RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.QTyLho/RM_3039666.SatFeb151805492025 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: 1739671548 Database = /dev/shm/rModeler.QTyLho/GCA_905231915.1_Snec_CCMP2469 - Sequences = 104583 - Bases = 767953253 - N50 = 14529 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 1253992-1343492 | [ 1 ] 1164493-1253992 | [ ] 1074993-1164492 | [ ] 985494-1074993 | [ ] 895994-985493 | [ ] 806495-895994 | [ 1 ] 716995-806494 | [ ] 627496-716995 | [ ] 537996-627495 | [ 2 ] 448497-537996 | [ ] 358997-448496 | [ 1 ] 269498-358997 | [ ] 179998-269497 | [ 4 ] 90499-179998 | [ 52 ] 1000-90499 |************************************************** [ 104522 ] Storage Throughput = excellent ( 1788.60 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40221885 bp ( 40001107 non ambiguous ) - Num Contigs Represented = 5534 - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:06:20 (hh:mm:ss) Elapsed Time Round Time: 00:07:09 (hh:mm:ss) Elapsed Time : 129 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 8748 repeats masked totaling 710755 bp(s). - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10083419 bp Num Contigs Represented = 1419 Non ambiguous bp: Initial: 10026711 bp After Masking: 8656585 bp Masked: 13.66 % -- Input Database Coverage: 10083419 bp out of 767953253 bp ( 1.31 % ) Sampling Time: 00:00:21 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 1006071 Comparison Time: 00:06:13 (hh:mm:ss) Elapsed Time, 35933 HSPs Collected Number of families returned by RECON: 2123 Round Time: 00:07:09 (hh:mm:ss) Elapsed Time : 26 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:54 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 35847 repeats masked totaling 4043818 bp(s). - TE Masking time 00:00:12 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30177111 bp Num Contigs Represented = 4122 Non ambiguous bp: Initial: 30012700 bp After Masking: 24008487 bp Masked: 20.01 % -- Input Database Coverage: 40260530 bp out of 767953253 bp ( 5.24 % ) Sampling Time: 00:01:08 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 8514001 Comparison Time: 00:21:43 (hh:mm:ss) Elapsed Time, 32941 HSPs Collected Number of families returned by RECON: 5074 Round Time: 00:23:29 (hh:mm:ss) Elapsed Time : 29 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:00:04 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:02:40 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 104010 repeats masked totaling 11957153 bp(s). - TE Masking time 00:00:34 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90511711 bp Num Contigs Represented = 12490 Non ambiguous bp: Initial: 90013517 bp After Masking: 72336067 bp Masked: 19.64 % -- Input Database Coverage: 130772241 bp out of 767953253 bp ( 17.03 % ) Sampling Time: 00:03:22 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 78469128 Comparison Time: 01:42:16 (hh:mm:ss) Elapsed Time, 176833 HSPs Collected Number of families returned by RECON: 22723 Round Time: 01:50:12 (hh:mm:ss) Elapsed Time : 159 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:00:12 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:07:55 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 346898 repeats masked totaling 40869352 bp(s). - TE Masking time 00:02:18 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 271525899 bp Num Contigs Represented = 37589 Non ambiguous bp: Initial: 270007484 bp After Masking: 211903752 bp Masked: 21.52 % -- Input Database Coverage: 402298140 bp out of 767953253 bp ( 52.39 % ) Sampling Time: 00:10:35 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 715876041 Comparison Time: 10:22:01 (hh:mm:ss) Elapsed Time, 1242261 HSPs Collected Number of families returned by RECON: 96082 Round Time: 11:42:02 (hh:mm:ss) Elapsed Time : 753 families discovered. RepeatScout/RECON discovery complete: 1096 families found Classification Time: 00:35:39 (hh:mm:ss) Elapsed Time Program Time: 14:45:40 (hh:mm:ss) Elapsed Time