RepeatMasker icon indicating copy to clipboard operation
RepeatMasker copied to clipboard
verified publisher icon rmhubley

Can't locate 'setThreadByQuery' via package "NCBIBlastSearchEngine" at RepeatModeler/Refiner

Open tania-k opened this issue 2 years ago • 1 comments

Hi folks, I have been attempting to load in RepeatModeler through your usual installation description and am running into this one main issue I can't figure out.

I am on a campus cluster so I'm not sure if I have the proper root access I might need to remedy this.

I am not honest how I can reproduce this error for you, but it comes through running the RepeatModeler program on my genomes. The BuildDatabase program runs just fine. My error as mentioned in my subject keeps indicating the setThreadByQuery function cannot be found in my NCBIBlastSearchEngine program when running RepeatModeler/Refiner. All programs are in my RepeatModeler/bin directory of which I have configured to through your configuration steps.

I've done what I could, updated programs, created a conda environment with RepeatModeler and added all the dependent programs into the same environment, ran configure on different directories of each program, ran configure on one main directory where all the dependent programs were copied into, and etc scenario.

If I let the program run to completion it always fails and never generates my .fa or .stk files I need to progress with my analysis. Please let me know what I can do to remedy this.

Thank you!

My copied error looks like this.

Histoplasma_capsulatum_HcMV3 Building database repeat_library/Histoplasma_capsulatum_HcMV3: Reading genomes/Histoplasma_capsulatum_HcMV3.sorted.fasta... Number of sequences (bp) added to database: 95 ( 5675239 bp ) RepeatModeler Version 2.0.5 =========================== Using output directory = /work/users/t/a/taniak/Annotation/RM_2590771.MonOct231255012023 Search Engine = rmblast 2.14.1+ Threads = 4 Dependencies: TRF 4.10, RECON , RepeatScout 1.0.5, RepeatMasker 4.1.5 LTR Structural Analysis: Enabled ( GenomeTools 1.6.2, LTR_Retriever v2.9.5, Ninja 0.97-cluster_only, MAFFT 7.490, CD-HIT 4.8.1 ) Random Number Seed: 1698080101 Database = /work/users/t/a/taniak/Annotation/repeat_library/Histoplasma_capsulatum_HcMV3 .

  • Sequences = 95
  • Bases = 5675239 Storage Throughput = fair ( 390.19 MB/s )

Ready to start the sampling process. INFO: The runtime of RepeatModeler heavily depends on the quality of the assembly and the repetitive content of the sequences. It is not imperative that RepeatModeler completes all rounds in order to obtain useful results. At the completion of each round, the files ( consensi.fa, and families.stk ) found in: /work/users/t/a/taniak/Annotation/RM_2590771.MonOct231255012023/ will contain all results produced thus far. These files may be manually copied and run through RepeatClassifier should the program be terminated early.

RepeatModeler Round # 1 ======================== Searching for Repeats -- Sampling from the database...

  • Gathering up to 40000000 bp
  • Final Sample Size = 5675160 bp ( 5667012 non ambiguous )
  • Num Contigs Represented = 95
  • Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences...
  • RepeatScout: Running build_lmer_table ( l = 13 )..
  • RepeatScout: Running RepeatScout.. : 95 raw families identified
  • RepeatScout: Running filtering stage.. 90 families remaining
  • RepeatScout: 00:01:01 (hh:mm:ss) Elapsed Time
  • Large Satellite Filtering.. : 3 found in 00:00:15 (hh:mm:ss) Elapsed Time
  • Collecting repeat instances...slurmstepd: error: *** JOB 20955013 ON c0310 CANCELLED AT 2023-10-23T12:57:01 *** (base) [taniak@longleaf-login4 logs]$ cat repeatmodeler_attempt.17.log Histoplasma_capsulatum_HcMZ5 Building database repeat_library/Histoplasma_capsulatum_HcMZ5: Reading genomes/Histoplasma_capsulatum_HcMZ5.sorted.fasta... Number of sequences (bp) added to database: 999 ( 14298302 bp ) RepeatModeler Version 2.0.5 =========================== Using output directory = /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023 Search Engine = rmblast 2.14.1+ Threads = 4 Dependencies: TRF 4.10, RECON , RepeatScout 1.0.6, RepeatMasker 4.1.5 LTR Structural Analysis: Enabled ( GenomeTools 1.6.2, LTR_Retriever v2.9.5, Ninja 0.97-cluster_only, MAFFT 7.490, CD-HIT 4.8.1 ) Random Number Seed: 1698000022 Database = /work/users/t/a/taniak/Annotation/repeat_library/Histoplasma_capsulatum_HcMZ5 .
  • Sequences = 999
  • Bases = 14298302
  • N50 = 1923913
  • Contig Histogram: Size(bp) Count

2296636-2460646 | [ 1 ] 2132626-2296635 | [ ] 1968616-2132625 | [ 1 ] 1804607-1968616 | [ 1 ] 1640597-1804606 | [ ] 1476587-1640596 | [ ] 1312577-1476586 | [ ] 1148568-1312577 | [ 2 ] 984558-1148567 | [ 1 ] 820548-984557 | [ ] 656538-820547 | [ ] 492529-656538 | [ ] 328519-492528 | [ ] 164509-328518 | [ ] 500-164509 |************************************************** [ 993 ]

Storage Throughput = fair ( 332.84 MB/s )

Ready to start the sampling process. INFO: The runtime of RepeatModeler heavily depends on the quality of the assembly and the repetitive content of the sequences. It is not imperative that RepeatModeler completes all rounds in order to obtain useful results. At the completion of each round, the files ( consensi.fa, and families.stk ) found in: /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/ will contain all results produced thus far. These files may be manually copied and run through RepeatClassifier should the program be terminated early.

