# Core-metrics-phylogenetic crashed: free(): invalid next size
**URL:** https://forum.qiime2.org/t/core-metrics-phylogenetic-crashed-free-invalid-next-size/8408
**Category:** Technical Support
**Created:** [February 17, 2019, 9:10pm UTC](https://forum.qiime2.org/t/core-metrics-phylogenetic-crashed-free-invalid-next-size/8408 "2019-02-17T21:10:24Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@zhan\_xw](https://forum.qiime2.org/u/zhan_xw)
#### Post date: [February 17, 2019, 9:10pm UTC](https://forum.qiime2.org/t/core-metrics-phylogenetic-crashed-free-invalid-next-size/8408/1 "2019-02-17T21:10:24Z")
My QIIME version is 2019.01
The command is:
(qiime2-2019.1) [xzhan9@Nucleus005 another.16s]$ rm -rf core-metrics-results/ && qiime diversity core-metrics-phylogenetic --i-phylogeny rooted-tree.qza --i-table table.qza --p-sampling-depth 38005 --m-metadata-file sample-metadata.tsv --output-dir core-metrics-results --verbose
The error message is:
/home2/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/site-packages/sklearn/utils/validation.py:595: DataConversionWarning: Data with input dtype float64 was converted to bool by check\_pairwise\_arrays.
warnings.warn(msg, DataConversionWarning)
/home2/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/site-packages/skbio/stats/ordination/\_principal\_coordinate\_analysis.py:188: RuntimeWarning: invalid value encountered in true\_divide
proportion\_explained = eigvals / sum\_eigenvalues
/home2/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/site-packages/emperor/core.py:614: RuntimeWarning: invalid value encountered in true\_divide
c\_data = (coords / np.max(np.abs(coords)))
\*\*\* Error in `/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python': free(): invalid next size (fast): 0x0000555557a472f0 \*\*\*
======= Backtrace: =========
/lib64/libc.so.6(+0x7c619)[0x2aaaaaf67619]
/home2/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/site-packages/unifrac/\_api.cpython-36m-x86\_64-linux-gnu.so(\_ZNSt10\_HashtableINSt7\_\_cxx1112basic\_stringIcSt11char\_traitsIcESaIcEEES5\_SaIS5\_ENSt8\_\_detail9\_IdentityESt8equal\_toIS5\_ESt4hashIS5\_ENS7\_18\_Mod\_range\_hashingENS7\_20\_Default\_ranged\_hashENS7\_20\_Prime\_rehash\_policyENS7\_17\_Hashtable\_traitsILb1ELb1ELb1EEEE5clearEv+0x32)[0x2aaac8a4aa12]
/home2/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/site-packages/unifrac/\_api.cpython-36m-x86\_64-linux-gnu.so(\_ZNSt10\_HashtableINSt7\_\_cxx1112basic\_stringIcSt11char\_traitsIcESaIcEEES5\_SaIS5\_ENSt8\_\_detail9\_IdentityESt8equal\_toIS5\_ESt4hashIS5\_ENS7\_18\_Mod\_range\_hashingENS7\_20\_Default\_ranged\_hashENS7\_20\_Prime\_rehash\_policyENS7\_17\_Hashtable\_traitsILb1ELb1ELb1EEEED2Ev+0xa)[0x2aaac8a4aa5a]
/home2/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/site-packages/unifrac/\_api.cpython-36m-x86\_64-linux-gnu.so(one\_off+0xaa1)[0x2aaac8a4a621]
/home2/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/site-packages/unifrac/\_api.cpython-36m-x86\_64-linux-gnu.so(+0x22807)[0x2aaac8a44807]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyCFunction\_FastCallDict+0x154)[0x555555667754]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x1a15ac)[0x5555556f55ac]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x30a)[0x55555571a28a]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16d801)[0x5555556c1801]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16e84f)[0x5555556c284f]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x1a1685)[0x5555556f5685]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x10c7)[0x55555571b047]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(PyEval\_EvalCodeEx+0x329)[0x5555556c5eb9]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x172dd6)[0x5555556c6dd6]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(PyObject\_Call+0x3e)[0x55555566755e]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x184f)[0x55555571b7cf]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16e60b)[0x5555556c260b]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x1a1685)[0x5555556f5685]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x30a)[0x55555571a28a]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16dc4e)[0x5555556c1c4e]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16e84f)[0x5555556c284f]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x1a1685)[0x5555556f5685]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x30a)[0x55555571a28a]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16d801)[0x5555556c1801]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16e84f)[0x5555556c284f]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x1a1685)[0x5555556f5685]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x10c7)[0x55555571b047]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(PyEval\_EvalCodeEx+0x329)[