rarefaction.single() in v.1.11.0 creates broken output

mothur bugs
1

Hi everybody,

I have rabund data (generated by a custom perl script that reads uclust output), which I feed into mothur using

mothur ‘#read.otu(rabund=filename); rarefaction.single()’

My input file contains 2 lines, representing data for clustering at 90 and 93 percent sequence identity; the format
is tab-separated, containing a label in the first field, the number of clusters in the second field, and the invididual
cluster sizes (sorted, descending) afterwards. The resulting output file, however, seems to be broken:

numsampled      90      lci     hci     93      lci     hci
1       1.0000  1.0000  1.0000  1.0000  1.0000  1.0000
100     87.8700 81.2777 94.4623 91.6270 85.8623 97.3917
200     160.4370        149.0420        171.8320        171.2700        161.4293        181.1107
300     224.8030        210.3882        239.2178        243.2590        230.1044        256.4136
400     282.6750        265.8762        299.4738        310.2860        294.1978        326.3742
500     336.3700        317.9398        354.8002        372.7680        354.5306        391.0054
600     386.4050        365.8174        406.9926        432.4530        411.8782        453.0278
[...]
119900  4721.9880       4721.7745       4722.2015       8930.7790       8926.2508       8935.3072
120000  4721.9930       4721.8295       4722.1565       8930.9890       8926.5932       8935.3848
120100  4721.9980       4721.9104       4722.0856       8931.2000       8926.9351       8935.4649
120200  4721.9990       4721.9370       4722.0610       8931.4180       8927.2116       8935.6244
120300  4722.0000       4722.0000       4722.0000       8931.6160       8927.5645       8935.6675
120307  4722.0000       4722.0000       4722.0000       8931.8170       8927.8660       8935.7680
ÿ       8931.9920       8928.1443       8935.8397
        8932.1810       8928.4283       8935.9337
        8932.3500       8928.6953       8936.0047
        8932.5340       8928.9540       8936.1140
        8932.7270       8929.2630       8936.1910
        8932.9170       8929.5729       8936.2611
[...]

(Please note the ‘ÿ’ char in the first column and the missing values in this column below.)

I’m attaching sample input data. Any help would be appreciated.

2

file upload complains about forbidden extension (.txt). What extensions are allowed?

3

Could you send your .rabund file to mothur.bugs@gmail.com?

4

I just sent the file.

5

Thanks for sending your file. When I took a look, the label 90 has 120307 sequences, but the label 93 has 124521 sequences. The number of sequences needs to be the same across the various distances to make sense. The extra lines are mothur outputting the values for the label 93 as it processes the extra sequences.