RepeatModeler Round # 1

Searching for Repeats -- Sampling from the database...

  • Gathering up to 40000000 bp
  • Final Sample Size = 14298197 bp ( 14255281 non ambiguous )
  • Num Contigs Represented = 999
  • Sequence extraction : 00:00:01 (hh:mm:ss) Elapsed Time -- Running RepeatScout on the sequences...
  • RepeatScout: Running build_lmer_table ( l = 13 )..
  • RepeatScout: Running RepeatScout.. : 155 raw families identified
  • RepeatScout: Running filtering stage.. 146 families remaining
  • RepeatScout: 00:03:32 (hh:mm:ss) Elapsed Time
  • Large Satellite Filtering.. : 4 found in 00:00:05 (hh:mm:ss) Elapsed Time
  • Collecting repeat instances...: 00:02:44 (hh:mm:ss) Elapsed Time Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Refinement: 00:18:30 (hh:mm:ss) Elapsed Time WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-28.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-23.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-11.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-39.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-45.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-47.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-22.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-41.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-0.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-48.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-33.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-3.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-5.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-30.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-8.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-18.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-16.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-6.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-25.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-12.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-20.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-27.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-1.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-36.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-19.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-21.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-15.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-24.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-50.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-26.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-44.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-37.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-49.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-2.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-43.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-9.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-38.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-31.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-40.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-14.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-4.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-13.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-52.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-34.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-46.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-51.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-29.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-17.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-10.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-35.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-7.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-42.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-1/family-32.fa. Family Refinement: 00:18:30 (hh:mm:ss) Elapsed Time Round Time: 00:24:53 (hh:mm:ss) Elapsed Time : 0 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... 851 Tandem Repeats Masked
  • TRFMask time 00:00:25 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 10030276 bp Num Contigs Represented = 669 Non ambiguous bp: Initial: 10001027 bp After Masking: 9951556 bp Masked: 0.49 % -- Input Database Coverage: 10030276 bp out of 14298302 bp ( 70.15 % ) Sampling Time: 00:00:26 (hh:mm:ss) Elapsed Time Running all-by-other comparisons...
