Hi, Thank you very much for your tool. I was using it on a fastq file I have and successfully ran the species function, however, when I ran the genes function I got the following error (after 6 hours of it running successfully)
`
MIDAS: Metagenomic Intra-species Diversity Analysis System
version 1.2.1; github.com/snayfach/MIDAS
Copyright (C) 2015-2016 Stephen Nayfach
Freely distributed under the GNU General Public License (GPLv3)
Parameters
Command: ./MIDAS/scripts/run_midas.py genes ./data_out/poolA_res/ -1 ../FASTQ_Files/poolA_S17_L005_R1_001.fastq
Script: run_midas.py genes
Database: midas_db_v1.2
Output directory: ./data_out/poolA_res/
Remove temporary files: False
Pipeline options:
build bowtie2 database of pangenomes
align reads to bowtie2 pangenome database
quantify coverage of pangenomes genes
Database options:
include all species with >=3.0X genome coverage
Read alignment options:
input reads (1st mate): ../FASTQ_Files/poolA_S17_L005_R1_001.fastq
input reads (2nd mate): None
alignment speed/sensitivity: very-sensitive
number of reads to use from input: use all
number of threads for database search: 1
Gene coverage options:
minimum alignment percent identity: 94.0
minimum alignment coverage of reads: 0.75
minimum read quality score: 20
minimum mapping quality score: 0
trim 0 base-pairs from 3'/right end of read
Reading reference data
0.56 minutes
0.2 Gb maximum memory
Building pangenome database
total species: 11
total genes: 576240
total base-pairs: 497291760
33.44 minutes
1.16 Gb maximum memory
Aligning reads to pangenomes
finished aligning
checking bamfile integrity
293.88 minutes
1.16 Gb maximum memory
Computing coverage of pangenomes
total aligned reads: 29207158
total mapped reads: 22242407
Traceback (most recent call last):
File "./MIDAS/scripts/run_midas.py", line 699, in
run_program(program, args)
File "./MIDAS/scripts/run_midas.py", line 78, in run_program
genes.run_pipeline(args)
File "/Users/williampascucci/Documents/Research/MIDAS/MIDAS/midas/run/genes.py", line 274, in run_pipeline
pangenome_coverage(args, species, genes)
File "/Users/williampascucci/Documents/Research/MIDAS/MIDAS/midas/run/genes.py", line 151, in pangenome_coverage
normalize(args, species, genes)
File "/Users/williampascucci/Documents/Research/MIDAS/MIDAS/midas/run/genes.py", line 201, in normalize
sp.marker_coverage = np.median(sp.markers.values())
File "//anaconda/lib/python3.5/site-packages/numpy/lib/function_base.py", line 3944, in median
overwrite_input=overwrite_input)
File "//anaconda/lib/python3.5/site-packages/numpy/lib/function_base.py", line 3858, in _ureduce
r = func(a, **kwargs)
File "//anaconda/lib/python3.5/site-packages/numpy/lib/function_base.py", line 4002, in _median
return mean(part[indexer], axis=axis, out=out)
File "//anaconda/lib/python3.5/site-packages/numpy/core/fromnumeric.py", line 2889, in mean
out=out, **kwargs)
File "//anaconda/lib/python3.5/site-packages/numpy/core/_methods.py", line 82, in _mean
ret = ret / rcount
TypeError: unsupported operand type(s) for /: 'dict_values' and 'int'`
I am not sure where I am going wrong, thank you for any help you can provide!