Segmentation fault make.biom

mothur bugs
1

Hi,

I am trying to make a biom file using this command, but it hives a Segmentation fault:

mothur > make.biom(shared=final.shhh.trim.unique.good.filter.unique.precluster.pick.an.shared, label=0.03)
0.03
Segmentation fault

The shared file looks like this (excerpt):

label   Group   numOtus Otu0001 Otu0002 Otu0003 Otu0004 Otu0005 Otu0006 Otu0007 Otu0008 Otu0009 Otu0010 Otu0011 Otu0012 Otu0013 Otu0014 Otu0015 Otu0016 Otu0017 Otu0018 Otu0019 Otu0020 Otu0021 Otu0022 Otu0023
unique  SAMPLE1    2737    59      0       0       32      0       0       0       0       0       0       0       0       0       0       0       29      0       0       0       0       0       0       0       0
unique  SAMPLE2    2737    18      0       10      9       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0
unique  SAMPLE3    2737    0       0       0       0       0       0       0       0       0       0       0       0       0       30      0       0       0       0       0       0       0       0       0       0
unique  SAMPLE4    2737    27      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0
unique  SAMPLE5    2737    0       53      32      0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0
unique  SAMPLE6    2737    0       0       0       1       0       0       0       0       0       0       31      0       0       0       0       0       0       28      0       0       0       0       0       0
unique  SAMPLE7    2737    0       0       3       0       40      35      31      31      31      31      0       0       30      0       29      0       0       0       0       28      0       27      27      26
unique  SAMPLE8    2737    0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       0       29      0       0       0       0       0       0       0
unique  SAMPLE9    2737    0       0       0       0       0       0       0       0       0       0       0       30      0       0       0       0       0       0       28      0       28      0       0       0
0.01    SAMPLE1    2284    76      1       32      0       0       0       0       0       11      0       0       0       0       0       0       0       0       0       1       0       0       0       0       0
0.01    SAMPLE2    2284    24      0       9       11      2       0       0       10      0       0       0       0       7       3       1       2       0       1       0       0       0       18      0       17
0.01    SAMPLE3    2284    8       14      0       4       0       0       2       1       3       0       9       2       18      8       1       1       0       2       0       0       2       0       0       0
0.01    SAMPLE4    2284    34      7       9       2       0       15      0       0       0       0       0       0       1       1       9       10      1       4       0       0       0       0       0       0
0.01    SAMPLE5    2284    71      15      0       0       0       0       19      32      11      0       0       0       0       11      0       0       22      1       0       0       0       4       0       0
0.01    SAMPLE6    2284    8       1       1       3       0       1       1       0       3       0       0       0       7       12      2       8       1       2       5       31      0       0       0       0
0.01    SAMPLE7    2284    0       35      34      40      28      34      21      3       2       40      21      35      2       0       1       13      8       20      26      0       29      9       31      6
0.01    SAMPLE8    2284    42      27      0       7       0       1       6       0       12      0       9       0       0       0       19      0       0       2       0       1       0       0       0       8
0.01    SAMPLE9    2284    0       12      0       0       22      0       0       0       0       0       0       0       0       0       1       0       0       0       0       0       0       0       0       0
0.03    SAMPLE1    1314    103     1       3       7       0       35      0       1       0       0       1       0       4       0       1       13      3       0       12      0       4       4       0       6
0.03    SAMPLE2    1314    25      0       2       0       29      15      0       0       17      1       0       0       5       0       0       0       0       0       0       0       0       0       0       0
0.03    SAMPLE3    1314    9       43      18      9       4       0       41      6       0       5       4       16      6       6       9       4       18      7       15      0       19      15      0       30
0.03    SAMPLE4    1314    41      25      8       19      2       12      0       2       1       3       0       0       6       0       0       3       0       0       0       0       1       0       1       0
0.03    SAMPLE5    1314    81      15      2       1       4       3       0       5       2       3       1       0       6       0       19      21      0       19      0       2       14      3       28      0
0.03    SAMPLE6    1314    20      4       4       17      3       2       0       2       3       7       0       0       13      3       0       7       0       2       1       0       4       2       2       0
0.03    SAMPLE7    1314    0       48      94      66      74      36      33      61      44      35      52      49      21      59      37      4       26      26      33      51      10      31      23      0
0.03    SAMPLE8    1314    42      32      15      38      15      0       8       6       8       19      13      7       4       0       0       12      15      7       0       4       4       0       1       13
0.03    SAMPLE9    1314    0       13      23      0       0       0       13      1       5       5       1       0       7       0       0       0       0       1       0       1       0       0       0       4

Any idea what causes this error and how to debug this?

Thanks!

2

I tracked down the cause of the problem. I ran make.shared with multiple labels. Using only 1 distance level per time it worked. So there seems to be a bug in make.biom reading in a shared file containing multiple labels.

This command works:

make.shared(list=final.shhh.trim.unique.good.filter.unique.precluster.pick.an.list,group=final.good.pick.groups,label=0.01)
make.biom(shared=final.shhh.trim.unique.good.filter.unique.precluster.pick.an.shared,label=0.01)

This doesn’t:

make.shared(list=final.shhh.trim.unique.good.filter.unique.precluster.pick.an.list,group=final.good.pick.groups,label=unique-0.01)
make.biom(shared=final.shhh.trim.unique.good.filter.unique.precluster.pick.an.shared,label=0.01)
0.01
Segmentation fault
3

Thanks for bringing this bug to our attention. It will be fixed in our next release.