  • Total Comparisons = 354061 1% completed, 01:1:09 (hh:mm:ss) est. time remaining. 1% completed, 01:8:13 (hh:mm:ss) est. time remaining. 2% completed, 00:53:43 (hh:mm:ss) est. time remaining. 3% completed, 00:50:18 (hh:mm:ss) est. time remaining. 6% completed, 00:45:59 (hh:mm:ss) est. time remaining. 7% completed, 00:43:37 (hh:mm:ss) est. time remaining. 7% completed, 00:44:37 (hh:mm:ss) est. time remaining. 8% completed, 00:55:15 (hh:mm:ss) est. time remaining. 9% completed, 00:59:37 (hh:mm:ss) est. time remaining. 9% completed, 00:56:39 (hh:mm:ss) est. time remaining. 12% completed, 00:47:49 (hh:mm:ss) est. time remaining. 12% completed, 00:46:58 (hh:mm:ss) est. time remaining. 13% completed, 00:48:46 (hh:mm:ss) est. time remaining. 13% completed, 00:48:36 (hh:mm:ss) est. time remaining. 13% completed, 00:48:32 (hh:mm:ss) est. time remaining. 14% completed, 00:46:03 (hh:mm:ss) est. time remaining. 15% completed, 00:46:06 (hh:mm:ss) est. time remaining. 17% completed, 00:41:54 (hh:mm:ss) est. time remaining. 17% completed, 00:41:22 (hh:mm:ss) est. time remaining. 18% completed, 00:41:13 (hh:mm:ss) est. time remaining. 19% completed, 00:39:26 (hh:mm:ss) est. time remaining. 20% completed, 00:38:48 (hh:mm:ss) est. time remaining. 20% completed, 00:39:20 (hh:mm:ss) est. time remaining. 22% completed, 00:36:38 (hh:mm:ss) est. time remaining. 22% completed, 00:36:15 (hh:mm:ss) est. time remaining. 23% completed, 00:39:28 (hh:mm:ss) est. time remaining. 25% completed, 00:37:27 (hh:mm:ss) est. time remaining. 25% completed, 00:37:21 (hh:mm:ss) est. time remaining. 25% completed, 00:37:17 (hh:mm:ss) est. time remaining. 26% completed, 00:36:56 (hh:mm:ss) est. time remaining. 26% completed, 00:36:50 (hh:mm:ss) est. time remaining. 26% completed, 00:37:06 (hh:mm:ss) est. time remaining. 27% completed, 00:36:46 (hh:mm:ss) est. time remaining. 27% completed, 00:37:14 (hh:mm:ss) est. time remaining. 27% completed, 00:36:54 (hh:mm:ss) est. time remaining. 27% completed, 00:36:52 (hh:mm:ss) est. time remaining. 28% completed, 00:35:24 (hh:mm:ss) est. time remaining. 31% completed, 00:32:44 (hh:mm:ss) est. time remaining. 32% completed, 00:32:05 (hh:mm:ss) est. time remaining. 33% completed, 00:31:24 (hh:mm:ss) est. time remaining. 33% completed, 00:31:10 (hh:mm:ss) est. time remaining. 33% completed, 00:31:35 (hh:mm:ss) est. time remaining. 34% completed, 00:31:22 (hh:mm:ss) est. time remaining. 34% completed, 00:31:41 (hh:mm:ss) est. time remaining. 34% completed, 00:31:26 (hh:mm:ss) est. time remaining. 35% completed, 00:30:36 (hh:mm:ss) est. time remaining. 37% completed, 00:29:04 (hh:mm:ss) est. time remaining. 38% completed, 00:28:49 (hh:mm:ss) est. time remaining. 39% completed, 00:28:43 (hh:mm:ss) est. time remaining. 39% completed, 00:28:42 (hh:mm:ss) est. time remaining. 39% completed, 00:28:30 (hh:mm:ss) est. time remaining. 40% completed, 00:28:22 (hh:mm:ss) est. time remaining. 40% completed, 00:28:18 (hh:mm:ss) est. time remaining. 40% completed, 00:28:13 (hh:mm:ss) est. time remaining. 41% completed, 00:28:08 (hh:mm:ss) est. time remaining. 41% completed, 00:28:04 (hh:mm:ss) est. time remaining. 41% completed, 00:27:53 (hh:mm:ss) est. time remaining. 42% completed, 00:27:20 (hh:mm:ss) est. time remaining. 43% completed, 00:27:42 (hh:mm:ss) est. time remaining. 43% completed, 00:27:35 (hh:mm:ss) est. time remaining. 43% completed, 00:27:25 (hh:mm:ss) est. time remaining. 44% completed, 00:27:33 (hh:mm:ss) est. time remaining. 44% completed, 00:27:44 (hh:mm:ss) est. time remaining. 45% completed, 00:27:12 (hh:mm:ss) est. time remaining. 45% completed, 00:27:07 (hh:mm:ss) est. time remaining. 47% completed, 00:26:33 (hh:mm:ss) est. time remaining. 47% completed, 00:26:21 (hh:mm:ss) est. time remaining. 48% completed, 00:26:30 (hh:mm:ss) est. time remaining. 48% completed, 00:26:07 (hh:mm:ss) est. time remaining. 48% completed, 00:26:01 (hh:mm:ss) est. time remaining. 49% completed, 00:25:39 (hh:mm:ss) est. time remaining. 50% completed, 00:25:43 (hh:mm:ss) est. time remaining. 50% completed, 00:25:39 (hh:mm:ss) est. time remaining. 50% completed, 00:25:38 (hh:mm:ss) est. time remaining. 51% completed, 00:25:17 (hh:mm:ss) est. time remaining. 51% completed, 00:25:08 (hh:mm:ss) est. time remaining. 52% completed, 00:24:26 (hh:mm:ss) est. time remaining. 53% completed, 00:24:14 (hh:mm:ss) est. time remaining. 53% completed, 00:24:08 (hh:mm:ss) est. time remaining. 53% completed, 00:24:03 (hh:mm:ss) est. time remaining. 53% completed, 00:23:55 (hh:mm:ss) est. time remaining. 53% completed, 00:24:01 (hh:mm:ss) est. time remaining. 54% completed, 00:23:38 (hh:mm:ss) est. time remaining. 54% completed, 00:23:34 (hh:mm:ss) est. time remaining. 54% completed, 00:23:30 (hh:mm:ss) est. time remaining. 54% completed, 00:23:22 (hh:mm:ss) est. time remaining. 55% completed, 00:23:17 (hh:mm:ss) est. time remaining. 55% completed, 00:23:13 (hh:mm:ss) est. time remaining. 56% completed, 00:22:33 (hh:mm:ss) est. time remaining. 57% completed, 00:22:08 (hh:mm:ss) est. time remaining. 57% completed, 00:21:54 (hh:mm:ss) est. time remaining. 58% completed, 00:21:40 (hh:mm:ss) est. time remaining. 59% completed, 00:21:25 (hh:mm:ss) est. time remaining. 59% completed, 00:21:17 (hh:mm:ss) est. time remaining. 59% completed, 00:21:15 (hh:mm:ss) est. time remaining. 59% completed, 00:21:11 (hh:mm:ss) est. time remaining. 59% completed, 00:21:10 (hh:mm:ss) est. time remaining. 60% completed, 00:21:16 (hh:mm:ss) est. time remaining. 60% completed, 00:21:09 (hh:mm:ss) est. time remaining. 60% completed, 00:21:05 (hh:mm:ss) est. time remaining. 60% completed, 00:20:59 (hh:mm:ss) est. time remaining. 60% completed, 00:20:55 (hh:mm:ss) est. time remaining. 60% completed, 00:20:47 (hh:mm:ss) est. time remaining. 61% completed, 00:20:43 (hh:mm:ss) est. time remaining. 61% completed, 00:20:50 (hh:mm:ss) est. time remaining. 