RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.SgJXHS/RM_162728.SunJan151512272023 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: 1673824346 Database = /dev/shm/rModeler.SgJXHS/GCF_014108245.1_mPipKuh1.p - Sequences = 202 - Bases = 1775688541 - N50 = 80685825 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 184059808-197205563 | [ 3 ] 170914053-184059807 | [ ] 157768299-170914053 | [ ] 144622544-157768298 | [ ] 131476789-144622543 | [ ] 118331035-131476789 | [ ] 105185280-118331034 | [ ] 92039525-105185279 | [ ] 78893771-92039525 |* [ 4 ] 65748016-78893770 | [ 2 ] 52602261-65748015 | [ 1 ] 39456507-52602261 |* [ 5 ] 26310752-39456506 | [ 3 ] 13164997-26310751 | [ 3 ] 19243-13164997 |************************************************** [ 181 ] Storage Throughput = excellent ( 1233.04 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40358829 bp ( 40018416 non ambiguous ) - Num Contigs Represented = 79 - Sequence extraction : 00:02:33 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:28 (hh:mm:ss) Elapsed Time Round Time: 00:25:40 (hh:mm:ss) Elapsed Time : 341 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:37 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:35 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 15213 repeats masked totaling 2258158 bp(s). - TE Masking time 00:00:08 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10083069 bp Num Contigs Represented = 46 Non ambiguous bp: Initial: 10028335 bp After Masking: 7584516 bp Masked: 24.37 % -- Input Database Coverage: 10083069 bp out of 1775688541 bp ( 0.57 % ) Sampling Time: 00:01:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:06:27 (hh:mm:ss) Elapsed Time, 6480 HSPs Collected Number of families returned by RECON: 895 Round Time: 00:08:25 (hh:mm:ss) Elapsed Time : 15 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 00:01:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 49617 repeats masked totaling 7643384 bp(s). - TE Masking time 00:00:23 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30315605 bp Num Contigs Represented = 72 Non ambiguous bp: Initial: 30029926 bp After Masking: 21843490 bp Masked: 27.26 % -- Input Database Coverage: 40398674 bp out of 1775688541 bp ( 2.28 % ) Sampling Time: 00:03:51 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 287661 Comparison Time: 00:30:29 (hh:mm:ss) Elapsed Time, 25877 HSPs Collected Number of families returned by RECON: 2452 Round Time: 00:35:17 (hh:mm:ss) Elapsed Time : 70 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:05:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:09 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 158400 repeats masked totaling 25271671 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90522049 bp Num Contigs Represented = 110 Non ambiguous bp: Initial: 90034276 bp After Masking: 63214126 bp Masked: 29.79 % -- Input Database Coverage: 130920723 bp out of 1775688541 bp ( 7.37 % ) Sampling Time: 00:11:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2573046 Comparison Time: 03:24:45 (hh:mm:ss) Elapsed Time, 112690 HSPs Collected Number of families returned by RECON: 8909 Round Time: 03:45:20 (hh:mm:ss) Elapsed Time : 220 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:15:56 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:04 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 506914 repeats masked totaling 82062949 bp(s). - TE Masking time 00:05:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271859763 bp Num Contigs Represented = 166 Non ambiguous bp: Initial: 270036444 bp After Masking: 183248402 bp Masked: 32.14 % -- Input Database Coverage: 402780486 bp out of 1775688541 bp ( 22.68 % ) Sampling Time: 00:37:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23245971 Comparison Time: 22:47:38 (hh:mm:ss) Elapsed Time, 236725 HSPs Collected Number of families returned by RECON: 37682 Round Time: 23:48:36 (hh:mm:ss) Elapsed Time : 418 families discovered. RepeatScout/RECON discovery complete: 1064 families found Classification Time: 00:31:08 (hh:mm:ss) Elapsed Time Program Time: 29:14:26 (hh:mm:ss) Elapsed Time