RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.8SmsKO/RM_969343.ThuDec70839262023 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: 1701967165 Database = /dev/shm/rModeler.8SmsKO/GCA_963264785.1_bPsiEch3.1 - Sequences = 172 - Bases = 1203831919 - N50 = 122792946 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 156870048-168074981 | [ 2 ] 145665116-156870048 | [ ] 134460184-145665116 | [ ] 123255252-134460184 | [ 1 ] 112050320-123255252 | [ 1 ] 100845388-112050320 | [ 1 ] 89640456-100845388 | [ 1 ] 78435524-89640456 | [ 1 ] 67230592-78435524 | [ ] 56025660-67230592 | [ 1 ] 44820728-56025660 | [ ] 33615796-44820728 | [ ] 22410864-33615796 | [ 3 ] 11205932-22410864 |* [ 6 ] 1000-11205932 |************************************************** [ 155 ] Storage Throughput = excellent ( 1032.66 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40016595 bp ( 40014795 non ambiguous ) - Num Contigs Represented = 61 - Sequence extraction : 00:02:23 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:16:51 (hh:mm:ss) Elapsed Time Round Time: 00:22:31 (hh:mm:ss) Elapsed Time : 88 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:34 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:36 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 3496 repeats masked totaling 1152037 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10033314 bp Num Contigs Represented = 33 Non ambiguous bp: Initial: 10032914 bp After Masking: 8451713 bp Masked: 15.76 % -- Input Database Coverage: 10033314 bp out of 1203831919 bp ( 0.83 % ) Sampling Time: 00:01:18 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31626 Comparison Time: 00:06:41 (hh:mm:ss) Elapsed Time, 1372 HSPs Collected Number of families returned by RECON: 194 Round Time: 00:08:05 (hh:mm:ss) Elapsed Time : 5 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:52 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 10984 repeats masked totaling 3475245 bp(s). - TE Masking time 00:00:16 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30023277 bp Num Contigs Represented = 55 Non ambiguous bp: Initial: 30021877 bp After Masking: 25019037 bp Masked: 16.66 % -- Input Database Coverage: 40056591 bp out of 1203831919 bp ( 3.33 % ) Sampling Time: 00:03:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:31:57 (hh:mm:ss) Elapsed Time, 3339 HSPs Collected Number of families returned by RECON: 1156 Round Time: 00:36:04 (hh:mm:ss) Elapsed Time : 3 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:04:30 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:22 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 30871 repeats masked totaling 9560249 bp(s). - TE Masking time 00:00:48 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90032099 bp Num Contigs Represented = 66 Non ambiguous bp: Initial: 90027499 bp After Masking: 76470610 bp Masked: 15.06 % -- Input Database Coverage: 130088690 bp out of 1203831919 bp ( 10.81 % ) Sampling Time: 00:10:47 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 03:55:55 (hh:mm:ss) Elapsed Time, 28370 HSPs Collected Number of families returned by RECON: 8140 Round Time: 04:08:12 (hh:mm:ss) Elapsed Time : 48 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:05 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:17:27 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 102196 repeats masked totaling 32428288 bp(s). - TE Masking time 00:02:42 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270023332 bp Num Contigs Represented = 107 Non ambiguous bp: Initial: 270005303 bp After Masking: 225696755 bp Masked: 16.41 % -- Input Database Coverage: 400112022 bp out of 1203831919 bp ( 33.24 % ) Sampling Time: 00:33:33 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22960476 Comparison Time: 27:11:29 (hh:mm:ss) Elapsed Time, 167103 HSPs Collected Number of families returned by RECON: 54502 Round Time: 28:15:39 (hh:mm:ss) Elapsed Time : 192 families discovered. RepeatScout/RECON discovery complete: 336 families found Classification Time: 00:26:08 (hh:mm:ss) Elapsed Time Program Time: 33:56:39 (hh:mm:ss) Elapsed Time