Hey, I wanted to perform unifrac on my fungal LSU data. I used make_phylogeny.py to generate a compatible tree for my biom file. However ,I got this errror message:
beta_significance.py -i fung.biom -t temp_aligned.tre -s unweighted_unifrac -o uw_sig.txt
Traceback (most recent call last):
File "/macqiime/bin/beta_significance.py", line 4, in <module>
__import__('pkg_resources').run_script('qiime==1.9.0', 'beta_significance.py')
File "/macqiime/lib/python2.7/site-packages/setuptools-12.2-py2.7.egg/pkg_resources/__init__.py", line 698, in run_script
File "/macqiime/lib/python2.7/site-packages/setuptools-12.2-py2.7.egg/pkg_resources/__init__.py", line 1616, in run_script
File "/macqiime/lib/python2.7/site-packages/qiime-1.9.0-py2.7.egg/EGG-INFO/scripts/beta_significance.py", line 210, in <module>
main()
File "/macqiime/lib/python2.7/site-packages/qiime-1.9.0-py2.7.egg/EGG-INFO/scripts/beta_significance.py", line 122, in main
raise ValueError(e.message + " and that the otu abundance is"
ValueError: No valid samples/environments found. Check whether tree tips match otus/taxa present in samples/environments and that the otu abundance is not relative.
I checked the tree tips and otu names and didn't see any anomalies. I found this command worked fine on my 16S data.
Thanks.
make_phylogeny.py to generate a compatible tree for my biom file
align_seqs.py -i temp.fasta -m muscle -o alitemp/
make_phylogeny.py -i temp_aligned.fasta
beta_significance.py -i fung.biom -t temp_aligned.tre -s unweighted_unifrac -o uw_sig.txt
Thanks
validate_demultiplexed_fasta.py -i temp.fasta -m mapping_corrected.txt -b -p -t /Users/FLFLFLLF/Desktop/geochip2isme/alitemp/temp_aligned.tre -e
# fasta file temp.fasta validation report
Percent duplicate labels: 0.000
Percent QIIME-incompatible fasta labels: 1.000
Percent of labels that fail to map to SampleIDs: 1.000
Percent of sequences with invalid characters: 0.000
Percent of sequences with barcodes detected: 0.000
Percent of sequences with barcodes detected at the beginning of the sequence: 0.000
Percent of sequences with primers detected: 0.000
Fasta label/tree tip exact match report
The following labels were not in tree tips:
fung.OTU.83
fung.OTU.68
fung.OTU.81
fung.OTU.80
fung.OTU.101
fung.OTU.86
fung.OTU.85
fung.OTU.82
fung.OTU.61
fung.OTU.60
fung.OTU.89
fung.OTU.62
fung.OTU.65
fung.OTU.118
fung.OTU.67
fung.OTU.66
fung.OTU.46
fung.OTU.93
fung.OTU.41
fung.OTU.40
fung.OTU.24
fung.OTU.111
fung.OTU.26
fung.OTU.38
fung.OTU.49
fung.OTU.48
fung.OTU.96
fung.OTU.119
fung.OTU.84
fung.OTU.104
fung.OTU.112
fung.OTU.102
fung.OTU.99
fung.OTU.116
fung.OTU.22
fung.OTU.106
fung.OTU.91
fung.OTU.92
fung.OTU.88
fung.OTU.94
fung.OTU.95
fung.OTU.78
fung.OTU.79
fung.OTU.98
fung.OTU.77
fung.OTU.110
fung.OTU.75
fung.OTU.72
fung.OTU.70
fung.OTU.71
fung.OTU.33
fung.OTU.56
fung.OTU.57
fung.OTU.36
fung.OTU.51
fung.OTU.34
fung.OTU.53
fung.OTU.10
fung.OTU.12
fung.OTU.120
fung.OTU.59
fung.OTU.113
fung.OTU.17
fung.OTU.8
fung.OTU.105
fung.OTU.2
fung.OTU.1
fung.OTU.6
fung.OTU.7
fung.OTU.4
fung.OTU.5
fung.OTU.103
The following tips were not in fasta labels:
'fung.OTU.106'
'fung.OTU.86'
'fung.OTU.80'
'fung.OTU.96'
'fung.OTU.104'
'fung.OTU.111'
'fung.OTU.4'
'fung.OTU.2'
'fung.OTU.53'
'fung.OTU.98'
'fung.OTU.113'
'fung.OTU.83'
'fung.OTU.56'
'fung.OTU.68'
'fung.OTU.72'
'fung.OTU.89'
'fung.OTU.40'
'fung.OTU.94'
'fung.OTU.41'
'fung.OTU.102'
'fung.OTU.82'
'fung.OTU.65'
'fung.OTU.48'
'fung.OTU.12'
'fung.OTU.10'
'fung.OTU.51'
'fung.OTU.36'
'fung.OTU.99'
'fung.OTU.75'
'fung.OTU.67'
'fung.OTU.46'
'fung.OTU.6'
'fung.OTU.70'
'fung.OTU.84'
'fung.OTU.59'
'fung.OTU.110'
'fung.OTU.38'
'fung.OTU.5'
'fung.OTU.112'
'fung.OTU.1'
'fung.OTU.93'
'fung.OTU.91'
'fung.OTU.62'
'fung.OTU.81'
'fung.OTU.79'
'fung.OTU.85'
'fung.OTU.119'
'fung.OTU.57'
'fung.OTU.118'
'fung.OTU.24'
'fung.OTU.101'
'fung.OTU.22'
'fung.OTU.92'
'fung.OTU.66'
'fung.OTU.105'
'fung.OTU.26'
'fung.OTU.34'
'fung.OTU.116'
'fung.OTU.103'
'fung.OTU.95'
'fung.OTU.49'
'fung.OTU.71'
'fung.OTU.77'
'fung.OTU.60'
'fung.OTU.120'
'fung.OTU.88'
'fung.OTU.33'
'fung.OTU.7'
'fung.OTU.8'
'fung.OTU.61'
'fung.OTU.17'
'fung.OTU.78'
Percent QIIME-incompatible fasta labels: 1.000