SourceTracker Help Please

[Andy]

I am trying to run source tracker on my dataset combined with some human references.  I ran closed OTU picking with gg reference dataset and my OTU table seems ok (I have shared phylotypes across the dataset)  I have attached my otu table, and mapping file.  I was able to successfully run sourcetracker with the tutorial files. Any help would be greatly appreciated.

R --slave --valnilla --args -i otus/filtered_otu_table.txt -m humans.txt -o sourcetracker_out_1 <SOURCETRACKER_PATH/sourcetracker_for_qiime_r

Error in x[1, ] : subscript out of bounds

Calls: sourcetracker -> rarefy

Execution halted

Thanks in advance for any assistance,

Andy

[Andy]

I figured it out.  Just in case others have some error message, I read under QIIME blog about mapping files with additional spaces from leading and trailing whitespaces which can cause some issues when using compiler in R.  The post has python file to strip out these white spaces and way to download it from GitHub.  Script is strip_mapping_file_fields.py

Andy

[Barvaz Sini]

Hi Andy,

Thanks for posting this solution!

Cheers,

Amnon

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