I am trying to run RepeatExplorer2 on some NGS paired-end reads. I followed the protocol for sampling the reads and uploaded them to Galaxy. Upon running RepeatExplorer2 on these sampled paired-end NGS reads, I got the following error which looks like something to do with the Galaxy servers? Please let me know how I can go about troubleshooting this.
edit: As a note, I have had success running RepeatExplorer in the past (earlier this year), so i believe I am following the instructions appropriately.
Thanks!
2024-06-28 19:45:16,206 - __main__ - INFO -
--------------------------------------------------------------------------
PIPELINE VERSION : version of pipeline is not available!
PROTEIN DATABASE VERSION : protein_database_viridiplantae_v3.0.fasta
md5 checksum : a36362f4e8b024f1ce97589aac1e6f1a
DNA DATABASE VERSION : dna_database_masked.fasta
md5 checksum : 86bab7cdd3e70374cd756de13680240d
--------------------------------------------------------------------------
2024-06-28 19:45:19,128 - __main__ - INFO -
Namespace(assembly_min=5, automatic_filtering=False, cleanup=True, cpu=10, database=None, domain_search='BLASTX_W3', keep_names=False, logfile=<_io.TextIOWrapper name='/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/staging/11186/outputs/dataset_a144f903-5398-4964-92db-0bb97816e63e.dat' mode='w' encoding='UTF-8'>, max_memory=4096000, 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 0x148e7ab2a160>}, 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 0x148e7ab2a0d0>}, 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 0x148e7ab2a1f0>})), output_dir='tarean_output', paired=True, prefix_length=0, sample=0, sequences=<_io.TextIOWrapper name='/storage/brno11-elixir/home/galaxyelixir/pulsar-re/files/staging/11186/inputs/dataset_cec4c4fd-5047-446d-9d38-ae52ad76ee88.dat' mode='r' encoding='UTF-8'>, tarean_mode=False, taxon='VIRIDIPLANTAE3.0')
2024-06-28 19:45:19,128 - __main__ - INFO -
creating directory structure
2024-06-28 19:45:19,156 - __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
connection to Rserve refused, server is probably already down
STDERR CONTENT:
fatal: detected dubious ownership in repository at '/opt/repex_tarean'
To add an exception for this directory, call:
git config --global --add safe.directory /opt/repex_tarean
Traceback (most recent call last):
File "/usr/local/bin/seqclust", line 820, in <module>
main()
File "/usr/local/bin/seqclust", line 655, in main
run_info = DataInfo(args, paths)
File "/usr/local/bin/seqclust", line 198, in __init__
self.number_of_input_sequences = seqtools.SequenceSet.fasta_length(
File "/opt/repex_tarean/lib/seqtools.py", line 785, in fasta_length
for i in f:
File "/usr/lib/python3.8/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte