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  • Python commands not found at all in QIIME

    Hello all,

    I am very new to qiime, and bioinformatics in general. I'm going to try and explain this the best that I can, but if something is unclear please tell me.

    I'm trying to analyze data from one (1) environmental sample using the Illumina MiSeq. I have the data, the lab I'm working in primarily uses QIIME to look at MiSeq data. Yesterday, I was able to work through enough of our lab's protocol to check for chimera sequences, and to filter them out (I'm pretty sure). Now that I have the chimera sequences filtered out, I'm trying to pick my OTUs.

    I went in today and tried using the pick_open_reference_otus.py command and got the following error: pick_open_reference_otus.py: command not found

    I tried to backtrack a little to see if I could filter the chimeras again and create another filtered file, just to see if it worked. So I used the filter_fasta.py command and got the same error. These commands worked yesterday and so I'm not sure why they wouldn't be working now?

    I should mention that I'm working on and through my lab's server, they have qiime installed with all the packages also on the server. I'm not sure if that makes any difference though.

    As I said, I'm very new at this, any help at all would be greatly appreciated!

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