RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.ImeiHB/RM_318165.SunJan10920192023 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: 1672593617 Database = /dev/shm/rModeler.ImeiHB/GCF_902148845.1_fSalaFa1.1 - Sequences = 203 - Bases = 797507141 - N50 = 33379828 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 38925303-41705463 |* [ 4 ] 36145144-38925303 | [ 1 ] 33364985-36145144 |* [ 5 ] 30584826-33364985 |* [ 4 ] 27804667-30584826 |* [ 4 ] 25024507-27804666 | [ 3 ] 22244348-25024507 | [ 1 ] 19464189-22244348 | [ 1 ] 16684030-19464189 | [ 1 ] 13903871-16684030 | [ ] 11123711-13903870 | [ ] 8343552-11123711 | [ ] 5563393-8343552 | [ ] 2783234-5563393 | [ 1 ] 3075-2783234 |************************************************** [ 178 ] Storage Throughput = excellent ( 1394.35 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40394128 bp ( 40028036 non ambiguous ) - Num Contigs Represented = 57 - Sequence extraction : 00:00:30 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:10:31 (hh:mm:ss) Elapsed Time Round Time: 00:15:25 (hh:mm:ss) Elapsed Time : 402 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:08 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:38 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 5620 repeats masked totaling 1210942 bp(s). - TE Masking time 00:00:07 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030762 bp Num Contigs Represented = 34 Non ambiguous bp: Initial: 10025903 bp After Masking: 8302363 bp Masked: 17.19 % -- Input Database Coverage: 10030762 bp out of 797507141 bp ( 1.26 % ) Sampling Time: 00:00:54 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31375 Comparison Time: 00:06:37 (hh:mm:ss) Elapsed Time, 4889 HSPs Collected Number of families returned by RECON: 1306 Round Time: 00:07:43 (hh:mm:ss) Elapsed Time : 11 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:00:19 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 16451 repeats masked totaling 3393168 bp(s). - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30363286 bp Num Contigs Represented = 51 Non ambiguous bp: Initial: 30002053 bp After Masking: 25517565 bp Masked: 14.95 % -- Input Database Coverage: 40394048 bp out of 797507141 bp ( 5.07 % ) Sampling Time: 00:02:07 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 290703 Comparison Time: 00:26:22 (hh:mm:ss) Elapsed Time, 37201 HSPs Collected Number of families returned by RECON: 5248 Round Time: 00:29:41 (hh:mm:ss) Elapsed Time : 63 families discovered. RepeatModeler Round # 4 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 90000000 bp - Sequence extraction : 00:01:07 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:05:18 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 57572 repeats masked totaling 12330219 bp(s). - TE Masking time 00:00:56 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 91073434 bp Num Contigs Represented = 95 Non ambiguous bp: Initial: 90030487 bp After Masking: 74000668 bp Masked: 17.80 % -- Input Database Coverage: 131467482 bp out of 797507141 bp ( 16.48 % ) Sampling Time: 00:07:27 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2616328 Comparison Time: 02:39:53 (hh:mm:ss) Elapsed Time, 292267 HSPs Collected Number of families returned by RECON: 19458 Round Time: 02:56:26 (hh:mm:ss) Elapsed Time : 466 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:02:59 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:19:11 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 232025 repeats masked totaling 52061307 bp(s). - TE Masking time 00:08:35 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 273708033 bp Num Contigs Represented = 145 Non ambiguous bp: Initial: 270039546 bp After Masking: 207251752 bp Masked: 23.25 % -- Input Database Coverage: 405175515 bp out of 797507141 bp ( 50.81 % ) Sampling Time: 00:31:00 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 23636250 Comparison Time: 18:01:30 (hh:mm:ss) Elapsed Time, 890701 HSPs Collected Number of families returned by RECON: 72614 Round Time: 19:49:30 (hh:mm:ss) Elapsed Time : 1225 families discovered. RepeatScout/RECON discovery complete: 2167 families found Classification Time: 02:03:02 (hh:mm:ss) Elapsed Time Program Time: 25:41:47 (hh:mm:ss) Elapsed Time