(base) [dengcl.life@login02 text]$TEsorter-test
Running the following command: TEsorter /gpfs1/home/life/dengcl/anaconda3/lib/python3.9/site-packages/TEsorter/test/rice6.9.5.liban
2022-03-02 10:30:36,340 -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
2022-03-02 10:30:36,490 -INFO- VARS: {'sequence': '/gpfs1/home/life/dengcl/anaconda3/lib/python3.9/site-packages/TEsorter/test/rice6.9.5.liban', 'hmm_database': 'rexdb', 'seq_type': 'nucl', 'prefix': 'rice6.9.5.liban.rexdb', 'force_write_hmmscan': False, 'processors': 4, 'tmp_dir': './tmp', 'min_coverage': 20, 'max_evalue': 0.001, 'disable_pass2': False, 'pass2_rule': '80-80-80', 'no_library': False, 'no_reverse': False, 'no_cleanup': False, 'p2_identity': 80.0, 'p2_coverage': 80.0, 'p2_length': 80.0}
2022-03-02 10:30:36,490 -INFO- checking dependencies:
2022-03-02 10:30:36,659 -INFO- hmmer	3.3.2	OK
2022-03-02 10:30:44,756 -INFO- blastn	2.12.0+	OK
2022-03-02 10:30:44,757 -INFO- check database rexdb
2022-03-02 10:30:44,758 -INFO- db path: /gpfs1/home/life/dengcl/anaconda3/lib/python3.9/site-packages/TEsorter/database
2022-03-02 10:30:44,758 -INFO- db file: REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm
2022-03-02 10:30:44,774 -INFO- REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm	OK
2022-03-02 10:30:44,774 -INFO- Start classifying pipeline
2022-03-02 10:30:45,932 -INFO- total 2431 sequences
2022-03-02 10:30:45,932 -INFO- translating `/gpfs1/home/life/dengcl/anaconda3/lib/python3.9/site-packages/TEsorter/test/rice6.9.5.liban` in six frames
/gpfs1/home/life/dengcl/anaconda3/lib/python3.9/site-packages/Bio/Seq.py:2334: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.
  warnings.warn(
2022-03-02 10:30:52,655 -INFO- HMM scanning against `/gpfs1/home/life/dengcl/anaconda3/lib/python3.9/site-packages/TEsorter/database/REXdb_protein_database_viridiplantae_v3.0_plus_metazoa_v3.hmm`
2022-03-02 10:30:53,067 -INFO- Creating server instance (pp-1.6.4.4)
2022-03-02 10:30:53,067 -INFO- Running on Python 3.9.7 linux
2022-03-02 10:30:53,491 -INFO- pp local server started with 4 workers
2022-03-02 10:30:53,516 -INFO- Task 0 started
2022-03-02 10:30:53,517 -INFO- Task 1 started
2022-03-02 10:30:53,517 -INFO- Task 2 started
2022-03-02 10:30:53,517 -INFO- Task 3 started
2022-03-02 10:31:51,008 -INFO- generating gene anntations
2022-03-02 10:31:51,955 -INFO- 569 sequences classified by HMM
2022-03-02 10:31:51,955 -INFO- see protein domain sequences in `rice6.9.5.liban.rexdb.dom.faa` and annotation gff3 file in `rice6.9.5.liban.rexdb.dom.gff3`
2022-03-02 10:31:51,955 -INFO- classifying the unclassified sequences by searching against the classified ones
2022-03-02 10:31:52,367 -INFO- using the 80-80-80 rule
2022-03-02 10:31:52,367 -INFO- run CMD: `makeblastdb -in ./tmp/pass1_classified.fa -dbtype nucl`
2022-03-02 10:31:55,131 -INFO- run CMD: `blastn -query ./tmp/pass1_unclassified.fa -db ./tmp/pass1_classified.fa -out ./tmp/pass1_unclassified.fa.blastout -outfmt '6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen qcovs qcovhsp sstrand' -num_threads 4`
2022-03-02 10:31:58,924 -INFO- 15 sequences classified in pass 2
2022-03-02 10:31:58,925 -INFO- total 584 sequences classified.
2022-03-02 10:31:58,925 -INFO- see classified sequences in `rice6.9.5.liban.rexdb.cls.tsv`
2022-03-02 10:31:58,925 -INFO- writing library for RepeatMasker in `rice6.9.5.liban.rexdb.cls.lib`
2022-03-02 10:31:59,102 -INFO- writing classified protein domains in `rice6.9.5.liban.rexdb.cls.pep`
2022-03-02 10:31:59,195 -INFO- Summary of classifications:
Order           Superfamily      # of Sequences# of Clade Sequences    # of Clades# of full Domains
LTR             Copia                       143            143              8            106
LTR             Gypsy                       189            187              7            136
pararetrovirus  unknown                       4              0              0              0
LINE            unknown                      46              0              0              0
TIR             EnSpm_CACTA                  25              0              0              0
TIR             MuDR_Mutator                 80              0              0              0
TIR             PIF_Harbinger                34              0              0              0
TIR             Tc1_Mariner                  17              0              0              0
TIR             hAT                          25              0              0              0
Helitron        unknown                      19              0              0              0
mixture         mixture                       2              0              0              0
2022-03-02 10:31:59,196 -INFO- Pipeline done.
2022-03-02 10:31:59,196 -INFO- cleaning the temporary directory ./tmp