0x5555556c5eb9]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x172dd6)[0x5555556c6dd6]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(PyObject\_Call+0x3e)[0x55555566755e]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x184f)[0x55555571b7cf]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16e60b)[0x5555556c260b]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x1a1685)[0x5555556f5685]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x30a)[0x55555571a28a]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16dc4e)[0x5555556c1c4e]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16e84f)[0x5555556c284f]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x1a1685)[0x5555556f5685]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x30a)[0x55555571a28a]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(PyEval\_EvalCodeEx+0x329)[0x5555556c5eb9]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x172dd6)[0x5555556c6dd6]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(PyObject\_Call+0x3e)[0x55555566755e]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x178fc7)[0x5555556ccfc7]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(PyObject\_Call+0x3e)[0x55555566755e]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x184f)[0x55555571b7cf]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16d801)[0x5555556c1801]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyFunction\_FastCallDict+0x3d7)[0x5555556c2f17]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyObject\_FastCallDict+0x26f)[0x555555667b1f]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyObject\_Call\_Prepend+0x63)[0x55555566c7b3]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(PyObject\_Call+0x3e)[0x55555566755e]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x178fc7)[0x5555556ccfc7]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(PyObject\_Call+0x3e)[0x55555566755e]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x184f)[0x55555571b7cf]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16d801)[0x5555556c1801]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyFunction\_FastCallDict+0x3d7)[0x5555556c2f17]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyObject\_FastCallDict+0x26f)[0x555555667b1f]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyObject\_Call\_Prepend+0x63)[0x55555566c7b3]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(PyObject\_Call+0x3e)[0x55555566755e]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x184f)[0x55555571b7cf]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16e60b)[0x5555556c260b]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x1a1685)[0x5555556f5685]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(\_PyEval\_EvalFrameDefault+0x30a)[0x55555571a28a]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16dc4e)[0x5555556c1c4e]
/home2/xzhan9/.conda/envs/qiime2-2019.1/bin/python(+0x16e84f)[0x5555556c284f]
======= Memory map: ========
2aaaaaaab000-2aaaaaacc000 r-xp 00000000 08:01 39109043 /usr/lib64/ld-2.17.so
2aaaaaacc000-2aaaaaace000 r-xp 00000000 00:00 0 [vdso]
2aaaaaace000-2aaaaaacf000 rw-p 00000000 00:00 0
2aaaaaacf000-2aaaaaad6000 r--s 00000000 08:01 6426948 /usr/lib64/gconv/gconv-modules.cache
2aaaaaad6000-2aaaaaad7000 r--p 00000000 00:32 580100053 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_heapq.cpython-36m-x86\_64-linux-gnu.so
2aaaaaad7000-2aaaaaad9000 r-xp 00001000 00:32 580100053 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_heapq.cpython-36m-x86\_64-linux-gnu.so
2aaaaaad9000-2aaaaaada000 r--p 00003000 00:32 580100053 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_heapq.cpython-36m-x86\_64-linux-gnu.so
2aaaaaada000-2aaaaaadb000 r--p 00003000 00:32 580100053 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_heapq.cpython-36m-x86\_64-linux-gnu.so
2aaaaaadb000-2aaaaaadd000 rw-p 00004000 00:32 580100053 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_heapq.cpython-36m-x86\_64-linux-gnu.so
2aaaaaadd000-2aaaaaade000 r--p 00000000 00:32 580100035 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_opcode.cpython-36m-x86\_64-linux-gnu.so
2aaaaaade000-2aaaaaadf000 r-xp 00001000 00:32 580100035 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_opcode.cpython-36m-x86\_64-linux-gnu.so
2aaaaaadf000-2aaaaaae0000 r--p 00002000 00:32 580100035 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_opcode.cpython-36m-x86\_64-linux-gnu.so
2aaaaaae0000-2aaaaaae1000 r--p 00002000 00:32 580100035 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_opcode.cpython-36m-x86\_64-linux-gnu.so
2aaaaaae1000-2aaaaaae2000 rw-p 00003000 00:32 580100035 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_opcode.cpython-36m-x86\_64-linux-gnu.so
2aaaaaae2000-2aaaaaae5000 r--p 00000000 00:32 580100069 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/math.cpython-36m-x86\_64-linux-gnu.so
