Map File problem

[Deb Colman]

Hi, I'm a new QIIME user. I have one 454 metadate file (16S rRNA). It has 7 barcodes, because I have 7 different samples. I've splitted the seqs in 7 fasta files (by Bioedit program). Now, I want to create and validate the map file in QIIME.

I have doubts about how I must create the map file. I've done a map file with sequences related to one barcode and I tried to execute but I couldn't. I send you a screenshot of the error message. I don't know if the message is for the script or about the map file.

When I have different barcodes, I have to create one map file each one? And each map file must have all sequences assigned to that barcode?

For more information, I've installed QIIME Virtual Box. 

I hope that someone understand me.

Thanks!!

[Daniel McDonald]

Hi Deb,

The error in your traceback is from attempting to create a directory in the shared folder on your VirtualBox in a directory where you do not have permission to do so. If you specify "-o $HOME/mapping_output" it should proceed further. 

Your mapping file is your study. It is what relates your samples to covariates. You should have a single file which associates each sample to all the information you have about the physical specimen. For example, please see an example mapping file here:

https://github.com/biocore/qiime/blob/master/qiime_test_data/filter_distance_matrix/Fasting_Map.txt

Best,

Daniel

[Deb Colman]

Hi Daniel! Thanks for your soon answer. It was very useful! I'm running the script as you told me. 

I guess this is taking time because of the large number of sequences to be analyzed (+ 200,000).

If there is any problem, I do not hesitate to write to the forum!!

Thank you for all!

[Daniel McDonald]

Glad to help, and good luck!

Best,

Daniel