Hello,
I am running core_div_analyses as such
core_diversity_analyses.py -i fruit.biom -o core_div_analyses_fruita/ -m mapping_fruita.txt -c Description -t gg_13_8_otus/trees/97_otus.tree -e 50234
But am getting this error:
*** ERROR RAISED DURING STEP: Make emperor plots, weighted_unifrac)
Command run was:
make_emperor.py -i core_div_analyses_fruita//bdiv_even50234//weighted_unifrac_pc.txt -o core_div_analyses_fruita//bdiv_even50234//weighted_unifrac_emperor_pcoa_plot/ -m mapping_fruita.txt
Command returned exit status: 2
Stdout:
Stderr
Error in make_emperor.py: The metadata mapping file has fewer sample identifiers than the coordinates file. Verify you are using a mapping file that contains at least all the samples contained in the coordinates file(s). You can force the script to ignore these samples by passing the '--ignore_missing_samples' flag.
I have double-checked my mapping file and it has the 123 samples, whilst the I expect I have run 122. Hence, I am not sure why it is saying it is missing files since it appears to have one extra. Is there a script to automatically cross-ref both files? Otherwise, I have tried the --ignore_missing_files flag but its tells me Error in core_diversity_analyses.py: no such option: --ignore_missing_samples
Can someone please offer any help as to how to get the core_div_analyses to run?
Best,
Sofia