61% completed, 00:20:41 (hh:mm:ss) est. time remaining. 61% completed, 00:20:36 (hh:mm:ss) est. time remaining. 62% completed, 00:20:17 (hh:mm:ss) est. time remaining. 62% completed, 00:20:23 (hh:mm:ss) est. time remaining. 63% completed, 00:19:58 (hh:mm:ss) est. time remaining. 63% completed, 00:19:54 (hh:mm:ss) est. time remaining. 63% completed, 00:19:52 (hh:mm:ss) est. time remaining. 64% completed, 00:19:35 (hh:mm:ss) est. time remaining. 64% completed, 00:19:14 (hh:mm:ss) est. time remaining. 65% completed, 00:19:08 (hh:mm:ss) est. time remaining. 65% completed, 00:19:12 (hh:mm:ss) est. time remaining. 65% completed, 00:18:41 (hh:mm:ss) est. time remaining. 66% completed, 00:18:19 (hh:mm:ss) est. time remaining. 66% completed, 00:18:04 (hh:mm:ss) est. time remaining. 67% completed, 00:17:59 (hh:mm:ss) est. time remaining. 67% completed, 00:17:30 (hh:mm:ss) est. time remaining. 68% completed, 00:16:54 (hh:mm:ss) est. time remaining. 68% completed, 00:16:50 (hh:mm:ss) est. time remaining. 69% completed, 00:16:47 (hh:mm:ss) est. time remaining. 69% completed, 00:16:43 (hh:mm:ss) est. time remaining. 69% completed, 00:16:39 (hh:mm:ss) est. time remaining. 69% completed, 00:16:36 (hh:mm:ss) est. time remaining. 70% completed, 00:16:06 (hh:mm:ss) est. time remaining. 70% completed, 00:15:46 (hh:mm:ss) est. time remaining. 71% completed, 00:15:07 (hh:mm:ss) est. time remaining. 71% completed, 00:15:06 (hh:mm:ss) est. time remaining. 72% completed, 00:14:31 (hh:mm:ss) est. time remaining. 72% completed, 00:14:26 (hh:mm:ss) est. time remaining. 73% completed, 00:14:26 (hh:mm:ss) est. time remaining. 73% completed, 00:14:18 (hh:mm:ss) est. time remaining. 73% completed, 00:14:17 (hh:mm:ss) est. time remaining. 73% completed, 00:14:12 (hh:mm:ss) est. time remaining. 73% completed, 00:14:09 (hh:mm:ss) est. time remaining. 75% completed, 00:13:20 (hh:mm:ss) est. time remaining. 75% completed, 00:13:08 (hh:mm:ss) est. time remaining. 75% completed, 00:13:03 (hh:mm:ss) est. time remaining. 75% completed, 00:13:00 (hh:mm:ss) est. time remaining. 76% completed, 00:12:15 (hh:mm:ss) est. time remaining. 78% completed, 00:11:30 (hh:mm:ss) est. time remaining. 78% completed, 00:11:09 (hh:mm:ss) est. time remaining. 78% completed, 00:11:04 (hh:mm:ss) est. time remaining. 79% completed, 00:11:01 (hh:mm:ss) est. time remaining. 79% completed, 00:10:45 (hh:mm:ss) est. time remaining. 79% completed, 00:10:43 (hh:mm:ss) est. time remaining. 79% completed, 00:10:40 (hh:mm:ss) est. time remaining. 80% completed, 00:10:38 (hh:mm:ss) est. time remaining. 80% completed, 00:10:34 (hh:mm:ss) est. time remaining. 80% completed, 00:10:31 (hh:mm:ss) est. time remaining. 80% completed, 00:10:12 (hh:mm:ss) est. time remaining. 81% completed, 00:10:10 (hh:mm:ss) est. time remaining. 81% completed, 00:10:06 (hh:mm:ss) est. time remaining. 81% completed, 00:9:50 (hh:mm:ss) est. time remaining. 82% completed, 00:9:14 (hh:mm:ss) est. time remaining. 83% completed, 00:8:56 (hh:mm:ss) est. time remaining. 83% completed, 00:8:42 (hh:mm:ss) est. time remaining. 83% completed, 00:8:39 (hh:mm:ss) est. time remaining. 83% completed, 00:8:36 (hh:mm:ss) est. time remaining. 84% completed, 00:8:17 (hh:mm:ss) est. time remaining. 84% completed, 00:8:14 (hh:mm:ss) est. time remaining. 84% completed, 00:8:11 (hh:mm:ss) est. time remaining. 84% completed, 00:8:01 (hh:mm:ss) est. time remaining. 84% completed, 00:7:59 (hh:mm:ss) est. time remaining. 85% completed, 00:7:57 (hh:mm:ss) est. time remaining. 85% completed, 00:7:55 (hh:mm:ss) est. time remaining. 85% completed, 00:7:26 (hh:mm:ss) est. time remaining. 86% completed, 00:7:14 (hh:mm:ss) est. time remaining. 86% completed, 00:6:53 (hh:mm:ss) est. time remaining. 87% completed, 00:6:38 (hh:mm:ss) est. time remaining. 87% completed, 00:6:30 (hh:mm:ss) est. time remaining. 87% completed, 00:6:27 (hh:mm:ss) est. time remaining. 87% completed, 00:6:25 (hh:mm:ss) est. time remaining. 87% completed, 00:6:24 (hh:mm:ss) est. time remaining. 88% completed, 00:6:23 (hh:mm:ss) est. time remaining. 88% completed, 00:6:20 (hh:mm:ss) est. time remaining. 88% completed, 00:6:07 (hh:mm:ss) est. time remaining. 88% completed, 00:5:59 (hh:mm:ss) est. time remaining. 88% completed, 00:5:56 (hh:mm:ss) est. time remaining. 88% completed, 00:5:54 (hh:mm:ss) est. time remaining. 89% completed, 00:5:35 (hh:mm:ss) est. time remaining. 89% completed, 00:5:33 (hh:mm:ss) est. time remaining. 89% completed, 00:5:31 (hh:mm:ss) est. time remaining. 90% completed, 00:5:13 (hh:mm:ss) est. time remaining. 90% completed, 00:4:56 (hh:mm:ss) est. time remaining. 90% completed, 00:4:54 (hh:mm:ss) est. time remaining. 90% completed, 00:4:52 (hh:mm:ss) est. time remaining. 91% completed, 00:4:33 (hh:mm:ss) est. time remaining. 91% completed, 00:4:25 (hh:mm:ss) est. time remaining. 91% completed, 00:4:22 (hh:mm:ss) est. time remaining. 91% completed, 00:4:20 (hh:mm:ss) est. time remaining. 91% completed, 00:4:18 (hh:mm:ss) est. time remaining. 92% completed, 00:4:03 (hh:mm:ss) est. time remaining. 92% completed, 00:3:51 (hh:mm:ss) est. time remaining. 