RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.EKDz7B/RM_3688924.SunJan140824592024 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: 1705249499 Database = /dev/shm/rModeler.EKDz7B/GCA_028858805.1_NHGRI_mPanTro3-v1.1-hic.freeze_alt - Sequences = 119 - Bases = 3015383096 - N50 = 146345972 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 217758882-233312453 | [ 1 ] 202205311-217758881 | [ ] 186651740-202205310 |* [ 2 ] 171098169-186651739 |* [ 3 ] 155544598-171098168 | [ 1 ] 139991027-155544597 |* [ 3 ] 124437456-139991026 |* [ 2 ] 108883886-124437456 | [ 1 ] 93330315-108883885 |** [ 5 ] 77776744-93330314 |* [ 2 ] 62223173-77776743 | [ 1 ] 46669602-62223172 |* [ 2 ] 31116031-46669601 | [ ] 15562460-31116030 | [ ] 8890-15562460 |************************************************** [ 96 ] Storage Throughput = excellent ( 1245.98 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40115442 bp ( 40035439 non ambiguous ) - Num Contigs Represented = 27 - Sequence extraction : 00:02:15 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:15:50 (hh:mm:ss) Elapsed Time Round Time: 00:26:30 (hh:mm:ss) Elapsed Time : 238 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:39 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:43 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11522 repeats masked totaling 2865893 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10000311 bp Num Contigs Represented = 25 Non ambiguous bp: Initial: 10000311 bp After Masking: 6219517 bp Masked: 37.81 % -- Input Database Coverage: 10000311 bp out of 3015383096 bp ( 0.33 % ) Sampling Time: 00:02:39 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:06:58 (hh:mm:ss) Elapsed Time, 4820 HSPs Collected Number of families returned by RECON: 725 Round Time: 00:10:21 (hh:mm:ss) Elapsed Time : 20 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:45 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:42 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 38808 repeats masked totaling 9452468 bp(s). - TE Masking time 00:00:32 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30115051 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30035048 bp After Masking: 17614204 bp Masked: 41.35 % -- Input Database Coverage: 40115362 bp out of 3015383096 bp ( 1.33 % ) Sampling Time: 00:08:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283881 Comparison Time: 00:34:10 (hh:mm:ss) Elapsed Time, 25623 HSPs Collected Number of families returned by RECON: 2266 Round Time: 00:43:24 (hh:mm:ss) Elapsed Time : 69 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:58 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 125372 repeats masked totaling 29746112 bp(s). - TE Masking time 00:01:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90175764 bp Num Contigs Represented = 36 Non ambiguous bp: Initial: 90020779 bp After Masking: 51350175 bp Masked: 42.96 % -- Input Database Coverage: 130291126 bp out of 3015383096 bp ( 4.32 % ) Sampling Time: 00:23:36 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2545896 Comparison Time: 02:50:11 (hh:mm:ss) Elapsed Time, 91639 HSPs Collected Number of families returned by RECON: 8068 Round Time: 03:17:40 (hh:mm:ss) Elapsed Time : 163 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:14:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:54:33 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 402297 repeats masked totaling 96513960 bp(s). - TE Masking time 00:05:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270520962 bp Num Contigs Represented = 53 Non ambiguous bp: Initial: 270011382 bp After Masking: 145989027 bp Masked: 45.93 % -- Input Database Coverage: 400812088 bp out of 3015383096 bp ( 13.29 % ) Sampling Time: 01:15:16 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22906296 Comparison Time: 20:26:46 (hh:mm:ss) Elapsed Time, 357074 HSPs Collected Number of families returned by RECON: 31221 Round Time: 22:23:25 (hh:mm:ss) Elapsed Time : 426 families discovered. RepeatScout/RECON discovery complete: 916 families found Classification Time: 00:38:27 (hh:mm:ss) Elapsed Time Program Time: 27:39:47 (hh:mm:ss) Elapsed Time