# Segmentation fault make.biom

**URL:** <https://forum.mothur.org/t/segmentation-fault-make-biom/1494>\
**Category:** mothur bugs\
**Created:** [September 9, 2013, 1:11pm UTC](https://forum.mothur.org/t/segmentation-fault-make-biom/1494 "2013-09-09T13:11:50Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![mattias](https://avatars.discourse-cdn.com/v4/letter/m/cab0a1/32.png) [@mattias](https://forum.mothur.org/u/mattias)\
**Post date:** [September 9, 2013, 1:11pm UTC](https://forum.mothur.org/t/segmentation-fault-make-biom/1494/1 "2013-09-09T13:11:50Z")

</div>

Hi,

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

```nohighlight
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):

```nohighlight
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!

---

<div class="post-metadata">

**Author:** ![mattias](https://avatars.discourse-cdn.com/v4/letter/m/cab0a1/32.png) [@mattias](https://forum.mothur.org/u/mattias)\
**Post date:** [September 9, 2013, 2:30pm UTC](https://forum.mothur.org/t/segmentation-fault-make-biom/1494/2 "2013-09-09T14:30:45Z")

</div>

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:

```nohighlight
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:

```nohighlight
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

```

---

<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [September 10, 2013, 11:39am UTC](https://forum.mothur.org/t/segmentation-fault-make-biom/1494/3 "2013-09-10T11:39:16Z")

</div>

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