# Help in performing alpha-rarefaction diversity analysis
**URL:** https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510
**Category:** User Support
**Tags:** diversity, alpha-rarefaction
**Created:** [August 30, 2023, 3:41pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510 "2023-08-30T15:41:52Z")
**Posts on this page:** 16
**Page:** 1
### Author:  [@vasanth\_mandla](https://forum.qiime2.org/u/vasanth_mandla)
#### Post date: [August 30, 2023, 3:41pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/1 "2023-08-30T15:41:53Z")
I am using the emp-single-end-sequences dataset to run the Qiime2 workflow.
I was able to generate the phylogenetic tree for the diversity analysis. But, after this step I was unable to generate the visualization file (qzv) for the alpha-rarefaction. It is giving the error, as following. I have removed and reinstalled Qiime2, even then the error is not solved.
**Error**
Plugin error from diversity:
[Errno 8] Exec format error: 'faithpd'
Debug info has been saved to /tmp/qiime2-q2cli-err-\_i4csh25.log
**Command used:**
qiime diversity alpha-rarefaction --i-table table-dada2.qza --i-phylogeny rooted-tree.qza --p-max-depth 4000 --m-metadata-file sample-metadata.tsv --o-visualization alpha-rarefaction.qzv --qverbose
**Verbose Output:**
(qiime2-2023.7) bioinfo@AHLL09533:~/meta\_geneome$ qiime diversity alpha-rarefaction --i-table table-dada2.qza --i-phylogeny rooted-tree.qza --p-max-depth 4000 --m-metadata-file sample-metadata.tsv --o-visualization alpha-rarefaction.qzv --verbose
Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.
Command:
faithpd -i /tmp/qiime2/bioinfo/data/991d9934-d26f-4aa9-8f42-f228edadc328/data/feature-table.biom -t /tmp/qiime2/bioinfo/data/f51690f0-8a8a-46b3-a425-39e1d3b31dbd/data/tree.nwk -o /tmp/q2-AlphaDiversityFormat-u0w7r459
Traceback (most recent call last):
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 478, in **call**
results = self.\_execute\_action(
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/commands.py", line 539, in \_execute\_action
results = action(\*\*arguments)
File "", line 2, in alpha\_rarefaction
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable
outputs = self._callable\_executor_(
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 615, in _callable\_executor_
ret\_val = self.\_callable(output\_dir=temp\_dir, \*\*view\_args)
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2\_diversity/\_alpha/\_visualizer.py", line 375, in alpha\_rarefaction
data = \_compute\_rarefaction\_data(table, min\_depth, max\_depth,
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2\_diversity/\_alpha/\_visualizer.py", line 306, in \_compute\_rarefaction\_data
vector, = alpha\_phylo(table=rt, metric=metric,
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/context.py", line 140, in deferred\_action
return action\_obj.\_bind(
File "", line 2, in alpha\_phylogenetic
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable
outputs = self._callable\_executor_(
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 647, in _callable\_executor_
outputs = self.\_callable(scope.ctx, \*\*view\_args)
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2\_diversity/\_alpha/\_pipeline.py", line 16, in alpha\_phylogenetic
vector, = action(table, phylogeny)
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/context.py", line 140, in deferred\_action
return action\_obj.\_bind(
File "", line 2, in faith\_pd
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 342, in bound\_callable
outputs = self._callable\_executor_(
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/action.py", line 566, in _callable\_executor_
output\_views = self.\_callable(\*\*view\_args)
File "", line 2, in faith\_pd
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 69, in \_disallow\_empty\_tables
return wrapped\_function(\*args, \*\*kwargs)
File "", line 2, in faith\_pd
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 112, in \_validate\_requested\_cpus
return wrapped\_function(\*bound\_arguments.args, \*\*bound\_arguments.kwargs)
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2\_diversity\_lib/alpha.py", line 53, in faith\_pd
\_omp\_cmd\_wrapper(threads, cmd)
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 128, in \_omp\_cmd\_wrapper
return \_run\_external\_cmd(cmd, verbose=verbose, env=env)
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2\_diversity\_lib/\_util.py", line 122, in \_run\_external\_cmd
return subprocess.run(cmd, check=True, env=env)
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/subprocess.py", line 493, in run
with Popen(\*popenargs, \*\*kwargs) as process:
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/subprocess.py", line 858, in **init**
self.\_execute\_child(args, executable, preexec\_fn, close\_fds,
File "/home/bioinfo/anaconda3/envs/qiime2-2023.7/lib/python3.8/subprocess.py", line 1704, in \_execute\_child
raise child\_exception\_type(errno\_num, err\_msg, err\_filename)
OSError: [Errno 8] Exec format error: 'faithpd'
Plugin error from diversity:
[Errno 8] Exec format error: 'faithpd'
See above for debug info.
