RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.dZ17yh/RM_541800.SunMar310610572024 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: 1711890657 Database = /dev/shm/rModeler.dZ17yh/GCA_963932015.1_bAnaAcu1.1 - Sequences = 395 - Bases = 1189313589 - N50 = 119285422 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 191341003-205008147 | [ 1 ] 177673860-191341003 | [ ] 164006717-177673860 | [ ] 150339574-164006717 | [ 1 ] 136672431-150339574 | [ ] 123005288-136672431 | [ ] 109338145-123005288 | [ 1 ] 95671001-109338144 | [ ] 82003858-95671001 | [ ] 68336715-82003858 | [ 2 ] 54669572-68336715 | [ 1 ] 41002429-54669572 | [ ] 27335286-41002429 | [ 4 ] 13668143-27335286 |* [ 9 ] 1000-13668143 |************************************************** [ 376 ] Storage Throughput = excellent ( 1141.36 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40033879 bp ( 40027654 non ambiguous ) - Num Contigs Represented = 75 - Sequence extraction : 00:01:54 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:17:45 (hh:mm:ss) Elapsed Time Round Time: 00:27:31 (hh:mm:ss) Elapsed Time : 89 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:46 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 1834 repeats masked totaling 688157 bp(s). - TE Masking time 00:00:06 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10028689 bp Num Contigs Represented = 39 Non ambiguous bp: Initial: 10026889 bp After Masking: 8856730 bp Masked: 11.67 % -- Input Database Coverage: 10028689 bp out of 1189313589 bp ( 0.84 % ) Sampling Time: 00:01:23 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31878 Comparison Time: 00:07:22 (hh:mm:ss) Elapsed Time, 1174 HSPs Collected Number of families returned by RECON: 245 Round Time: 00:09:38 (hh:mm:ss) Elapsed Time : 1 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:19 (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... 6403 repeats masked totaling 2317457 bp(s). - TE Masking time 00:00:14 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30005189 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 30000764 bp After Masking: 26122622 bp Masked: 12.93 % -- Input Database Coverage: 40033878 bp out of 1189313589 bp ( 3.37 % ) Sampling Time: 00:03:44 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 284635 Comparison Time: 00:37:24 (hh:mm:ss) Elapsed Time, 5105 HSPs Collected Number of families returned by RECON: 1542 Round Time: 00:41:22 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:03:51 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:06:24 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 17786 repeats masked totaling 6112119 bp(s). - TE Masking time 00:00:36 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90027921 bp Num Contigs Represented = 127 Non ambiguous bp: Initial: 90020121 bp After Masking: 78768675 bp Masked: 12.50 % -- Input Database Coverage: 130061799 bp out of 1189313589 bp ( 10.94 % ) Sampling Time: 00:10:58 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2570778 Comparison Time: 04:24:34 (hh:mm:ss) Elapsed Time, 42706 HSPs Collected Number of families returned by RECON: 9670 Round Time: 04:40:01 (hh:mm:ss) Elapsed Time : 58 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:11:50 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:21:02 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 65105 repeats masked totaling 22071419 bp(s). - TE Masking time 00:02:49 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270044813 bp Num Contigs Represented = 232 Non ambiguous bp: Initial: 270016374 bp After Masking: 231327813 bp Masked: 14.33 % -- Input Database Coverage: 400106612 bp out of 1189313589 bp ( 33.64 % ) Sampling Time: 00:35:59 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23143806 Comparison Time: 34:52:27 (hh:mm:ss) Elapsed Time, 246246 HSPs Collected Number of families returned by RECON: 59819 Round Time: 36:09:20 (hh:mm:ss) Elapsed Time : 232 families discovered. RepeatScout/RECON discovery complete: 385 families found Classification Time: 00:31:38 (hh:mm:ss) Elapsed Time Program Time: 42:39:30 (hh:mm:ss) Elapsed Time