92% completed, 00:3:49 (hh:mm:ss) est. time remaining. 92% completed, 00:3:47 (hh:mm:ss) est. time remaining. 92% completed, 00:3:45 (hh:mm:ss) est. time remaining. 92% completed, 00:3:43 (hh:mm:ss) est. time remaining. 93% completed, 00:3:41 (hh:mm:ss) est. time remaining. 93% completed, 00:3:39 (hh:mm:ss) est. time remaining. 93% completed, 00:3:37 (hh:mm:ss) est. time remaining. 93% completed, 00:3:35 (hh:mm:ss) est. time remaining. 93% completed, 00:3:15 (hh:mm:ss) est. time remaining. 93% completed, 00:3:10 (hh:mm:ss) est. time remaining. 94% completed, 00:2:57 (hh:mm:ss) est. time remaining. 94% completed, 00:2:46 (hh:mm:ss) est. time remaining. 94% completed, 00:2:38 (hh:mm:ss) est. time remaining. 95% completed, 00:2:36 (hh:mm:ss) est. time remaining. 95% completed, 00:2:25 (hh:mm:ss) est. time remaining. 95% completed, 00:2:23 (hh:mm:ss) est. time remaining. 95% completed, 00:2:17 (hh:mm:ss) est. time remaining. 96% completed, 00:2:00 (hh:mm:ss) est. time remaining. 96% completed, 00:1:58 (hh:mm:ss) est. time remaining. 96% completed, 00:1:57 (hh:mm:ss) est. time remaining. 96% completed, 00:1:45 (hh:mm:ss) est. time remaining. 96% completed, 00:1:44 (hh:mm:ss) est. time remaining. 97% completed, 00:1:26 (hh:mm:ss) est. time remaining. 97% completed, 00:1:22 (hh:mm:ss) est. time remaining. 97% completed, 00:1:10 (hh:mm:ss) est. time remaining. 97% completed, 00:1:02 (hh:mm:ss) est. time remaining. 98% completed, 00:0:57 (hh:mm:ss) est. time remaining. 98% completed, 00:0:54 (hh:mm:ss) est. time remaining. 98% completed, 00:0:51 (hh:mm:ss) est. time remaining. 98% completed, 00:0:49 (hh:mm:ss) est. time remaining. 98% completed, 00:0:44 (hh:mm:ss) est. time remaining. 98% completed, 00:0:39 (hh:mm:ss) est. time remaining. 98% completed, 00:0:35 (hh:mm:ss) est. time remaining. 99% completed, 00:0:29 (hh:mm:ss) est. time remaining. 99% completed, 00:0:28 (hh:mm:ss) est. time remaining. 99% completed, 00:0:27 (hh:mm:ss) est. time remaining. 99% completed, 00:0:27 (hh:mm:ss) est. time remaining. 99% completed, 00:0:26 (hh:mm:ss) est. time remaining. 99% completed, 00:0:19 (hh:mm:ss) est. time remaining. 99% completed, 00:0:18 (hh:mm:ss) est. time remaining. 99% completed, 00:0:18 (hh:mm:ss) est. time remaining. 99% completed, 00:0:17 (hh:mm:ss) est. time remaining. 99% completed, 00:0:13 (hh:mm:ss) est. time remaining. 99% completed, 00:0:09 (hh:mm:ss) est. time remaining. 99% completed, 00:0:09 (hh:mm:ss) est. time remaining. 99% completed, 00:0:08 (hh:mm:ss) est. time remaining. 99% completed, 00:0:07 (hh:mm:ss) est. time remaining. 99% completed, 00:0:07 (hh:mm:ss) est. time remaining. 99% completed, 00:0:06 (hh:mm:ss) est. time remaining. 99% completed, 00:0:03 (hh:mm:ss) est. time remaining. 99% completed, 00:0:02 (hh:mm:ss) est. time remaining. 99% completed, 00:0:02 (hh:mm:ss) est. time remaining. 99% completed, 00:0:01 (hh:mm:ss) est. time remaining. 99% completed, 00:0:01 (hh:mm:ss) est. time remaining. 99% completed, 00:0:01 (hh:mm:ss) est. time remaining. 99% completed, 00:0:01 (hh:mm:ss) est. time remaining. 99% completed, 00:0:01 (hh:mm:ss) est. time remaining. 99% completed, 00:0:01 (hh:mm:ss) est. time remaining. 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 100% completed, 00:0:00 (hh:mm:ss) est. time remaining. Comparison Time: 00:52:11 (hh:mm:ss) Elapsed Time, 512525 HSPs Collected
  • RECON: Running imagespread.. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time
  • RECON: Running initial definition of elements ( eledef ).. RECON Elapsed: 00:01:01 (hh:mm:ss) Elapsed Time
  • RECON: Running re-definition of elements ( eleredef ).. RECON Elapsed: 00:04:10 (hh:mm:ss) Elapsed Time
  • RECON: Running re-definition of edges ( edgeredef ).. RECON Elapsed: 00:03:54 (hh:mm:ss) Elapsed Time
  • RECON: Running family definition ( famdef ).. RECON Elapsed: 00:00:02 (hh:mm:ss) Elapsed Time
  • Obtaining element sequences Number of families returned by RECON: 634 Processing families with greater than 15 elements Instance Gathering: 00:00:01 (hh:mm:ss) Elapsed Time Refining 15 families Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-253.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-87.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-51.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-20.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-22.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-41.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-27.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-74.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-19.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-26.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-133.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-89.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-319.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-43.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-2/family-63.fa. Family Refinement: 00:33:32 (hh:mm:ss) Elapsed Time Round Time: 01:35:42 (hh:mm:ss) Elapsed Time : 0 families discovered.
  • Increasing sample size to include end piece now = 34298302