**Files in directory**
(qiime2-2023.7) bioinfo@AHLL09533:~/meta\_geneome$ ls -ltr
total 54624
-rw-r--r-- 1 bioinfo bioinfo 12885 Aug 26 17:00 qiime2-2023.7-py38-linux-conda.yml
-rw-r--r-- 1 bioinfo bioinfo 2094 Aug 26 17:35 sample-metadata.tsv
drwxr-xr-x 1 bioinfo bioinfo 4096 Aug 26 17:45 single\_end\_sequences
-rw-r--r-- 1 bioinfo bioinfo 29102196 Aug 29 17:15 empsingle-end-sequences.qza
-rw-r--r-- 1 bioinfo bioinfo 20603392 Aug 29 18:07 demux.qza
-rw-r--r-- 1 bioinfo bioinfo 3502245 Aug 29 18:07 demuxdetails.qza
-rw-r--r-- 1 bioinfo bioinfo 302578 Aug 29 18:09 demux.qzv
-rw-r--r-- 1 bioinfo bioinfo 54459 Aug 29 18:30 table-dada2.qza
-rw-r--r-- 1 bioinfo bioinfo 50610 Aug 29 18:30 rep-seqs-dada2.qza
-rw-r--r-- 1 bioinfo bioinfo 17883 Aug 29 18:30 stats-dada2.qza
-rw-r--r-- 1 bioinfo bioinfo 1223783 Aug 29 18:38 stats-dada2.qzv
-rw-r--r-- 1 bioinfo bioinfo 453782 Aug 30 10:29 table.qzv
-rw-r--r-- 1 bioinfo bioinfo 284451 Aug 30 10:57 rep-seqs.qzv
-rw-r--r-- 1 bioinfo bioinfo 62633 Aug 30 11:16 aligned-rep-seqs.qza
-rw-r--r-- 1 bioinfo bioinfo 65293 Aug 30 11:40 masked-aligned-rep-seqs.qza
-rw-r--r-- 1 bioinfo bioinfo 63171 Aug 30 11:40 unrooted-tree.qza
-rw-r--r-- 1 bioinfo bioinfo 67614 Aug 30 11:40 rooted-tree.qza
**Qiime2 Version:**
(qiime2-2023.7) bioinfo@AHLL09533:~/meta\_geneome$ qiime info
System versions
Python version: 3.8.15
QIIME 2 release: 2023.7
QIIME 2 version: 2023.7.0
q2cli version: 2023.7.0
Installed plugins
alignment: 2023.7.0
composition: 2023.7.0
cutadapt: 2023.7.0
dada2: 2023.7.0
deblur: 2023.7.0
demux: 2023.7.0
diversity: 2023.7.0
diversity-lib: 2023.7.0
emperor: 2023.7.0
feature-classifier: 2023.7.0
feature-table: 2023.7.0
fragment-insertion: 2023.7.0
gneiss: 2023.7.0
longitudinal: 2023.7.0
metadata: 2023.7.0
phylogeny: 2023.7.0
quality-control: 2023.7.0
quality-filter: 2023.7.0
sample-classifier: 2023.7.0
taxa: 2023.7.0
types: 2023.7.0
vsearch: 2023.7.0
Application config directory
/home/bioinfo/anaconda3/envs/qiime2-2023.7/var/q2cli
Getting help
To get help with QIIME 2, visit [https://qiime2.org](https://qiime2.org)
**Qiime2 Installation Method**
Conda
Windows 10 Pro --\> Ubuntu --\> conda --\> Qiime2
**Ubuntu Version**
Ubuntu 20.04.6 LTS (GNU/Linux 4.4.0-19041-Microsoft x86\_64)
command:
conda env create -n qiime2-2023.7 --file qiime2-2023.7-py38-linux-conda.yml
**Please, let me know if you need any further information
Thanks in advance**
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [August 30, 2023, 6:04pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/2 "2023-08-30T18:04:12Z")
Hello @vasanth_mandla,
What happens when you try to run the `faithpd` command alone in your environment?
