Debugging the QIIME 1.5 virtual box

I was trying to run pick_otus.py on the iMac QIIME 1.5 Virtual Box (Illumina GOM data), but ran into an error about uclust.

Command I ran:

pick_otus.py -m uclust -s 0.99 -t -z -i /home/qiime/Desktop/Shared_Folder/sl_out/GOM_illumina_demultiplexed_fwd_concat_1to12_1 -o /home/qiime/Desktop/Shared_Folder/GOM_uclust99_otus/

Error I got:

raise ApplicationError, (‘Error running uclust. Possible causes are ‘ cogent.app.util.ApplicationError: Error running uclust. Possible causes are unsupported version (current supported version is v1.2.22) is installed or improperly formatted input file was provided

ran print_qiime_config.py -t to see if there were any errors in the qiime configuration, and I was getting an error saying that usearch wasn’t installed. Downloaded the usearch binary (32 bit usearch 5.2.23 version) and copied the (renamed file) to a new folder on the Virtual Box /home/qiime/qiime_software/usearch-5.2.23-release/usearch.  Next had to set my environmental parameters:

cd
echo “export PATH=./home/qiime/qiime_software/usearch-5.2.23-release/:$PATH” >> ./.bashrc
source ./.bashrc
export PATH=$PATH:/home/qiime/qiime_software/usearch-5.2.23-release/
chmod 777 /home/qiime/qiime_software/usearch-5.2.23-release/usearch
usearch –version

After that, I was able to do usearch –version and get the current version pop up on the command line. Re-running the qiime config script showed that everything was OK and I had no errors. Now running the original command again to see if I can avoid this error — if not, I’ll have to post to the developer forum.

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