source tracker halted

[ravibiokr]

Dear QIIME,

I have tried sourcetracker on my dataset with qiime 1.8 vm halted 

R --slave --vanilla --args -i ST_filtered_otu_table_rare_even1000_9.txt -m ST_1_8_metadata.txt -o sourcetracker_1_8_out < $SOURCETRACKER_PATH/sourcetracker_for_qiime.r

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

Calls: sourcetracker -> rarefy

Execution halted

Thank you 

Ravi

[Tony Walters]

Ravi,

I can't claim much experience with sourcetracker. Does the tutorial data on this page (http://qiime.org/tutorials/source_tracking.html) generate the expected results without error? If so, can you post the ST_1_8_metadata.txt file?

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[ravibiokr]

Hi 

Thank you for the information 

I did not bothered about the tutorial and just followed the method... 

Here is my metadata file

Thank you 

Ravi

[Tony Walters]

Ravi, this may not be the only issue, but I noticed that the "source" values were capitalized under SourceSink (most of the scripts will be sensitive to this). I fixed that in the attached file, which you can try to see if it works.

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[ravibiokr]

Dear Tony

Thank you the metadata file worked.... 

R --slave --vanilla --args -i ST_filtered_otu_table_w_tax_even1000.txt -m ST_1_8_metadata_modified.txt -o sourcetracker_out < $SOURCETRACKER_PATH/sourcetracker_for_qiime.r

Rarefying training data at 1000

                                             CS    Unknown

..........   1 of    6, depth=  353:  0.50 (0.07) 0.50 (0.07)

..........   2 of    6, depth=  354:  0.50 (0.05) 0.50 (0.05)

..........   3 of    6, depth=  358:  0.38 (0.05) 0.62 (0.05)

..........   4 of    6, depth=  359:  0.37 (0.07) 0.63 (0.07)

..........   5 of    6, depth=  391:  0.00 (0.00) 1.00 (0.00)

..........   6 of    6, depth=  376:  0.51 (0.08) 0.49 (0.08)

Ravi 

[DV]

Hello,

I resolved this issue formatting my otu table:

Your otu_table.txt most have this format:

Note that "#" most appear.

Good luck!