ ] 15533269-17474812 | [ 1 ] 13591725-15533268 | [ ] 11650182-13591725 | [ ] 9708639-11650182 | [ 1 ] 7767096-9708639 | [ ] 5825553-7767096 | [ ] 3884010-5825553 | [ ] 1942467-3884010 |* [ 3 ] 924-1942467 |************************************************** [ 96 ] Storage Throughput = excellent ( 1130.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40979963 bp ( 40007433 non ambiguous ) - Num Contigs Represented = 43 - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:19:42 (hh:mm:ss) Elapsed Time Round Time: 00:24:28 (hh:mm:ss) Elapsed Time : 264 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:09 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3947 repeats masked totaling 1237325 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10398108 bp Num Contigs Represented = 31 Non ambiguous bp: Initial: 10011095 bp After Masking: 8623103 bp Masked: 13.86 % -- Input Database Coverage: 10398108 bp out of 591951591 bp ( 1.76 % ) Sampling Time: 00:00:41 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 33670 Comparison Time: 00:07:06 (hh:mm:ss) Elapsed Time, 5184 HSPs Collected Number of families returned by RECON: 1111 Round Time: 00:08:01 (hh:mm:ss) Elapsed Time : 10 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:58 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 12685 repeats masked totaling 3498300 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30661801 bp Num Contigs Represented = 37 Non ambiguous bp: Initial: 30037975 bp After Masking: 26128685 bp Masked: 13.01 % -- Input Database Coverage: 41059909 bp out of 591951591 bp ( 6.94 % ) Sampling Time: 00:01:50 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 295296 Comparison Time: 00:38:49 (hh:mm:ss) Elapsed Time, 30074 HSPs Collected Number of families returned by RECON: 4381 Round Time: 00:41:48 (hh:mm:ss) Elapsed Time : 54 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:03:14 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 43903 repeats masked totaling 12068778 bp(s). - TE Masking time 00:01:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 92031257 bp Num Contigs Represented = 64 Non ambiguous bp: Initial: 90014207 bp After Masking: 76691158 bp Masked: 14.80 % -- Input Database Coverage: 133091166 bp out of 591951591 bp ( 22.48 % ) Sampling Time: 00:05:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2683086 Comparison Time: 04:38:22 (hh:mm:ss) Elapsed Time, 202307 HSPs Collected Number of families returned by RECON: 18379 Round Time: 04:58:35 (hh:mm:ss) Elapsed Time : 333 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:03:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:09:10 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 175423 repeats masked totaling 44309838 bp(s). - TE Masking time 00:08:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 276132669 bp Num Contigs Represented = 93 Non ambiguous bp: Initial: 270002686 bp After Masking: 221952016 bp Masked: 17.80 % -- Input Database Coverage: 409223835 bp out of 591951591 bp ( 69.13 % ) Sampling Time: 00:21:55 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23995128 Comparison Time: 36:20:20 (hh:mm:ss) Elapsed Time, 679496 HSPs Collected Number of families returned by RECON: 78312 Round Time: 38:59:09 (hh:mm:ss) Elapsed Time : 860 families discovered. RepeatScout/RECON discovery complete: 1521 families found Classification Time: 01:28:35 (hh:mm:ss) Elapsed Time Program Time: 46:40:36 (hh:mm:ss) Elapsed Time