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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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phyluce_snp_bwa_multiple_align issue #150

Closed mprebus closed 5 years ago

mprebus commented 5 years ago

I'm attempting to work through the UCE phasing protocol, but I've run into an error with the ConfigParser:

2019-03-05 12:51:23,387 - phyluce_snp_bwa_multiple_align - INFO - ============ Starting phyluce_snp_bwa_multiple_align ============ 2019-03-05 12:51:23,387 - phyluce_snp_bwa_multiple_align - INFO - Version: git fatal: Not a git repository: '/home/mborowiec/phyluce-master/.git' 2019-03-05 12:51:23,387 - phyluce_snp_bwa_multiple_align - INFO - Argument --config: /home/mborowiec/Matt/temno-salvini-group/phasing.conf 2019-03-05 12:51:23,388 - phyluce_snp_bwa_multiple_align - INFO - Argument --cores: 9 2019-03-05 12:51:23,388 - phyluce_snp_bwa_multiple_align - INFO - Argument --log_path: /home/mborowiec/Matt/temno-salvini-group 2019-03-05 12:51:23,388 - phyluce_snp_bwa_multiple_align - INFO - Argument --mem: True 2019-03-05 12:51:23,388 - phyluce_snp_bwa_multiple_align - INFO - Argument --no_remove_duplicates: False 2019-03-05 12:51:23,388 - phyluce_snp_bwa_multiple_align - INFO - Argument --output: /home/mborowiec/Matt/temno-salvini-group/multialign-bams 2019-03-05 12:51:23,388 - phyluce_snp_bwa_multiple_align - INFO - Argument --subfolder: 2019-03-05 12:51:23,389 - phyluce_snp_bwa_multiple_align - INFO - Argument --verbosity: INFO 2019-03-05 12:51:23,389 - phyluce_snp_bwa_multiple_align - INFO - ============ Starting phyluce_snp_bwa_multiple_align ============ 2019-03-05 12:51:23,391 - phyluce_snp_bwa_multiple_align - INFO - Getting input filenames and creating output directories 2019-03-05 12:51:23,391 - phyluce_snp_bwa_multiple_align - INFO - Need to create BWA index file for reference 2019-03-05 12:51:23,391 - phyluce_snp_bwa_multiple_align - INFO - Running bwa indexing against /home/mborowiec/Matt/temno-salvini-group/salvini_group-incomplete/mafft-nexus-edge-trimmed-exploded/Temnothorax_aztecus_BZ_P192.fasta Traceback (most recent call last): File "/home/mborowiec/phyluce-master/bin/snps/phyluce_snp_bwa_multiple_align", line 193, in main() File "/home/mborowiec/phyluce-master/bin/snps/phyluce_snp_bwa_multiple_align", line 136, in main references_individuals = get_input_data(log, conf, args.output) File "/home/mborowiec/phyluce-master/bin/snps/phyluce_snp_bwa_multiple_align", line 109, in get_input_data bwa.create_index_files(log, reference[1]) File "/home/mborowiec/phyluce-master/phyluce/bwa.py", line 27, in create_index_files cmd = [get_user_path("binaries", "bwa"), "index", reference] File "/home/mborowiec/phyluce-master/phyluce/pth.py", line 29, in get_user_path pth = config.get(program, binary) File "/home/mborowiec/anaconda2/envs/Py27/lib/python2.7/ConfigParser.py", line 607, in get raise NoSectionError(section) ConfigParser.NoSectionError: No section: 'binaries'

brantfaircloth commented 5 years ago

Looks like this is an old git repository. Please install phyluce using conda as described in the manual - that should fix this issue.

mprebus commented 5 years ago

Thanks! This fixed the issue.