RepeatModeler Version 2.0.4 =========================== Using output directory = /dev/shm/rModeler.O7uCag/RM_3506544.SunMar102057502024 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: 1710129470 Database = /dev/shm/rModeler.O7uCag/GCA_026936385.1_BBF_mMolNig1_v1 - Sequences = 146 - Bases = 2407891554 - N50 = 87249243 - Contig Histogram: Size(bp) Count ----------------------------------------------------------------------- 225037811-241110514 | [ 1 ] 208965109-225037811 | [ ] 192892407-208965109 | [ ] 176819704-192892406 | [ ] 160747002-176819704 | [ ] 144674300-160747002 | [ ] 128601597-144674299 | [ ] 112528895-128601597 | [ 1 ] 96456193-112528895 | [ 2 ] 80383490-96456192 |*** [ 9 ] 64310788-80383490 | [ 2 ] 48238086-64310788 |** [ 5 ] 32165383-48238085 | [ 1 ] 16092681-32165383 |**** [ 11 ] 19979-16092681 |************************************************** [ 114 ] Storage Throughput = excellent ( 1209.78 MB/s ) RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 40000000 bp - Final Sample Size = 40022618 bp ( 40020618 non ambiguous ) - Num Contigs Represented = 86 - Sequence extraction : 00:01:36 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences... - RepeatScout: 00:13:36 (hh:mm:ss) Elapsed Time Round Time: 00:24:31 (hh:mm:ss) Elapsed Time : 185 families discovered. RepeatModeler Round # 2 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 10000000 bp - Sequence extraction : 00:00:25 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:00:26 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 11128 repeats masked totaling 2844527 bp(s). - TE Masking time 00:00:09 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10005647 bp Num Contigs Represented = 57 Non ambiguous bp: Initial: 10005647 bp After Masking: 7058363 bp Masked: 29.46 % -- Input Database Coverage: 10005647 bp out of 2407891554 bp ( 0.42 % ) Sampling Time: 00:01:02 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 31125 Comparison Time: 00:05:32 (hh:mm:ss) Elapsed Time, 5497 HSPs Collected Number of families returned by RECON: 758 Round Time: 00:06:57 (hh:mm:ss) Elapsed Time : 15 families discovered. RepeatModeler Round # 3 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 30000000 bp - Sequence extraction : 00:01:22 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:01:17 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 36630 repeats masked totaling 8643234 bp(s). - TE Masking time 00:00:22 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 30016965 bp Num Contigs Represented = 78 Non ambiguous bp: Initial: 30014965 bp After Masking: 21015965 bp Masked: 29.98 % -- Input Database Coverage: 40022612 bp out of 2407891554 bp ( 1.66 % ) Sampling Time: 00:03:04 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 282376 Comparison Time: 00:26:21 (hh:mm:ss) Elapsed Time, 33959 HSPs Collected Number of families returned by RECON: 2334 Round Time: 00:30:23 (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 : 00:03:44 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:04:29 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 121675 repeats masked totaling 29769066 bp(s). - TE Masking time 00:01:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 90023063 bp Num Contigs Represented = 98 Non ambiguous bp: Initial: 90018563 bp After Masking: 59031055 bp Masked: 34.42 % -- Input Database Coverage: 130045675 bp out of 2407891554 bp ( 5.40 % ) Sampling Time: 00:09:30 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 2534626 Comparison Time: 02:37:26 (hh:mm:ss) Elapsed Time, 136001 HSPs Collected Number of families returned by RECON: 7607 Round Time: 02:50:09 (hh:mm:ss) Elapsed Time : 173 families discovered. RepeatModeler Round # 5 ======================== Searching for Repeats -- Sampling from the database... - Gathering up to 270000000 bp - Sequence extraction : 00:13:36 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... - TRFMask time 00:15:28 (hh:mm:ss) Elapsed Time -- Masking repeats from the previous rounds... 397413 repeats masked totaling 95631539 bp(s). - TE Masking time 00:05:04 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 270030768 bp Num Contigs Represented = 128 Non ambiguous bp: Initial: 270018768 bp After Masking: 170834309 bp Masked: 36.73 % -- Input Database Coverage: 400076443 bp out of 2407891554 bp ( 16.62 % ) Sampling Time: 00:34:37 (hh:mm:ss) Elapsed Time Running all-by-other comparisons... - Total Comparisons = 22838661 Comparison Time: 21:28:42 (hh:mm:ss) Elapsed Time, 622749 HSPs Collected Number of families returned by RECON: 33352 Round Time: 22:24:22 (hh:mm:ss) Elapsed Time : 375 families discovered. RepeatScout/RECON discovery complete: 811 families found Classification Time: 00:35:05 (hh:mm:ss) Elapsed Time Program Time: 26:51:27 (hh:mm:ss) Elapsed Time