2aaaaaae5000-2aaaaaaeb000 r-xp 00003000 00:32 580100069 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/math.cpython-36m-x86\_64-linux-gnu.so
2aaaaaaeb000-2aaaaaaed000 r--p 00009000 00:32 580100069 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/math.cpython-36m-x86\_64-linux-gnu.so
2aaaaaaed000-2aaaaaaee000 r--p 0000a000 00:32 580100069 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/math.cpython-36m-x86\_64-linux-gnu.so
2aaaaaaee000-2aaaaaaf0000 rw-p 0000b000 00:32 580100069 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/math.cpython-36m-x86\_64-linux-gnu.so
2aaaaaaf0000-2aaaaaaf1000 rwxp 00000000 00:00 0
2aaaaaaf1000-2aaaaacb6000 rw-p 00000000 00:00 0
2aaaaacb6000-2aaaaacb9000 r--p 00000000 00:32 580100073 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_struct.cpython-36m-x86\_64-linux-gnu.so
2aaaaacb9000-2aaaaacbf000 r-xp 00003000 00:32 580100073 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_struct.cpython-36m-x86\_64-linux-gnu.so
2aaaaacbf000-2aaaaacc1000 r--p 00009000 00:32 580100073 /work/PCDC/xzhan9/.conda/envs/qiime2-2019.1/lib/python3.6/lib-dynload/\_struct.cpython-36m-x86\_64-linux-gnu.soAborted (core dumped)
I also shared the input files:
[https://www.dropbox.com/sh/oqtffyctdnduugn/AABAJD4clJ\_mx4X8tBPETaSHa?dl=0](https://www.dropbox.com/sh/oqtffyctdnduugn/AABAJD4clJ_mx4X8tBPETaSHa?dl=0)
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 19, 2019, 1:14am UTC](https://forum.qiime2.org/t/core-metrics-phylogenetic-crashed-free-invalid-next-size/8408/2 "2019-02-19T01:14:44Z")
---
### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [February 25, 2019, 9:09pm UTC](https://forum.qiime2.org/t/core-metrics-phylogenetic-crashed-free-invalid-next-size/8408/3 "2019-02-25T21:09:10Z")
Hi @zhan_xw,
Apologies for the delay.
This looks like something strange happening in the unifrac package. How many samples are left after rarefying at 38005 (based on your feature-table summary)?
Could you also supply some information about your current environment:
```auto
uname --all
```
Is this running on a cluster? Is there a queuing system involved? Thanks, and sorry for the vague questions, I'm not 100% sure where to start looking yet.
cc @wasade
---
### Author:  [@ebolyen](https://forum.qiime2.org/u/ebolyen)
#### Post date: [February 25, 2019, 9:09pm UTC](https://forum.qiime2.org/t/core-metrics-phylogenetic-crashed-free-invalid-next-size/8408/4 "2019-02-25T21:09:17Z")
---
### Author:  [@zhan\_xw](https://forum.qiime2.org/u/zhan_xw)
#### Post date: [February 25, 2019, 10:55pm UTC](https://forum.qiime2.org/t/core-metrics-phylogenetic-crashed-free-invalid-next-size/8408/5 "2019-02-25T22:55:07Z")
I should have 1 samples with depth of 38005 (attached the qzv file).
(qiime2-2019.1) [xzhan9@Nucleus005 another.16s]$ uname --all
Linux Nucleus005 3.10.0-693.2.2.el7.x86\_64 #1 SMP[table.qzv](https://cdck-file-uploads-global.s3.dualstack.us-west-2.amazonaws.com/flex002/uploads/qiime21/original/2X/9/9d705c9e3a601f961287ef6dd83d69152ea55d8a.qzv) (294.0 KB)
Sat Sep 9 03:55:24 EDT 2017 x86\_64 x86\_64 x86\_64 GNU/Linux
yes, it is on a cluster with Python 3.6.7(Python 3.6.7 | packaged by conda-forge | (default, Nov 21 2018, 03:09:43)).no queue system involved.
---
### Author:  [@Nicholas\_Bokulich](https://forum.qiime2.org/u/Nicholas_Bokulich)
#### Post date: [February 25, 2019, 11:06pm UTC](https://forum.qiime2.org/t/core-metrics-phylogenetic-crashed-free-invalid-next-size/8408/6 "2019-02-25T23:06:20Z")
> [@zhan\_xw](#):
>
> I should have 1 samples with depth of 38005 (attached the qzv file).
That may be the problem: a sample size of 1 is not useful for running through `core-metrics`, since that pipeline performs diversity analyses comparing multiple samples. You cannot calculate a unifrac distance matrix with 1 sample, as there are no distances to calculate — distances are calculated between pairs of samples.
If you had more than 1 sample and other samples are being dropped because you are setting a high sampling depth, reduce the sampling depth. Otherwise do not bother using this pipeline. You can use `qiime diversity alpha` to calculate alpha diversity values from a single sample if that is meaningful to you, but none of the beta diversity metrics are meaningful or calculable if you have one sample.
I hope that helps!
---
### Author:  [@wasade](https://forum.qiime2.org/u/wasade)
#### Post date: [February 26, 2019, 6:14pm UTC](https://forum.qiime2.org/t/core-metrics-phylogenetic-crashed-free-invalid-next-size/8408/8 "2019-02-26T18:14:16Z")
Hi @Nicholas_Bokulich and @zhan_xw, just as a brief update, we've opened a new [issue](https://github.com/qiime2/q2-diversity/issues/241) for `q2-diversity` to check for this edge case, and to report appropriately back to the user.
Best,
Daniel