RepeatModeler Version 2.0.4 =========================== Using output directory = /hive/data/genomes/asmHubs/genbankBuild/GCA/011/078/405/GCA_011078405.1_mCalJac1.mat/trackData/repeatModeler/RM_16086.SatDec241330332022 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: 1671917433 Database = /hive/data/genomes/asmHubs/genbankBuild/GCA/011/078/405/GCA_011078405.1_mCalJac1.mat/trackData/repeatModeler/GCA_011078405.1_mCalJac1.mat - Sequences = 216 - Bases = 2811151840 - N50 = 155929068 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 203594275-218136636 | [ 1 ] 189051915-203594275 | [ 2 ] 174509555-189051915 | [ ] 159967195-174509555 | [ 3 ] 145424835-159967195 | [ 2 ] 130882475-145424835 | [ 2 ] 116340115-130882475 |* [ 4 ] 101797755-116340115 | [ 1 ] 87255395-101797755 | [ 2 ] 72713035-87255395 | [ 1 ] 58170675-72713035 | [ ] 43628315-58170675 |* [ 5 ] 29085955-43628315 | [ ] 14543595-29085955 | [ ] 1235-14543595 |************************************************** [ 193 ] Storage Throughput = good ( 727.71 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40205570 bp ( 40016092 non ambiguous ) - Num Contigs Represented = 28 - Sequence extraction : 00:02:45 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:32 (hh:mm:ss) Elapsed Time Round Time: 00:25:43 (hh:mm:ss) Elapsed Time : 275 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 14509 repeats masked totaling 3213556 bp(s). - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10080309 bp Num Contigs Represented = 24 Non ambiguous bp: Initial: 10018512 bp After Masking: 6671651 bp Masked: 33.41 % -- Input Database Coverage: 10080309 bp out of 2811151840 bp ( 0.36 % ) Sampling Time: 00:01:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:05:52 (hh:mm:ss) Elapsed Time, 22882 HSPs Collected Number of families returned by RECON: 1043 Round Time: 00:08:36 (hh:mm:ss) Elapsed Time : 17 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:02:24 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:08 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 46902 repeats masked totaling 9996695 bp(s). - TE Masking time 00:00:26 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30165258 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 30037577 bp After Masking: 19437345 bp Masked: 35.29 % -- Input Database Coverage: 40245567 bp out of 2811151840 bp ( 1.43 % ) Sampling Time: 00:05:01 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 285390 Comparison Time: 00:25:47 (hh:mm:ss) Elapsed Time, 64681 HSPs Collected Number of families returned by RECON: 2271 Round Time: 00:33:50 (hh:mm:ss) Elapsed Time : 68 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:06:20 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:56 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 148204 repeats masked totaling 32798460 bp(s). - TE Masking time 00:01:28 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90300113 bp Num Contigs Represented = 42 Non ambiguous bp: Initial: 90007453 bp After Masking: 55763530 bp Masked: 38.05 % -- Input Database Coverage: 130545680 bp out of 2811151840 bp ( 4.64 % ) Sampling Time: 00:12:52 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2557191 Comparison Time: 02:39:14 (hh:mm:ss) Elapsed Time, 123667 HSPs Collected Number of families returned by RECON: 7612 Round Time: 03:03:03 (hh:mm:ss) Elapsed Time : 172 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:19:29 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:16:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 476798 repeats masked totaling 105366922 bp(s). - TE Masking time 00:05:29 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271222465 bp Num Contigs Represented = 59 Non ambiguous bp: Initial: 270020458 bp After Masking: 160323072 bp Masked: 40.63 % -- Input Database Coverage: 401768145 bp out of 2811151840 bp ( 14.29 % ) Sampling Time: 00:41:29 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23035078 Comparison Time: 20:25:35 (hh:mm:ss) Elapsed Time, 1060533 HSPs Collected Number of families returned by RECON: 32383 Round Time: 22:35:03 (hh:mm:ss) Elapsed Time : 386 families discovered. RepeatScout/RECON discovery complete: 918 families found Classification Time: 00:33:38 (hh:mm:ss) Elapsed Time Program Time: 27:19:53 (hh:mm:ss) Elapsed Time