Limit to number of Samples

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Samuel Major

Jul 25, 2016, 10:13:19 PM7/25/16
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I wanted to split my otu table and ran the command and recieved the error:

shared_samples = list(set(mdata[:, 0]).intersection(bt.ids(axis='sample')))
IndexError: too many indices for array

This gave me the idea that I may have too much going on in the mapping file. so I tried to validate it: -m 16S_18S/16S_18S_map.txt -o 16S_18S/map_val -b --not_barcoded
 if len(mapping_data[curr_data][curr_ix]) == 0:
IndexError: list index out of range

I currently have 48 samples (16S and 18S). I'll have 46 after I remove any contamination and any erroneous samples. 
Is there a limit to the number of samples that a mapping file can carry? I've used up to 25 samples thus far in other analyses.


Justine Debelius

Jul 26, 2016, 11:15:08 AM7/26/16
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Hi Samuel,

I've used the on the American Gut data when it was at about 5000 samples using a MacBook. 

Sometimes, I've gotten this kind of error (or similar behavior) because QIIME detects an extra row in my mapping file. If you've used Excel and currently have a text file, you need to open it as text. If you're working on a Mac, you can do this by opening the file using the File -> Open, and then going through the import menu. Select all your columns as text. (This will make sure you don't have any changes in your mapping file, like inference around zipcode). I think the same is true of windows and Open Office, but I haven't tried it.

Then, highlight maybe 20 cells below your last sample, and delete those rows. I typically to this three or four times, just to be sure. I'll do the same thing with columns.


Samuel Major

Jul 26, 2016, 10:55:38 PM7/26/16
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Hi Justine,
Thanks for the advice. I tried a few of your suggestions and re-running the command again and received the same error. However, I then tried validating it and re-running the command with the validated X_corrected.txt file and it seemed to have done the trick. 
I appreciate the help tremendously!
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