run RepeatExplorer2 clustering on genome file encountered error

[tf s]

Hi,

I wanted to cluster a genome file using the RepeatExplorer2 clustering tool, but I encountered the following error. What should I do? Thanks for your attention.

2022-12-12 13:38:07,104 - main - INFO -

PIPELINE VERSION : version: 0.3.8.1-466(f549307) branch: devel

PROTEIN DATABASE VERSION : protein_database_viridiplantae_v3.0.fasta
md5 checksum : a36362f4e8b024f1ce97589aac1e6f1a

DNA DATABASE VERSION : dna_database_masked.fasta

md5 checksum : 86bab7cdd3e70374cd756de13680240d

2022-12-12 13:38:10,252 - main - INFO -
Namespace(assembly_min=5, automatic_filtering=False, cleanup=True, cpu=4, database=None, domain_search='BLASTX_W3', keep_names=False, logfile=<_io.TextIOWrapper name='/storage/brno11-elixir/home/galaxyelixir/galaxy/database/files/000/777/dataset_777583.dat' mode='w' encoding='UTF-8'>, max_memory=4000000, merge_threshold=0, min_lcov=55, mincl=0.01, options=Options(name='illumina', database='blastdb_legacy', all2all_search_params='mgblast -p 75 -W18 -UT -X40 -KT -JF -F "m D" -v100000000 -b100000000 -D4 -C 30 -H 30 -i {query} -d {blastdb}', filtering_threshold=FilteringThreshold(min_lcov=55, min_pid=90, min_ovl=0, min_scov=0, evalue=1), filter_self_hits=False, legacy_database=True, lastdb=False, annotation_search_params=AnnotationParams(blastn={'args': ' -task blastn -num_alignments 1 -evalue 0.01 ', 'output_columns': 'qseqid sseqid qlen slen length ppos bitscore', 'column_types': [<class 'str'>, <class 'str'>, <class 'float'>, <class 'float'>, <class 'float'>, <class 'float'>, <class 'float'>], 'program': 'blastn', 'filter_function': <function <lambda> at 0x151b80316b00>}, blastx={'args': ' -num_alignments 1 -word_size 3 -evalue 0.01 ', 'output_columns': 'qseqid sseqid qlen slen length ppos bitscore', 'column_types': [<class 'str'>, <class 'str'>, <class 'float'>, <class 'float'>, <class 'float'>, <class 'float'>, <class 'float'>], 'program': 'blastx', 'filter_function': <function <lambda> at 0x151b80316a70>}, blastn_trna={'args': ' -task blastn -num_alignments 1 -word_size 7', 'output_columns': 'qseqid sseqid qlen slen length ppos bitscore', 'column_types': [<class 'str'>, <class 'str'>, <class 'float'>, <class 'float'>, <class 'float'>, <class 'float'>, <class 'float'>], 'program': 'blastn', 'filter_function': <function <lambda> at 0x151b80316b90>})), output_dir='tarean_output', paired=False, prefix_length=0, sample=0, sequences=<_io.TextIOWrapper name='/storage/brno11-elixir/home/galaxyelixir/galaxy/database/files/000/777/dataset_777469.dat' mode='r' encoding='UTF-8'>, tarean_mode=False, taxon='VIRIDIPLANTAE3.0')

2022-12-12 13:38:10,252 - main - INFO -
creating directory structure

2022-12-12 13:38:10,254 - main - INFO -
getting information about input sequences

STDOUT CONTENT:
Rserv started in daemon mode.
Trying to start Rserve...
connection OK
R function loaded: add_preamble capitalize connect_to_databases create_main_reports df2html disconnect_database dummy_function get_comparative_codes is_comparative nested2named_list plot_rect_map preformatted rectMap reformat4html reformat_df_report reformat_df_to_profrep_classification reformat_header start_html summary_histogram
R function loaded: add_leaves_value add_preamble add_value_to_nodes annot2colors cluster_annotation common_ancestor connect_to_databases containLTR create_all_superclusters_report create_cluster_report create_single_supercluster_report df2html disconnect_database evaluate_LTR_detection filter_tree filter_tree2 find_best_hit find_best_hit_repeat formatWidth format_clinfo format_tree get_annotation_groups get_cluster_annotation_summary get_cluster_comparative_counts get_cluster_connection_info get_cluster_info get_comparative_codes get_ltr_info get_reads_annotation get_supercluster_graph get_supercluster_info get_supercluster_summary get_tarean_info html_insert_floating_image html_insert_image is_comparative make_final_annotation_template nested2named_list pasteDomains pieScatter plot_edges plot_rect_map plot_supercluster plotg preformatted radius_size read_annotation_to_tree rectMap rescale select_reads_id start_html summarize_annotation summary_histogram supercluster_size trmap
Shutting down Rserv...Done
STDERR CONTENT:
fatal: not a git repository (or any parent up to mount point /auto/brno11-elixir)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
/storage/brno11-elixir/home/galaxyelixir/files_test/tools_dependecy_dir/_cache/11e3bde0/lib/python3.7/site-packages/pyRserve/rparser.py:336: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead
dtype=numpyMap[lexeme.rTypeCode])
Traceback (most recent call last):
File "/storage/brno11-elixir/home/galaxyelixir/files_test/tools_dependecy_dir/repex_tarean/2.3.8.1/petr-novak/package_repex_tarean_2_3_8_1/b876ecefd6d8/seqclust", line 821, in <module>
main()
File "/storage/brno11-elixir/home/galaxyelixir/files_test/tools_dependecy_dir/repex_tarean/2.3.8.1/petr-novak/package_repex_tarean_2_3_8_1/b876ecefd6d8/seqclust", line 656, in main
run_info = DataInfo(args, paths)
File "/storage/brno11-elixir/home/galaxyelixir/files_test/tools_dependecy_dir/repex_tarean/2.3.8.1/petr-novak/package_repex_tarean_2_3_8_1/b876ecefd6d8/seqclust", line 220, in init
config.MINIMUM_NUMBER_OF_INPUT_SEQUENCES))
main.WrongInputDataError: provide more sequences for clustering, minumum 1000 is .required
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
File "/auto/brno11-elixir/home/galaxyelixir/files_test/tools_dependecy_dir/repex_tarean/2.3.8.1/petr-novak/package_repex_tarean_2_3_8_1/b876ecefd6d8/lib/r2py.py", line 11, in shutdown
conn = pyRserve.connect(port=port)
File "/storage/brno11-elixir/home/galaxyelixir/files_test/tools_dependecy_dir/_cache/11e3bde0/lib/python3.7/site-packages/pyRserve/rconn.py", line 70, in connect
return RConnector(host, port, atomicArray, defaultVoid, oobCallback)
File "/storage/brno11-elixir/home/galaxyelixir/files_test/tools_dependecy_dir/_cache/11e3bde0/lib/python3.7/site-packages/pyRserve/rconn.py", line 103, in init
self.connect()
File "/storage/brno11-elixir/home/galaxyelixir/files_test/tools_dependecy_dir/_cache/11e3bde0/lib/python3.7/site-packages/pyRserve/rconn.py", line 122, in connect
hdr = self.sock.recv(1024)
ConnectionResetError: [Errno 104] Connection reset by peer