rarefaction -min value

[abhishake lahiri]

Hello Qiimers,

I was running collate_alpha.py when qiime gave out an error: 'NoneType' object has no attribute 'index'. In order to debug when I inspected the input folder I found some of the files are empty. The exact order of commands was this:

 parallel_multiple_rarefactions.py -i otus/otu_table_rdp_nochimera.biom -O 20 -o otus/alpha_rars/ -m 100 -x 3100 -s 20 -n 20 [The minimum depth of my sample set was 3194].

 parallel_alpha_diversity.py -i otus/alpha_rars/ -o otus/alpha_div/ -O 20 -t otus/rep_set_chimerafree.tre -m chao1,observed_otus,PD_whole_tree,heip_e,shannon,observed_species,goods_coverage,simpson,simpson_e,ace

 collate_alpha.py -i otus/alpha_div/ -o otus/alpha_collated/

I found alpha_rarefaction_100_1.txt, 100_3, 100_7, 100_17, 140_15, 180_7 to be empty. Previously I have removed some of the lower depths as a round-about way-out. But I don't think that to be the right method. Can anyone suggest why this error occurring  and a probable solution.

Thanks in advance,

Abhishake.