RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ZULAuy/RM_32369.SatMay272051542023 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: 1685245912 Database = /dev/shm/rModeler.ZULAuy/GCF_021461395.2_iqSchAmer2.1 - Sequences = 1751 - Bases = 8990369808 - N50 = 994864580 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1183938540-1268505426 | [ 1 ] 1099371654-1183938539 | [ 1 ] 1014804768-1099371653 | [ ] 930237882-1014804767 | [ 2 ] 845670996-930237881 | [ 1 ] 761104110-845670995 | [ 1 ] 676537224-761104109 | [ ] 591970338-676537223 | [ 2 ] 507403452-591970337 | [ 1 ] 422836566-507403451 | [ ] 338269680-422836565 | [ ] 253702794-338269679 | [ ] 169135908-253702793 | [ 3 ] 84569022-169135907 | [ ] 2137-84569022 |************************************************** [ 1739 ] Storage Throughput = excellent ( 1197.86 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40018524 bp ( 40018024 non ambiguous ) - Num Contigs Represented = 62 - Sequence extraction : 00:16:53 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:44 (hh:mm:ss) Elapsed Time Round Time: 00:49:41 (hh:mm:ss) Elapsed Time : 727 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:04:15 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:34 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 13015 repeats masked totaling 4514357 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10015608 bp Num Contigs Represented = 27 Non ambiguous bp: Initial: 10015608 bp After Masking: 4555925 bp Masked: 54.51 % -- Input Database Coverage: 10015608 bp out of 8990369808 bp ( 0.11 % ) Sampling Time: 00:05:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:05:56 (hh:mm:ss) Elapsed Time, 14122 HSPs Collected Number of families returned by RECON: 1388 Round Time: 00:11:40 (hh:mm:ss) Elapsed Time : 12 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:12:33 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:51 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 39269 repeats masked totaling 13637205 bp(s). - TE Masking time 00:00:46 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30002836 bp Num Contigs Represented = 50 Non ambiguous bp: Initial: 30002336 bp After Masking: 13185697 bp Masked: 56.05 % -- Input Database Coverage: 40018444 bp out of 8990369808 bp ( 0.45 % ) Sampling Time: 00:15:14 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 283128 Comparison Time: 00:23:50 (hh:mm:ss) Elapsed Time, 49328 HSPs Collected Number of families returned by RECON: 4934 Round Time: 00:41:17 (hh:mm:ss) Elapsed Time : 108 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:37:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:06 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 128319 repeats masked totaling 43960124 bp(s). - TE Masking time 00:02:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90015391 bp Num Contigs Represented = 103 Non ambiguous bp: Initial: 90013391 bp After Masking: 37365661 bp Masked: 58.49 % -- Input Database Coverage: 130033835 bp out of 8990369808 bp ( 1.45 % ) Sampling Time: 00:45:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2550411 Comparison Time: 02:08:37 (hh:mm:ss) Elapsed Time, 326378 HSPs Collected Number of families returned by RECON: 13788 Round Time: 03:10:33 (hh:mm:ss) Elapsed Time : 616 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 01:54:14 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:41 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 457196 repeats masked totaling 154280007 bp(s). - TE Masking time 00:14:51 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270034106 bp Num Contigs Represented = 198 Non ambiguous bp: Initial: 270023974 bp After Masking: 89907831 bp Masked: 66.70 % -- Input Database Coverage: 400067941 bp out of 8990369808 bp ( 4.45 % ) Sampling Time: 02:25:20 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22892761 Comparison Time: 12:45:18 (hh:mm:ss) Elapsed Time, 910453 HSPs Collected Number of families returned by RECON: 30610 Round Time: 16:28:20 (hh:mm:ss) Elapsed Time : 1766 families discovered. RepeatScout/RECON discovery complete: 3229 families found Classification Time: 03:18:02 (hh:mm:ss) Elapsed Time Program Time: 24:39:33 (hh:mm:ss) Elapsed Time