(tesorter) msmith@n24-64-384-faith:~/scratch/rasps$ TEsorter-test
Running the following command: TEsorter /mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/test/rice6.9.5.liban
2025-04-17 09:46:10,055 -WARNING- Grid computing is not available because DRMAA not configured properly: Could not find drmaa library.  Please specify its full path using the environment variable DRMAA_LIBRARY_PATH
2025-04-17 09:46:10,055 -INFO- No DRMAA (see https://github.com/pygridtools/drmaa-python), Switching to local mode.
2025-04-17 09:46:10,069 -INFO- Command: /mnt/apps/users/msmith/conda/envs/tesorter/bin/TEsorter /mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/test/rice6.9.5.liban
2025-04-17 09:46:10,069 -INFO- Version: 1.4.7
2025-04-17 09:46:10,069 -INFO- VARS: {'sequence': '/mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/test/rice6.9.5.liban', 'hmm_database': 'rexdb', 'db_hmm': None, 'seq_type': 'nucl', 'prefix': None, 'force_write_hmmscan': False, 'processors': 4, 'tmp_dir': './tmp-68fb86ae-1b68-11f0-b95f-043201d8d740', 'min_coverage': 20, 'max_evalue': 0.001, 'min_probability': 0.5, 'min_score': 0.1, 'mask': None, 'no_cleanup': False, 'citation': False, 'disable_pass2': False, 'pass2_rule': '80-80-80', 'no_library': False, 'no_reverse': False, 'genome': False, 'win_size': 270000, 'win_ovl': 30000, 'p2_identity': 80.0, 'p2_coverage': 80.0, 'p2_length': 80.0}
2025-04-17 09:46:10,069 -INFO- checking dependencies:
2025-04-17 09:46:10,078 -INFO- hmmer    3.4     OK
2025-04-17 09:46:10,154 -INFO- blastn   2.14.1+ OK
2025-04-17 09:46:10,156 -INFO- check database /mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/database/REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm
2025-04-17 09:46:10,156 -INFO- db file: /mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/database/REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm
2025-04-17 09:46:10,156 -INFO- REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm    OK
2025-04-17 09:46:10,156 -INFO- Start classifying pipeline (ELEMENT mode)
2025-04-17 09:46:10,185 -INFO- total 2431 sequences
2025-04-17 09:46:10,202 -INFO- HMM scanning against `/mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/database/REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm`
Traceback (most recent call last):
  File "/mnt/apps/users/msmith/conda/envs/tesorter/bin/TEsorter", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "/mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/app.py", line 1265, in main
    pipeline(Args())
    ~~~~~~~~^^^^^^^^
  File "/mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/app.py", line 257, in pipeline
    gff, geneSeq = LTRlibAnn(
                   ~~~~~~~~~^
                ltrlib = args.sequence,
      ^^^^^^^^^^^^^^^^^^^^^^^
                seqtype = seq_type,
      ^^^^^^^^^^^^^^^^^^^
                **kargs
      ^^^^^^^
                )
      ^
  File "/mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/app.py", line 1165, in LTRlibAnn
    chunk_files = hmmscan_pp(ltrlib, hmmdb=hmmdb, hmmout=domtbl, tmpdir=tmpdir,
                processors=processors, bin=bin, seqtype=seqtype, force_write_hmmscan=force_write_hmmscan)
  File "/mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/app.py", line 1111, in hmmscan_pp
    _, _, _, chunk_files = split_fastx_by_chunk_num(
                           ~~~~~~~~~~~~~~~~~~~~~~~~^
        inSeq, prefix=chunk_prefix, chunk_num=chunk_num, seqfmt='fasta', suffix='')
     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/apps/users/msmith/conda/envs/tesorter/lib/python3.13/site-packages/TEsorter/modules/split_records.py", line 201, in split_fastx_by_chunk_num
    exec('%s.write(rc)' % (hname, ))
    ~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<string>", line 1, in <module>
NameError: name 'f1' is not defined