---
### Author:  [@vasanth\_mandla](https://forum.qiime2.org/u/vasanth_mandla)
#### Post date: [August 31, 2023, 8:02am UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/4 "2023-08-31T08:02:10Z")
Hi @colinvwood ,
Thank you, for your response.
The following is the output:
-bash: /home/bioinfo/anaconda3/envs/qiime2-2023.7/bin/faithpd: cannot execute binary file: Exec format error
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [August 31, 2023, 4:13pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/5 "2023-08-31T16:13:22Z")
Hello @vasanth_mandla,
It looks like you installed a binary that is incompatible with your machine somehow. You ran all of these commands inside of WSL with the qiime environment activated, correct?
Is it possible you followed installation instructions for a different architecture in the docs?
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [August 31, 2023, 4:16pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/6 "2023-08-31T16:16:12Z")
Hello @5cr34m,
The post you linked discusses a different error message from a different command. We're grateful for help on the forum, but please be a little more careful about making sure your responses are on topic.
---
### Author:  [@vasanth\_mandla](https://forum.qiime2.org/u/vasanth_mandla)
#### Post date: [September 1, 2023, 7:22am UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/7 "2023-09-01T07:22:57Z")
Dear @colinvwood,
Yes, you are right. I have installed the Ubuntu(20.04.6 LTS) in windows 10, installed the Qiime and followed the tutorial.
I have realised my mistake of installing qiime, by following instructions from the following link:
[QIIME 2 Library](https://docs.qiime2.org/2023.7/install/native/) (Linux)
I have reinstalled qiime by following instruction from the tab Windows (via WSL) and performed the analysis similarly (to my first post) and got stuck at the same step.
The error output when I ran faithpd command alone is same as previously mentioned.
I have provided the "conda info" and files used in rarefaction analysis, for reference.
[rooted-tree.qza](https://forum.qiime2.org/uploads/short-url/mi65VOdcy7UQIMzdzxhD4N8gLbk.qza) (66.0 KB)
[table.qza](https://forum.qiime2.org/uploads/short-url/4ASU24JAEF2iwsBoIMFCkozY177.qza) (53.2 KB)
**conda info from new qiime(WSL) environment**
(qiime2-2023.7\_WSL) bioinfo@AHLL09533:~/meta\_geneome/meta\_test$ conda info
```
active environment : qiime2-2023.7_WSL
active env location : /home/bioinfo/anaconda3/envs/qiime2-2023.7_WSL
shell level : 2
user config file : /home/bioinfo/.condarc
```
populated config files :
conda version : 23.7.3
conda-build version : 3.26.0
python version : 3.11.4.final.0
virtual packages : \_\_archspec=1=x86\_64
\_\_glibc=2.31=0
\_\_linux=4.4.0=0
\_\_unix=0=0
base environment : /home/bioinfo/anaconda3 (writable)
conda av data dir : /home/bioinfo/anaconda3/etc/conda
conda av metadata url : None
channel URLs : [main/linux-64](https://repo.anaconda.com/pkgs/main/linux-64)
[main/noarch](https://repo.anaconda.com/pkgs/main/noarch)
[r/linux-64](https://repo.anaconda.com/pkgs/r/linux-64)
[r/noarch](https://repo.anaconda.com/pkgs/r/noarch)
package cache : /home/bioinfo/anaconda3/pkgs
/home/bioinfo/.conda/pkgs
envs directories : /home/bioinfo/anaconda3/envs
/home/bioinfo/.conda/envs
platform : linux-64
user-agent : conda/23.7.3 requests/2.31.0 CPython/3.11.4 Linux/4.4.0-19041-Microsoft ubuntu/20.04.6 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
---
### Author:  [@5cr34m](https://forum.qiime2.org/u/5cr34m)
#### Post date: [September 1, 2023, 1:56pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/8 "2023-09-01T13:56:56Z")
Sorry, my fault.
