SourceTracker error

[Susan]

Hi,

keep getting this error with sourcetracker-0.9.8 and Qiime 1.9.1

$ R --slave --vanilla --args -i otu_filtered.txt -m mapping.txt -o sourcetracker_out < ~/bin/sourcetracker-0.9.8/sourcetracker_for_QIIME.r

Error in x[i, ] : subscript out of bounds
Calls: sourcetracker -> rarefy
Execution halted

I have checked the format of my mapping file and can find no errors.

Files attached, thanks for any help.

S

[Susan]

I corrected the white spaces and got the same error.

[Will Van Treuren]

Hi Susan, 

I believe the error is because the samples in your mapping file are of the form 'A19-7' (for example) and the samples in your OTU table are of the form 'A19-S7'. SourceTracker is erroring because it can't find any samples that match between the OTU table and the mapping file.

I replaced the sample names in the mapping file with the sample names in the OTU table (just added the extra S) and it seemed to run fine for me. 

Hope this helps,

Will 

[Susan]

Hi,

well spotted! I thought it must be some stupid mistake, just couldn't see it!

Thanks,

S.