RepeatModeler Round # 3

Searching for Repeats -- Sampling from the database...

  • Gathering up to 34298302 bp
  • Sequence extraction : 00:00:00 (hh:mm:ss) Elapsed Time -- Running TRFMask on the sequence... 372 Tandem Repeats Masked
  • TRFMask time 00:00:10 (hh:mm:ss) Elapsed Time -- Sample Stats: Sample Size 4267842 bp Num Contigs Represented = 338 Non ambiguous bp: Initial: 4254175 bp After Masking: 4232204 bp Masked: 0.52 % -- Input Database Coverage: 14298118 bp out of 14298302 bp ( 100.00 % ) Sampling Time: 00:00:11 (hh:mm:ss) Elapsed Time Running all-by-other comparisons...
  • Total Comparisons = 82621 0% completed, 00:10:07 (hh:mm:ss) est. time remaining. 1% completed, 00:15:01 (hh:mm:ss) est. time remaining. 4% completed, 00:12:04 (hh:mm:ss) est. time remaining. 5% completed, 00:11:13 (hh:mm:ss) est. time remaining. 5% completed, 00:10:47 (hh:mm:ss) est. time remaining. 6% completed, 00:13:09 (hh:mm:ss) est. time remaining. 9% completed, 00:10:07 (hh:mm:ss) est. time remaining. 14% completed, 00:7:16 (hh:mm:ss) est. time remaining. 15% completed, 00:7:00 (hh:mm:ss) est. time remaining. 19% completed, 00:7:10 (hh:mm:ss) est. time remaining. 21% completed, 00:7:07 (hh:mm:ss) est. time remaining. 24% completed, 00:7:39 (hh:mm:ss) est. time remaining. 26% completed, 00:7:09 (hh:mm:ss) est. time remaining. 26% completed, 00:7:06 (hh:mm:ss) est. time remaining. 27% completed, 00:7:05 (hh:mm:ss) est. time remaining. 29% completed, 00:6:35 (hh:mm:ss) est. time remaining. 29% completed, 00:6:30 (hh:mm:ss) est. time remaining. 30% completed, 00:6:41 (hh:mm:ss) est. time remaining. 33% completed, 00:6:13 (hh:mm:ss) est. time remaining. 35% completed, 00:5:57 (hh:mm:ss) est. time remaining. 38% completed, 00:5:45 (hh:mm:ss) est. time remaining. 40% completed, 00:5:26 (hh:mm:ss) est. time remaining. 43% completed, 00:5:10 (hh:mm:ss) est. time remaining. 46% completed, 00:4:51 (hh:mm:ss) est. time remaining. 46% completed, 00:4:48 (hh:mm:ss) est. time remaining. 46% completed, 00:4:57 (hh:mm:ss) est. time remaining. 47% completed, 00:4:55 (hh:mm:ss) est. time remaining. 48% completed, 00:4:46 (hh:mm:ss) est. time remaining. 48% completed, 00:4:43 (hh:mm:ss) est. time remaining. 50% completed, 00:4:45 (hh:mm:ss) est. time remaining. 50% completed, 00:4:44 (hh:mm:ss) est. time remaining. 53% completed, 00:4:22 (hh:mm:ss) est. time remaining. 54% completed, 00:4:15 (hh:mm:ss) est. time remaining. 54% completed, 00:4:12 (hh:mm:ss) est. time remaining. 54% completed, 00:4:10 (hh:mm:ss) est. time remaining. 56% completed, 00:4:01 (hh:mm:ss) est. time remaining. 57% completed, 00:3:58 (hh:mm:ss) est. time remaining. 57% completed, 00:4:03 (hh:mm:ss) est. time remaining. 57% completed, 00:4:00 (hh:mm:ss) est. time remaining. 57% completed, 00:3:59 (hh:mm:ss) est. time remaining. 58% completed, 00:3:58 (hh:mm:ss) est. time remaining. 59% completed, 00:3:50 (hh:mm:ss) est. time remaining. 59% completed, 00:3:49 (hh:mm:ss) est. time remaining. 64% completed, 00:3:13 (hh:mm:ss) est. time remaining. 64% completed, 00:3:11 (hh:mm:ss) est. time remaining. 65% completed, 00:3:06 (hh:mm:ss) est. time remaining. 66% completed, 00:3:00 (hh:mm:ss) est. time remaining. 67% completed, 00:2:55 (hh:mm:ss) est. time remaining. 67% completed, 00:2:53 (hh:mm:ss) est. time remaining. 68% completed, 00:2:55 (hh:mm:ss) est. time remaining. 68% completed, 00:2:51 (hh:mm:ss) est. time remaining. 69% completed, 00:2:49 (hh:mm:ss) est. time remaining. 69% completed, 00:2:48 (hh:mm:ss) est. time remaining. 72% completed, 00:2:35 (hh:mm:ss) est. time remaining. 72% completed, 00:2:30 (hh:mm:ss) est. time remaining. 73% completed, 00:2:26 (hh:mm:ss) est. time remaining. 73% completed, 00:2:25 (hh:mm:ss) est. time remaining. 74% completed, 00:2:23 (hh:mm:ss) est. time remaining. 74% completed, 00:2:23 (hh:mm:ss) est. time remaining. 75% completed, 00:2:19 (hh:mm:ss) est. time remaining. 76% completed, 00:2:13 (hh:mm:ss) est. time remaining. 