I'll try to.
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [September 1, 2023, 5:06pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/9 "2023-09-01T17:06:03Z")
Hello @vasanth_mandla,
What does `file $(which faithpd)` output?
---
### Author:  [@vasanth\_mandla](https://forum.qiime2.org/u/vasanth_mandla)
#### Post date: [September 2, 2023, 5:40am UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/10 "2023-09-02T05:40:24Z")
Hi @colinvwood ,
The following is the output:
(qiime2-2023.7\_WSL) bioinfo@AHLL09533:~/meta\_geneome/meta\_test$ file $(which faithpd)
/home/bioinfo/anaconda3/envs/qiime2-2023.7\_WSL/bin/faithpd: symbolic link to faithpd\_nv
Looks like, it does take the faithpd from where it supposed to. Did you get a chance to look at the files that I have provided. If so, did you find anything sceptical.
Thanks, for you time.
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [September 5, 2023, 4:46pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/11 "2023-09-05T16:46:01Z")
Hello @vasanth_mandla,
Can you run `file $(which faithpd_nv)`?
---
### Author:  [@vasanth\_mandla](https://forum.qiime2.org/u/vasanth_mandla)
#### Post date: [September 7, 2023, 5:06am UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/12 "2023-09-07T05:06:03Z")
Hi @colinvwood ,
Below is the output:
(qiime2-2023.7\_WSL) bioinfo@AHLL09533:~/meta\_geneome$ file $(which faithpd\_nv)
/home/bioinfo/anaconda3/envs/qiime2-2023.7\_WSL/bin/faithpd\_nv: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked, interpreter /lib64/ld-linux-x86-64.so.2, for GNU/Linux 2.6.18, with debug\_info, not stripped
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [September 7, 2023, 4:52pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/13 "2023-09-07T16:52:09Z")
Hello @vasanth_mandla,
And what does `uname -m` output in your linux terminal?
---
### Author:  [@vasanth\_mandla](https://forum.qiime2.org/u/vasanth_mandla)
#### Post date: [September 8, 2023, 5:54am UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/14 "2023-09-08T05:54:35Z")
Hi @colinvwood,
Output:
(qiime2-2023.7\_WSL) bioinfo@AHLL09533:~$ uname -m
x86\_64
---
### Author:  [@colinvwood](https://forum.qiime2.org/u/colinvwood)
#### Post date: [September 8, 2023, 5:37pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/15 "2023-09-08T17:37:58Z")
Hello @vasanth_mandla,
A possible solution is found [here](https://stackoverflow.com/questions/75249510/cannot-execute-binary-file-exec-format-error-for-a-binary-compiled-in-wsl-envir).
---
### Author:  [@vasanth\_mandla](https://forum.qiime2.org/u/vasanth_mandla)
#### Post date: [September 14, 2023, 6:31am UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/16 "2023-09-14T06:31:43Z")
Dear @colinvwood ,
I did try to resolve it by following your suggestion but, it did not solve the problem.
So, I have re-installed conda and qiime2 environment after completely removing them. Then the diversity analysis command started working as intended. In addition I have upgraded the WLS to version 2.
Thanks, for your time and patience in helping to resolve it.
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [October 15, 2023, 12:32pm UTC](https://forum.qiime2.org/t/help-in-performing-alpha-rarefaction-diversity-analysis/27510/17 "2023-10-15T12:32:24Z")
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