RuntimeError: Click will abort further execution because Python 3 was configured to use ASCII as encoding for the environment

Hi, everyone, I installed the QIIME2 with miniconda2, and when I source activate qiime2-2018.11,it shows errors

Traceback (most recent call last):
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 696, in main
    _verify_python3_env()
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/click/_unicodefun.py", line 124, in _verify_python3_env
    ' mitigation steps.' + extra
RuntimeError: Click will abort further execution because Python 3 was configured to use ASCII as encoding for the environment. Consult https://click.palletsprojects.com/en/7.x/python3/ for mitigation steps.

This system lists a couple of UTF-8 supporting locales that
you can pick from.  The following suitable locales were
discovered: aa_DJ.utf8, aa_ER.utf8, aa_ET.utf8, af_ZA.utf8, am_ET.utf8, an_ES.utf8, ar_AE.utf8, ar_BH.utf8, ar_DZ.utf8, ar_EG.utf8, ar_IN.utf8, ar_IQ.utf8, ar_JO.utf8, ar_KW.utf8, ar_LB.utf8, ar_LY.utf8, ar_MA.utf8, ar_OM.utf8, ar_QA.utf8, ar_SA.utf8, ar_SD.utf8, ar_SY.utf8, ar_TN.utf8, ar_YE.utf8, as_IN.utf8, ast_ES.utf8, az_AZ.utf8, be_BY.utf8, ber_DZ.utf8, ber_MA.utf8, bg_BG.utf8, bn_BD.utf8, bn_IN.utf8, bo_CN.utf8, bo_IN.utf8, br_FR.utf8, bs_BA.utf8, byn_ER.utf8, ca_AD.utf8, ca_ES.utf8, ca_FR.utf8, ca_IT.utf8, crh_UA.utf8, cs_CZ.utf8, csb_PL.utf8, cv_RU.utf8, cy_GB.utf8, da_DK.utf8, de_AT.utf8, de_BE.utf8, de_CH.utf8, de_DE.utf8, de_LU.utf8, dv_MV.utf8, dz_BT.utf8, el_CY.utf8, el_GR.utf8, en_AG.utf8, en_AU.utf8, en_BW.utf8, en_CA.utf8, en_DK.utf8, en_GB.utf8, en_HK.utf8, en_IE.utf8, en_IN.utf8, en_NG.utf8, en_NZ.utf8, en_PH.utf8, en_SG.utf8, en_US.utf8, en_ZA.utf8, en_ZW.utf8, es_AR.utf8, es_BO.utf8, es_CL.utf8, es_CO.utf8, es_CR.utf8, es_DO.utf8, es_EC.utf8, es_ES.utf8, es_GT.utf8, es_HN.utf8, es_MX.utf8, es_NI.utf8, es_PA.utf8, es_PE.utf8, es_PR.utf8, es_PY.utf8, es_SV.utf8, es_US.utf8, es_UY.utf8, es_VE.utf8, et_EE.utf8, eu_ES.utf8, fa_IR.utf8, fi_FI.utf8, fil_PH.utf8, fo_FO.utf8, fr_BE.utf8, fr_CA.utf8, fr_CH.utf8, fr_FR.utf8, fr_LU.utf8, fur_IT.utf8, fy_DE.utf8, fy_NL.utf8, ga_IE.utf8, gd_GB.utf8, gez_ER.utf8, gez_ET.utf8, gl_ES.utf8, gu_IN.utf8, gv_GB.utf8, ha_NG.utf8, he_IL.utf8, hi_IN.utf8, hne_IN.utf8, hr_HR.utf8, hsb_DE.utf8, ht_HT.utf8, hu_HU.utf8, hy_AM.utf8, id_ID.utf8, ig_NG.utf8, ik_CA.utf8, is_IS.utf8, it_CH.utf8, it_IT.utf8, iu_CA.utf8, iw_IL.utf8, ja_JP.utf8, ka_GE.utf8, kk_KZ.utf8, kl_GL.utf8, km_KH.utf8, kn_IN.utf8, ko_KR.utf8, kok_IN.utf8, ks_IN.utf8, ku_TR.utf8, kw_GB.utf8, ky_KG.utf8, lg_UG.utf8, li_BE.utf8, li_NL.utf8, lo_LA.utf8, lt_LT.utf8, lv_LV.utf8, mai_IN.utf8, mg_MG.utf8, mi_NZ.utf8, mk_MK.utf8, ml_IN.utf8, mn_MN.utf8, mr_IN.utf8, ms_MY.utf8, mt_MT.utf8, my_MM.utf8, nb_NO.utf8, nds_DE.utf8, nds_NL.utf8, ne_NP.utf8, nl_AW.utf8, nl_BE.utf8, nl_NL.utf8, nn_NO.utf8, no_NO.utf8, nr_ZA.utf8, nso_ZA.utf8, oc_FR.utf8, om_ET.utf8, om_KE.utf8, or_IN.utf8, pa_IN.utf8, pa_PK.utf8, pap_AN.utf8, pl_PL.utf8, ps_AF.utf8, pt_BR.utf8, pt_PT.utf8, ro_RO.utf8, ru_RU.utf8, ru_UA.utf8, rw_RW.utf8, sa_IN.utf8, sc_IT.utf8, sd_IN.utf8, se_NO.utf8, shs_CA.utf8, si_LK.utf8, sid_ET.utf8, sk_SK.utf8, sl_SI.utf8, so_DJ.utf8, so_ET.utf8, so_KE.utf8, so_SO.utf8, sq_AL.utf8, sq_MK.utf8, sr_ME.utf8, sr_RS.utf8, ss_ZA.utf8, st_ZA.utf8, sv_FI.utf8, sv_SE.utf8, ta_IN.utf8, te_IN.utf8, tg_TJ.utf8, th_TH.utf8, ti_ER.utf8, ti_ET.utf8, tig_ER.utf8, tk_TM.utf8, tl_PH.utf8, tn_ZA.utf8, tr_CY.utf8, tr_TR.utf8, ts_ZA.utf8, tt_RU.utf8, ug_CN.utf8, uk_UA.utf8, ur_PK.utf8, ve_ZA.utf8, vi_VN.utf8, wa_BE.utf8, wo_SN.utf8, xh_ZA.utf8, yi_US.utf8, yo_NG.utf8, zh_CN.utf8, zh_HK.utf8, zh_SG.utf8, zh_TW.utf8, zu_ZA.utf8