78% completed, 00:1:58 (hh:mm:ss) est. time remaining. 78% completed, 00:1:57 (hh:mm:ss) est. time remaining. 78% completed, 00:1:56 (hh:mm:ss) est. time remaining. 80% completed, 00:1:48 (hh:mm:ss) est. time remaining. 81% completed, 00:1:42 (hh:mm:ss) est. time remaining. 81% completed, 00:1:41 (hh:mm:ss) est. time remaining. 83% completed, 00:1:32 (hh:mm:ss) est. time remaining. 83% completed, 00:1:31 (hh:mm:ss) est. time remaining. 83% completed, 00:1:30 (hh:mm:ss) est. time remaining. 84% completed, 00:1:29 (hh:mm:ss) est. time remaining. 84% completed, 00:1:25 (hh:mm:ss) est. time remaining. 87% completed, 00:1:14 (hh:mm:ss) est. time remaining. 88% completed, 00:1:09 (hh:mm:ss) est. time remaining. 88% completed, 00:1:09 (hh:mm:ss) est. time remaining. 88% completed, 00:1:05 (hh:mm:ss) est. time remaining. 89% completed, 00:1:04 (hh:mm:ss) est. time remaining. 89% completed, 00:1:03 (hh:mm:ss) est. time remaining. 89% completed, 00:1:02 (hh:mm:ss) est. time remaining. 89% completed, 00:1:02 (hh:mm:ss) est. time remaining. 89% completed, 00:1:01 (hh:mm:ss) est. time remaining. 89% completed, 00:1:00 (hh:mm:ss) est. time remaining. 90% completed, 00:0:56 (hh:mm:ss) est. time remaining. 90% completed, 00:0:55 (hh:mm:ss) est. time remaining. 91% completed, 00:0:52 (hh:mm:ss) est. time remaining. 92% completed, 00:0:46 (hh:mm:ss) est. time remaining. 93% completed, 00:0:41 (hh:mm:ss) est. time remaining. 93% completed, 00:0:37 (hh:mm:ss) est. time remaining. 94% completed, 00:0:32 (hh:mm:ss) est. time remaining. 94% completed, 00:0:32 (hh:mm:ss) est. time remaining. 95% completed, 00:0:28 (hh:mm:ss) est. time remaining. 96% completed, 00:0:22 (hh:mm:ss) est. time remaining. 96% completed, 00:0:18 (hh:mm:ss) est. time remaining. 97% completed, 00:0:13 (hh:mm:ss) est. time remaining. 97% completed, 00:0:13 (hh:mm:ss) est. time remaining. 97% completed, 00:0:12 (hh:mm:ss) est. time remaining. 97% completed, 00:0:12 (hh:mm:ss) est. time remaining. 98% completed, 00:0:10 (hh:mm:ss) est. time remaining. 98% completed, 00:0:08 (hh:mm:ss) est. time remaining. 98% completed, 00:0:08 (hh:mm:ss) est. time remaining. 98% completed, 00:0:07 (hh:mm:ss) est. time remaining. 99% completed, 00:0:05 (hh:mm:ss) est. time remaining. 99% completed, 00:0:05 (hh:mm:ss) est. time remaining. 99% completed, 00:0:04 (hh:mm:ss) est. time remaining. 99% completed, 00:0:02 (hh:mm:ss) est. time remaining. 99% completed, 00:0:01 (hh:mm:ss) est. time remaining. 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 99% completed, 00:0:00 (hh:mm:ss) est. time remaining. 100% completed, 00:0:00 (hh:mm:ss) est. time remaining. Comparison Time: 00:10:15 (hh:mm:ss) Elapsed Time, 125632 HSPs Collected
  • RECON: Running imagespread.. RECON Elapsed: 00:00:00 (hh:mm:ss) Elapsed Time
  • RECON: Running initial definition of elements ( eledef ).. RECON Elapsed: 00:00:14 (hh:mm:ss) Elapsed Time
  • RECON: Running re-definition of elements ( eleredef ).. RECON Elapsed: 00:00:50 (hh:mm:ss) Elapsed Time
  • RECON: Running re-definition of edges ( edgeredef ).. RECON Elapsed: 00:01:11 (hh:mm:ss) Elapsed Time
  • RECON: Running family definition ( famdef ).. RECON Elapsed: 00:00:01 (hh:mm:ss) Elapsed Time
  • Obtaining element sequences Number of families returned by RECON: 237 Processing families with greater than 15 elements Instance Gathering: 00:00:00 (hh:mm:ss) Elapsed Time Refining 5 families Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-3/family-10.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-3/family-14.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-3/family-27.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-3/family-3.fa. WARNING: Refiner did not return a consensus for /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/round-3/family-45.fa. Family Refinement: 00:34:43 (hh:mm:ss) Elapsed Time Round Time: 00:47:33 (hh:mm:ss) Elapsed Time : 0 families discovered.

RepeatScout/RECON discovery complete: 0 families found

LTR Structural Analysis

Running LtrHarvest... : 00:00:09 (hh:mm:ss) Elapsed Time Running Ltr_retriever...LTR_retriever failed to generate a file. Please check /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023/LTR_453025.SunOct221728322023/LRET_453025.SunOct221728412023/LTR_retriever.log for details. at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/LTRPipeline line 693. LTRPipeline Time: 00:00:10 (hh:mm:ss) Elapsed Time

Program Time: 02:48:18 (hh:mm:ss) Elapsed Time Working directory: /work/users/t/a/taniak/Annotation/RM_345954.SunOct221440222023 may be deleted unless there were problems with the run. No families identified. Perhaps the database is too small or contains overly fragmented sequences.

tania-k avatar Oct 23 '23 17:10 tania-k

Sorry for the delay. Are you still having this problem? The issue appears to be with the installation of RepeatMasker. The function referenced in the error was introduced in RepeatMasker 4.1.4. It appears from the startup log you are using RepeatMasker 4.1.5 so that shouldn't a problem. However, I do find it a bit strange the the error message refers to a conda installation in your .conda directory. I wonder if you have more than one RepeatModeler installation this cluster?:

Can't locate object method "setThreadByQuery" via package "NCBIBlastSearchEngine" at /nas/longleaf/home/taniak/.conda/envs/RepeatModeler/Refiner line 602.

That shouldn't be a problem but I wonder if something is referencing an older RepeatMasker installation incorrectly. As an aside I rarely see Conda installations that work. I would recommend installing these programs outside of conda to avoid that as an issue.

rmhubley avatar Nov 28 '23 01:11 rmhubley