Empty file produced from 'parse_Taxonomy_Function.py' script

[Rachel Mugge]

Hi,

I am working through the MG SOPv3 with my own data and am at step 5.2 (Generate final normalized tables). After fixing a few errors with python on my machine, I got the script to run and it makes the output file, but the file is empty. I've double checked my manifest file ("master input file") to make sure the full path is pointing to the correct files in each column, and that those files have something in them (they do). I also ran 'ln -s /Users/firefly-hl/Microbiome_Helper2/MMSeqs2_db/*.pbz2 .' so the script knows where the ".pbz2" files are. I have tried each of the 4 commands within section 5.2 and each produces an empty files. 

For example, I run this: 

'/usr/local/bin/python /Users/firefly-hl/Microbiome_Helper2/Functional_Helper_Scripts/parse_TaxonomyFunction.py --multisample /Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/pipeline_2/08_mmseqs2/B001/master_input_file/B001_master_input_file.txt --outputf /Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/pipeline_2/08_mmseqs2/B001/output_tables/B001_unstrat_matrix_RPKM.txt --unstratified Y'

and get this output:

'MicrobeCensus report not provided; RPKG will not be calculated; will normalize to RPKM

Running multiple samples from file: /Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/pipeline_2/08_mmseqs2/B001/master_input_file/B001_master_input_file.txt

line: ['B001', '/Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/kraken2_testing/k2_standard_0.1/output.kraken.txt', 'kraken2', '/Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/pipeline_2/08_mmseqs2/B001/mmseqs_U90_out_tophit/mmseqs2_B001_output.m8-parsed.txt', 'uniref', '/Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/pipeline_2/08_mmseqs2/B001/m8_files/mmseqs2_B001_output.m8']

Current sample: /Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/kraken2_testing/k2_standard_0.1/output.kraken.txt kraken2 /Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/pipeline_2/08_mmseqs2/B001/mmseqs_U90_out_tophit/mmseqs2_B001_output.m8-parsed.txt uniref /Volumes/FireFly_Promise_Pegasus/RMugge/DISSERTATION/Ch3/Metagenome_Microcosm2.0/pipeline_2/08_mmseqs2/B001/m8_files/mmseqs2_B001_output.m8

In Core ... >>>: kraken2 uniref

Taxatype:Kraken2

Functype:uniref

In Uniref Parsed func ... 

m8 file given...processing

In m8 parse ... 

Total reads mapped: 2679734

Total reads mapped to taxa: 115386 percent 4.305875135367914

Total reads mapped to functions: 2679734 percent 100.0

Reads mapped to either taxa OR functions: 2795120 percent 104.30587513536791

Reads mapped to both taxa AND functions: 0 percent 0.0

resultant dictionary taxa and func: 

 {}

Total unique functions:  0

Index([], dtype='object', name='function')'

I'm only running one sample as opposed to multiple, but I don't think that is the issue. Any thoughts on how to resolve this?

Thanks!

Rachel