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Error with genotype #51

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R-Laksh opened this issue Jun 23, 2022 · 2 comments
Open

Error with genotype #51

R-Laksh opened this issue Jun 23, 2022 · 2 comments

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@R-Laksh
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R-Laksh commented Jun 23, 2022

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
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ltf2020 commented Jul 23, 2022

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
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Can you try installing muscle?

conda install muscle=3.8.1551

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3 participants
@Jong-hun-Park @ltf2020 @R-Laksh