RepeatModeler Version 2.0.7
===========================
Using output directory = /dev/shm/rModeler.3GIJV4/RM_1357071.MonFeb92012152026
Search Engine = rmblast 2.14.1+
Threads = 32
Dependencies: TRF 4.09, RECON , RepeatScout 1.0.7, RepeatMasker 4.2.1, RepeatAfterMe 0.0.7
LTR Structural Analysis: Disabled [use -LTRStruct to enable]
Random Number Seed: 1770696734
Database = /dev/shm/rModeler.3GIJV4/GCA_964014045.1_Leishmania_braziliensis_M2904-Dec2022 
  - Sequences = 51
  - Bases = 33507578
Storage Throughput = excellent ( 1508.20 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 33507498 bp ( 33506496 non ambiguous )
   - Num Contigs Represented = 51
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 179 raw families identified
   - RepeatScout: Running filtering stage.. 163 families remaining
   - RepeatScout: 00:02:04 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 148 families... 00:59:40 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 37 satellite(s), 29 contained, found in 00:00:27 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:27 (hh:mm:ss) Elapsed Time
Round Time: 01:02:15 (hh:mm:ss) Elapsed Time : 82 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       2570 repeats masked totaling 825004 bp(s).
   - TE Masking time 00:00:10 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10006958 bp
       Num Contigs Represented = 43
       Non ambiguous bp:
             Initial: 10006956 bp
             After Masking: 8960084 bp
             Masked: 10.46 % 
 -- Input Database Coverage: 10006958 bp out of 33507578 bp ( 29.86 % )
Sampling Time: 00:00:37 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 34191
Comparison Time: 00:04:17 (hh:mm:ss) Elapsed Time, 2348 HSPs Collected
Number of families returned by RECON: 714
Round Time: 00:05:14 (hh:mm:ss) Elapsed Time : 2 families discovered.


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 30000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:53 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       6215 repeats masked totaling 2037624 bp(s).
   - TE Masking time 00:00:17 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 23500460 bp
       Num Contigs Represented = 44
       Non ambiguous bp:
             Initial: 23499460 bp
             After Masking: 20983162 bp
             Masked: 10.71 % 
 -- Input Database Coverage: 33507418 bp out of 33507578 bp ( 100.00 % )
Sampling Time: 00:01:13 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 181503
Comparison Time: 00:13:24 (hh:mm:ss) Elapsed Time, 11587 HSPs Collected
Number of families returned by RECON: 2592
Round Time: 00:14:55 (hh:mm:ss) Elapsed Time : 11 families discovered.

RepeatScout/RECON discovery complete: 95 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /dev/shm/rModeler.3GIJV4/RM_1357071.MonFeb92012152026
# Protein Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatPeps.lib
#   - 18011 proteins
# Consensi Library: /hive/data/outside/RepeatMasker/RepeatMasker-4.2.1/Libraries/RepeatMasker.lib
#   - 26292 consensus sequences
  - Looking for simple/tandem and low complexity sequences..
  - Looking for similarity to known repeat proteins..
  - Looking for similarity to known repeat consensi..

Classification Time: 00:00:21 (hh:mm:ss) Elapsed Time


Program Time: 01:22:45 (hh:mm:ss) Elapsed Time