regarding filter_otu_from_table.py

[divyapr...@gmail.com]

Hi 

I am not able to filter_otu_from_table.py because i donot know which otus to filter. however running the command filter_otus_from_table.py gives me some error like no Json object could be decoded.  please some body help me out here.

As i am stuck in my analysis 

[Jenya Kopylov]

Hello,

Can you paste the exact command you ran for filter_otus_from_table.py and the full error that was output?

Thanks.

Jenya

[divyapr...@gmail.com]

qiime@qiime-VirtualBox:~$ filter_otus_from_otu_table.py -i Soil_otus/pynast_aligned_seqs/combined_seqs_rep_set_aligned.fasta -o filtered_otus -e Soil_otus/pynast_aligned_seqs/combined_seqs_rep_set_aligned.fasta.CPS 

Traceback (most recent call last):

  File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/filter_otus_from_otu_table.py", line 139, in <module>

    main()

  File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/filter_otus_from_otu_table.py", line 106, in main

    otu_table = parse_biom_table(open(opts.input_fp,'U'))

  File "/home/qiime/qiime_software/biom-format-1.3.1-release/lib/python2.7/site-packages/biom/parse.py", line 323, in parse_biom_table

    t = parse_biom_table_str(table_str, constructor=constructor)

  File "/home/qiime/qiime_software/biom-format-1.3.1-release/lib/python2.7/site-packages/biom/parse.py", line 588, in parse_biom_table_str

    json_table = json.loads(json_str)

  File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/json/__init__.py", line 326, in loads

    return _default_decoder.decode(s)

  File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/json/decoder.py", line 366, in decode

    obj, end = self.raw_decode(s, idx=_w(s, 0).end())

  File "/home/qiime/qiime_software/python-2.7.3-release/lib/python2.7/json/decoder.py", line 384, in raw_decode

    raise ValueError("No JSON object could be decoded")

ValueError: No JSON object could be decoded

[divyapr...@gmail.com]

Hi Jenya 

Secondly please tell me on what basis i will filter_otu_from_table.py so that i will get a phylogenetic tree and heat map but with different colors. i am getting a heat map but i am not able to visualize it.  for your convenience i am attaching the heat map pdf. So you can see it and help me out. 

[Jenya Kopylov]

Hello,

Have you looked at the documentation for filter_otus_from_otu_table.py? Or, have you tried searching the QIIME forum for the similar error? These are both excellent sources to obtain solutions quickly to various runtime problems.

The input to filter_otus_from_otu_table.py is a BIOM file, however you appear to be passing a FASTA file (-i Soil_otus/pynast_aligned_seqs/combined_seqs_rep_set_aligned.fasta). Please try using a BIOM file.

Jenya

[divyapr...@gmail.com]

Hi Jenya 

Do you mean i have to give otu_table.biom

[divyapr...@gmail.com]

Hi Jenya 

While running the command    filter_otus_from_otu_table.py -i Soil_otus/otu_table.biom -o Filtered_sequences2 -e Soil_otus/rep_set/combined_seqs_rep_set.fasta

 i have got the following error 

qiime@qiime-VirtualBox:~$ filter_otus_from_otu_table.py -i Soil_otus/otu_table.biom -o Filtered_sequences2 -e Soil_otus/rep_set/combined_seqs_rep_set.fasta

Traceback (most recent call last):

  File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/filter_otus_from_otu_table.py", line 139, in <module>

    main()

  File "/home/qiime/qiime_software/qiime-1.8.0-release/bin/filter_otus_from_otu_table.py", line 134, in main

    negate_ids_to_exclude)

  File "/home/qiime/qiime_software/qiime-1.8.0-release/lib/qiime/filter.py", line 512, in filter_otus_from_otu_table

    return otu_table.filterObservations(filter_f)

  File "/home/qiime/qiime_software/biom-format-1.3.1-release/lib/python2.7/site-packages/biom/table.py", line 626, in filterObservations

    raise TableException, "All observations were filtered out!"

biom.exception.TableException: All observations were filtered out!

i am attaching the file also 

[Jenya Kopylov]

The error says all OTUs were filtered out based on your criteria, producing an empty BIOM table.

The command you're using is removing all OTUs listed in Soil_otus/rep_set/combined_seqs_rep_set.fasta. Is that what you're looking to do?

Jenya

[divyapr...@gmail.com]

Hello Jenya 

Sorry to disturb you time and again

 

1. Am i running the correct command.

2. On what basis do i need to filter the otus 

i am attaching the otu file .

3.do i need to put otu-table.biom as input file.

4. After running the command successfully , what file i have to proceed with. i mean the filtered one or the exact table.biom

 

5. Please also mention how to change the color of heat map

[divyapr...@gmail.com]

Hi any one over here 

I have posted some of the queries. Being new to Qiime i am not able to do filtering. i mean i don't know whether i have to run filter_otus_from_otu_table.py or   filter_samples_from_otu_table.py or filter_taxa_from_otu_table.py.

I have got three samples, with otu count 3412. what is the better option for me . So that i can proceed forward to prepare phylogenetic tree and heatmap and can do other analysis. 

More over i want to known after filtering with which file i have to proceed with.

For convenience i am attaching the summarized biom file.  

[divyapr...@gmail.com]

Hi 

Any one here 

Please help me out here as i have posted many queries an waiting for the reply. 

[divyapr...@gmail.com]

Hi Colin

 Are u there 

[Colin Brislawn]

Hello,

Yes I'm here, but I don't know how to answer your question. Hopefully some else on the form can help.

Colin

[Kyle Bittinger]

I answered your question in the other thread, not sure if this is a different question or not.