So, what can I do for solving for this error?
THANKS!

Hi @JIM

I think I had a similar issue with set up. At some point, working on a non-english/non american cluster, I had to add the following lines to my bashrc to deal with some of the language issues. I’m not sure if it will work for you, but it’s work a try.

LC_ALL=en_US
export LC_ALL

Best,
Justine

1 Like

Thanks, Justine. I used this way export LC_ALL=en_AG.utf8, en_AU.utf8, en_BW.utf8, en_CA.utf8, en_DK.utf8, en_GB.utf8, en_HK.utf8, en_IE.utf8, en_IN.utf8,en_NG.utf8, en_NZ.utf8, en_PH.utf8, en_SG.utf8, en_US.utf8, en_ZA.utf8, en_ZW.utf8, every en_*.utf8 I tried, but, it didnt work. …

Did you try

LC_ALL=en_US
export LC_ALL

Rather than using the UTF-8 specification?

Best,
Justine

Thank you for your reply. And it doesn’t work.

(qiime2-2018.11) [[email protected] ~]$ LC_ALL=en_US
(qiime2-2018.11) [[email protected] ~]$ export LC_ALL
(qiime2-2018.11) [[email protected] ~]$ qiime --help
Traceback (most recent call last):
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 696, in main
    _verify_python3_env()
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/click/_unicodefun.py", line 124, in _verify_python3_env
    ' mitigation steps.' + extra
RuntimeError: Click will abort further execution because Python 3 was configured to use ASCII as encoding for the environment. Consult https://click.palletsprojects.com/en/7.x/python3/ for mitigation steps.

This system lists a couple of UTF-8 supporting locales that
you can pick from.  The following suitable locales were
discovered: aa_DJ.utf8, aa_ER.utf8, aa_ET.utf8, af_ZA.utf8, am_ET.utf8, an_ES.utf8, ar_AE.utf8, ar_BH.utf8, ar_DZ.utf8, ar_EG.utf8, ar_IN.utf8, ar_IQ.utf8, ar_JO.utf8, ar_KW.utf8, ar_LB.utf8, ar_LY.utf8, ar_MA.utf8, ar_OM.utf8, ar_QA.utf8, ar_SA.utf8, ar_SD.utf8, ar_SY.utf8, ar_TN.utf8, ar_YE.utf8, as_IN.utf8, ast_ES.utf8, az_AZ.utf8, be_BY.utf8, ber_DZ.utf8, ber_MA.utf8, bg_BG.utf8, bn_BD.utf8, bn_IN.utf8, bo_CN.utf8, bo_IN.utf8, br_FR.utf8, bs_BA.utf8, byn_ER.utf8, ca_AD.utf8, ca_ES.utf8, ca_FR.utf8, ca_IT.utf8, crh_UA.utf8, cs_CZ.utf8, csb_PL.utf8, cv_RU.utf8, cy_GB.utf8, da_DK.utf8,.....

