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mehrdadbakhtiari / adVNTR

A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data
http://advntr.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
39 stars 15 forks source link

Error with genotype #51

Open R-Laksh opened 2 years ago

R-Laksh commented 2 years ago

Hi,

I've been trying to follow the quickstart guide to test adVNTR using the sample data provided. However, the following error keeps occuring

Using Theano backend. WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions. Traceback (most recent call last): File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/bin/advntr", line 11, in sys.exit(main()) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/main.py", line 134, in main genotype(args, genotype_parser) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/advntr_commands.py", line 124, in genotype genome_analyzier.find_repeat_counts_from_alignment_file(input_file, average_coverage, args.update) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/genome_analyzer.py", line 241, in find_repeat_counts_from_alignment_file average_coverage, update) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/profiler.py", line 8, in wrapper retval = func(*args, kwargs) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/vntr_finder.py", line 707, in find_repeat_count_from_alignment_file selected_reads = self.select_illumina_reads(alignment_file, unmapped_filtered_reads, update) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/profiler.py", line 8, in wrapper retval = func(*args, *kwargs) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/vntr_finder.py", line 658, in select_illumina_reads hmm = self.get_vntr_matcher_hmm(read_length=read_length) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/vntr_finder.py", line 119, in get_vntr_matcher_hmm vntr_matcher = self.build_vntr_matcher_hmm(copies, flanking_region_size) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/profiler.py", line 8, in wrapper retval = func(args, kwargs) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/vntr_finder.py", line 101, in build_vntr_matcher_hmm vntr_matcher = get_read_matcher_model(left_flanking_region, right_flanking_region, patterns, copies) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/profiler.py", line 8, in wrapper retval = func(*args, kwargs) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/hmm_utils.py", line 529, in get_read_matcher_model repeats_matcher = get_variable_number_of_repeats_matcher_hmm(patterns, copies, vpaths) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/profiler.py", line 8, in wrapper retval = func(*args, *kwargs) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/hmm_utils.py", line 476, in get_variable_number_of_repeats_matcher_hmm model = get_constant_number_of_repeats_matcher_hmm(patterns, copies, vpaths) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/profiler.py", line 8, in wrapper retval = func(args, kwargs) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/hmm_utils.py", line 405, in get_constant_number_of_repeats_matcher_hmm transitions, emissions = build_profile_hmm_for_repeats(patterns, settings.MAX_ERROR_RATE) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/profiler.py", line 8, in wrapper retval = func(*args, **kwargs) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/advntr/profile_hmm.py", line 169, in build_profile_hmm_for_repeats stdout, stderr = muscle_cline(stdin=data) File "/home/users/astar/gis/ramul/miniconda3/envs/advntrenv/lib/python2.7/site-packages/Bio/Application/init.py", line 531, in call stdout_str, stderr_str) Bio.Application.ApplicationError: Non-zero return code 1 from 'muscle -clwstrict', message 'Invalid command line'

command: advntr genotype --vntr_id 301645 --alignment_file CSTB_2_5_testdata.bam --working_directory working_dir

A similar error also occurs when running the addmodel command. I'm at quite a loss so any help would be deeply appreciated.

ltf2020 commented 2 years ago

We also encountered similar errors File "/home/luotf/miniconda3/envs/python27/bin/advntr", line 11, in load_entry_point('advntr==1.4.1', 'console_scripts', 'advntr')() File "build/bdist.linux-x86_64/egg/advntr/main.py", line 134, in main File "build/bdist.linux-x86_64/egg/advntr/advntr_commands.py", line 124, in genotype File "build/bdist.linux-x86_64/egg/advntr/genome_analyzer.py", line 238, in find_repeat_counts_from_alignment_file File "build/bdist.linux-x86_64/egg/advntr/profiler.py", line 8, in wrapper File "build/bdist.linux-x86_64/egg/advntr/vntr_finder.py", line 710, in find_repeat_count_from_alignment_file File "build/bdist.linux-x86_64/egg/advntr/profiler.py", line 8, in wrapper File "build/bdist.linux-x86_64/egg/advntr/vntr_finder.py", line 660, in select_illumina_reads File "build/bdist.linux-x86_64/egg/advntr/vntr_finder.py", line 119, in get_vntr_matcher_hmm File "build/bdist.linux-x86_64/egg/advntr/profiler.py", line 8, in wrapper File "build/bdist.linux-x86_64/egg/advntr/vntr_finder.py", line 101, in build_vntr_matcher_hmm File "build/bdist.linux-x86_64/egg/advntr/profiler.py", line 8, in wrapper File "build/bdist.linux-x86_64/egg/advntr/hmm_utils.py", line 529, in get_read_matcher_model File "build/bdist.linux-x86_64/egg/advntr/profiler.py", line 8, in wrapper File "build/bdist.linux-x86_64/egg/advntr/hmm_utils.py", line 476, in get_variable_number_of_repeats_matcher_hmm File "build/bdist.linux-x86_64/egg/advntr/profiler.py", line 8, in wrapper File "build/bdist.linux-x86_64/egg/advntr/hmm_utils.py", line 405, in get_constant_number_of_repeats_matcher_hmm File "build/bdist.linux-x86_64/egg/advntr/profiler.py", line 8, in wrapper File "build/bdist.linux-x86_64/egg/advntr/profile_hmm.py", line 169, in build_profile_hmm_for_repeats File "/home/luotf/miniconda3/envs/python27/lib/python2.7/site-packages/Bio/Application/init.py", line 527, in call stdout_str, stderr_str) Bio.Application.ApplicationError: Non-zero return code 1 from 'muscle -clwstrict', message 'Invalid command line'

Jong-hun-Park commented 5 months ago

Can you try installing muscle?

conda install muscle=3.8.1551