error_in _running_RepeatModeler

Question

[manaswiniparija3]

I was running RepeatModeler and got the error as follows :

RepeatModeler  -engine ncbi -database GCA_902806645.1_cgigas_uk_roslin_v1_genomic
RepeatModeler Version open-1.0.8
================================
Search Engine = ncbi
Database = GCA_902806645.1_cgigas_uk_roslin_v1_genomic .
  - Sequences = 236
  - Bases = 647887097
Using output directory = /mnt/g/manaswini/transib_ancenstry/18th_april_2023_rag2/mollusca/Crassostrea gigas/repeat_modler/RM_2100.TueApr181550582023


RepeatModeler Round # 1
========================
Searching for Repeats
 -- Sampling from the database...
   - Gathering up to 40000000 bp
   - Final Sample Size = 40004654 bp ( 40003327 non ambiguous )
   - Num Contigs Represented = 76
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14 )..
Could not open sequence file /mnt/g/manaswini/transib_ancenstry/18th_april_2023_rag2/mollusca/Crassostrea
build_lmer_table failed. Exit code 256

I used the tool previously also but never got these type of error. unable to identify where I am doing it wrong. can anyone suggest me what should I do ???

[GenoMax]

Try removing the space in the directory name here --> Crassostrea gigas/ looks like the program is not able to handle that.

[manaswiniparija3]

i tried then i went one step forward and stopped

Storage Throughput = fair ( 544.35 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:
      /mnt/g/manaswini/repeat_modler/RM_25029.WedApr190950472023/
      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 = 40015601 bp ( 40014624 non ambiguous )
   - Num Contigs Represented = 78
   - Sequence extraction : 00:01:13 (hh:mm:ss) Elapsed Time
 -- Running RepeatScout on the sequences...
   - RepeatScout: Running build_lmer_table ( l = 14 )..
   - RepeatScout: Running RepeatScout.. : 2404 raw families identified
   - RepeatScout: Running filtering stage.. 2187 families remaining
   - RepeatScout: 00:17:33 (hh:mm:ss) Elapsed Time
cp: failed to clone '/mnt/g/manaswini/repeat_modler/RM_25029.WedApr190950472023/round-1/consensi.fa' from '/mnt/g/manaswini/repeat_modler/RM_25029.WedApr190950472023/round-1/sampleDB-1.fa.rscons.filtered': Inappropriate ioctl for device
NCBIBlastSearchEngine::search: Error...compressed subject database (/mnt/g/manaswini/repeat_modler/RM_25029.WedApr190950472023/round-1/consensi.fa) does not exist!
 at /home/neelesh/anaconda3/envs/EDTA/bin/RepeatModeler line 2340.