@JIM, forgive me if I’m wrong, but this does seem like a locale issue at first glance.
Please use the following commands to check the values of your system’s locale environment variables, and paste the output here.

echo $LC_ALL
echo $LANG

These snippets might help you get things patched up if the variables return no values, or similar.

Good luck!
CK

2 Likes

Thanks,@ChrisKeefe.
The output is

(qiime2-2018.11) [[email protected] envs]$ echo $LC_ALL
C
(qiime2-2018.11) [[email protected] envs]$ echo $LANG
en_US.UTF-8

@JIM, it looks like setting LC_ALL=en_US.UTF-8 either didn’t take, or has been reverted to C.

Try using this to set it again…

… then checking the value again using echo $LC_ALL.

If the setting has updated to en_US.UTF-8, try your commands again to see whether there’s a different outcome. If that doesn’t work, you might try the second approach Thermokarst suggests in this post, setting the variable on a temporary basis, while running your command.

If these suggestions don’t help, let us know what response you get and we’ll go from there. Thanks for your patience,
Chris

@ChrisKeefe Thank you very much! I open a new shell windows, and export LC_ALL=en_US.UTF-8, thenecho $LC_ALL,and it showsen_US.UTF-8,when I source activate qiime2-2018.11, it shows :

sh: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8)
Traceback (most recent call last):
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/click/core.py", line 696, in main
    _verify_python3_env()
  File "/public/home/mgb217/miniconda2/envs/qiime2-2018.11/lib/python3.5/site-packages/click/_unicodefun.py", line 124, in _verify_python3_env
    ' mitigation steps.' + extra
RuntimeError: Click will abort further execution because Python 3 was configured to use ASCII as encoding for the environment. Consult https://click.palletsprojects.com/en/7.x/python3/ for mitigation steps.

This system lists a couple of UTF-8 supporting locales that
you can pick from.  The following suitable locales were
discovered: aa_DJ.utf8, aa_ER.utf8, aa_ET.utf8.......
Click discovered that you exported a UTF-8 locale
but the locale system could not pick up from it because
it does not exist.  The exported locale is "en_US.UTF-8" but it
is not supported

And then, I use the method of @thermokarst export LC_ALL=en_US.UTF-8 && export LANG=en_US.UTF-8,source activate qiime2-2018.11,it shows same with above.Last, I used LC_ALL=C.UTF-8 LANG=C.UTF-8,it shows -bash: warning: setlocale: LC_ALL: cannot change locale (C.UTF-8): No such file or directory

@JIM. Is this a centOS system?
The Click documentation referenced in your error message mentions that

On some systems it was reported that UTF-8 has to be written as UTF8 and vice versa.

Try export LC_ALL=en_US.utf8
If that doesn’t work, try export LC_ALL=en_US.UTF8

Sorry this is taking so long to work out!
:thinking::pray::sweat:
Chris

Hello, I’m having a similar problem but I get an additional line about how to fix the problem. I’m looking at the site, but so far I don’t understand what to do since I am clueless about python. I use qiime1.9.1 with no problems by the way. I am reanalyzing some old data and wanted to use the newer qiime version.

RuntimeError: Click will abort further execution because Python 3 was configured to use ASCII as encoding for the environment. Consult https://click.palletsprojects.com/en/7.x/python3/ for mitigation steps.

I’m going to try and use the fixes you suggested to Jim but perhaps there is a better way???
Thanks.

Hi, I still got a weird error when I used the code but qiime 2 opened:

LC_ALL=en_US
export LC_ALL

I got:
Unable to revert mtime: /Library/Fonts

So I went back and read the mitigation stepson the website from my previous email and though I didn’t understand all the stuff about problems with python3 and click the suggested code did work perfectly. You have to run it before activating qiime2:

export LC_ALL=en_US.utf-8
export LANG=en_US.utf-8

Hopefully that is OK!!

4 Likes

@bmillerlab, I’m glad you were successful in fixing the original issue. In case it helps in the future, I believe this is roughly what’s going on: Python 3 thinks you are restricted to ASCII data. By setting your locale variables, you are telling Click, a Python package, how to handle unicode characters appropriately.

As for the second error (or warning?), it’s not something I’ve run into before. If it seems to create problems, please feel free to create a new post and we can try to help troubleshoot.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.