RepeatModeler Version 2.0.7
===========================
Using output directory = /data/tmp/rModeler.BKxZvf/RM_1043905.MonSep81244362025
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: 1757360675
Database = /data/tmp/rModeler.BKxZvf/GCA_000835815.1_Cryp_gatt_2001_935-1_V1 
  - Sequences = 24
  - Bases = 17566680
Storage Throughput = fair ( 652.55 MB/s )


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 17566539 bp ( 17377386 non ambiguous )
   - Num Contigs Represented = 24
   - Sequence extraction : 00:00:03 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14, min = 10 )..
   - RepeatScout: Running RepeatScout.. : 12 raw families identified
   - RepeatScout: Running filtering stage.. 11 families remaining
   - RepeatScout: 00:00:25 (hh:mm:ss) Elapsed Time
   - Collecting repeat instances...
   - Refining 11 families... 00:00:06 (hh:mm:ss) Elapsed Time
   - Redundant Families and Large Satellite Filtering.. 
      : 0 satellite(s), 0 contained, found in 00:00:01 (hh:mm:ss) Elapsed Time
Family Refinement: 00:00:01 (hh:mm:ss) Elapsed Time
Round Time: 00:00:38 (hh:mm:ss) Elapsed Time : 11 families discovered.


RepeatModeler Round # 2
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 10000000 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:11 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       199 repeats masked totaling 39876 bp(s).
   - TE Masking time 00:00:03 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 10134804 bp
       Num Contigs Represented = 22
       Non ambiguous bp:
             Initial: 10032053 bp
             After Masking: 9982290 bp
             Masked: 0.50 % 
 -- Input Database Coverage: 10134804 bp out of 17566680 bp ( 57.69 % )
Sampling Time: 00:00:18 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 34453
Comparison Time: 00:06:20 (hh:mm:ss) Elapsed Time, 2235 HSPs Collected
Number of families returned by RECON: 564
Round Time: 00:07:01 (hh:mm:ss) Elapsed Time : 3 families discovered.
   - Increasing sample size to include end piece now = 37566680


RepeatModeler Round # 3
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 37566680 bp
   - Sequence extraction : 00:00:02 (hh:mm:ss) Elapsed Time
 -- Running TRFMask on the sequence...
   - TRFMask time 00:00:09 (hh:mm:ss) Elapsed Time
 -- Masking repeats from the previous rounds...
       220 repeats masked totaling 46868 bp(s).
   - TE Masking time 00:00:02 (hh:mm:ss) Elapsed Time
 -- Sample Stats:
       Sample Size 7431655 bp
       Num Contigs Represented = 20
       Non ambiguous bp:
             Initial: 7345253 bp
             After Masking: 7289790 bp
             Masked: 0.76 % 
 -- Input Database Coverage: 17566459 bp out of 17566680 bp ( 100.00 % )
Sampling Time: 00:00:15 (hh:mm:ss) Elapsed Time
Running all-by-other comparisons...
  - Total Comparisons = 18145
Comparison Time: 00:04:41 (hh:mm:ss) Elapsed Time, 866 HSPs Collected
Number of families returned by RECON: 397
Round Time: 00:05:02 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 14 families found


#
# RepeatClassifier
#
# Version 2.0.7
# Threads: 32
# Current Working Directory: /data/tmp/rModeler.BKxZvf/RM_1043905.MonSep81244362025
# 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: 00:00:15 (hh:mm:ss) Elapsed Time


Program Time: 00:12:56 (hh:mm:ss) Elapsed Time