sam@sam-Precision-WorkStation-T7500[lib1] print_qiime_config.py -t    [ 9:17AM]

System information

==================

         Platform:        linux2

   Python version: 2.7.3 (default, Sep 26 2013, 20:03:06)  [GCC 4.6.3]

Python executable: /usr/bin/python

 

Dependency versions

===================

                     PyCogent version: 1.5.3

                        NumPy version:        1.6.1

                   matplotlib version:    1.1.1rc

                  biom-format version:  1.2.0

                QIIME library version:      1.7.0

                 QIIME script version:     1.7.0

        PyNAST version (if installed):   1.2

RDP Classifier version (if installed):        Not installed

          Java version (if installed):    1.7.0_45

QIIME config values

===================

Traceback (most recent call last):

  File "/usr/lib/qiime/bin/print_qiime_config.py", line 812, in

    main()

  File "/usr/lib/qiime/bin/print_qiime_config.py", line 801, in main

    max_len =  max([len(key) for key in qiime_config])

ValueError: max() arg is an empty sequence

解决办法：

My guess is that load_qiime_config is failing. Do you have a qiime config file?  see here for more information about how to set one up http://qiime.org/install/qiime_config.html

 

sam@sam-Precision-WorkStation-T7500[lib1] locate qiime_config        [12:05AM]

/etc/qiime/qiime_config

/usr/lib/qiime/bin/print_qiime_config.py

/usr/lib/qiime/bin/print_qiime_config.pyc

/usr/share/doc/qiime/doctrees/install/qiime_config.doctree.gz

/usr/share/doc/qiime/doctrees/scripts/print_qiime_config.doctree.gz

/usr/share/doc/qiime/html/_sources/install/qiime_config.txt

/usr/share/doc/qiime/html/_sources/scripts/print_qiime_config.txt

/usr/share/doc/qiime/html/install/qiime_config.html

/usr/share/doc/qiime/html/scripts/print_qiime_config.html

 

sam@sam-Precision-WorkStation-T7500[lib1] cat /etc/qiime/qiime_config [ 9:15AM]

# qiime_config

# WARNING: DO NOT EDIT OR DELETE Qiime/qiime_config

# To overwrite defaults, copy this file to $HOME/.qiime_config or a full path

# specified by $QIIME_CONFIG_FP and edit that copy of the file.

 

cluster_jobs_fp

python_exe_fp         python

working_dir      .

blastmat_dir    /usr/share/ncbi/data

blastall_fp        blastall

pynast_template_alignment_fp

pynast_template_alignment_blastdb

template_alignment_lanemask_fp

jobs_to_start  1

seconds_to_sleep   60

qiime_scripts_dir     /usr/lib/qiime/bin/

temp_dir /tmp

 

将这个qiime_config复制到$HOME/.qiime_config

cat /etc/qiime/qiime_config >/home/sam/.qiime_config

 

sam@sam-Precision-WorkStation-T7500[lib1]  print_qiime_config.py -t   [ 9:32AM]

这下子就正常了

上面的设置不对，连输入下面的这些命令，都会报错。

alpha_rarefaction.py -i otu_table/otu1_table.biom -m map.txt -o div_alpha/ -p alpha_params.txt -t rep_phylo_tre/rep1_phylo.tre

TypeError: int() argument must be a string or a number, not 'NoneType'

sam@sam-Precision-WorkStation-T7500[lib1] beta_diversity_through_plots.py

TypeError: int() argument must be a string or a number, not 'NoneType'

sam@sam-Precision-WorkStation-T7500[lib1] jackknifed_beta_diversity.py -i otu_table/otu1_table.biom -t rep_phylo_tre/rep1_phylo.tre -m map.txt -o div_jack -e 16705

 

TypeError: int() argument must be a string or a number, not 'NoneType'