Running qiime2 on a cluster

User Support
1

So I'm getting the following error when I try and run anything through qiime2 on a cluster, was wondering if anyone can offer insight of if it's a cluster module issue or a qiime issue, and any ideas how to fix it??

Thanks!!

Traceback (most recent call last):
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 696, in main
    _verify_python3_env()
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/lib/python3.6/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, ayc_PE.utf8, az_AZ.utf8, be_BY.utf8, bem_ZM.utf8, ber_DZ.utf8, ber_MA.utf8, bg_BG.utf8, bho_IN.utf8, bn_BD.utf8, bn_IN.utf8, bo_CN.utf8, bo_IN.utf8, br_FR.utf8, brx_IN.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, doi_IN.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_ZM.utf8, en_ZW.utf8, es_AR.utf8, es_BO.utf8, es_CL.utf8, es_CO.utf8, es_CR.utf8, es_CU.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, ff_SN.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, ia_FR.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, lb_LU.utf8, lg_UG.utf8, li_BE.utf8, li_NL.utf8, lij_IT.utf8, lo_LA.utf8, lt_LT.utf8, lv_LV.utf8, mag_IN.utf8, mai_IN.utf8, mg_MG.utf8, mhr_RU.utf8, mi_NZ.utf8, mk_MK.utf8, ml_IN.utf8, mn_MN.utf8, mni_IN.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, nhn_MX.utf8, niu_NU.utf8, niu_NZ.utf8, nl_AW.utf8, nl_BE.utf8, nl_NL.utf8, nn_NO.utf8, nr_ZA.utf8, nso_ZA.utf8, oc_FR.utf8, om_ET.utf8, om_KE.utf8, or_IN.utf8, os_RU.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, sat_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, sw_KE.utf8, sw_TZ.utf8, szl_PL.utf8, ta_IN.utf8, ta_LK.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, unm_US.utf8, ur_IN.utf8, ur_PK.utf8, ve_ZA.utf8, vi_VN.utf8, wa_BE.utf8, wae_CH.utf8, wal_ET.utf8, wo_SN.utf8, xh_ZA.utf8, yi_US.utf8, yo_NG.utf8, yue_HK.utf8, zh_CN.utf8, zh_HK.utf8, zh_SG.utf8, zh_TW.utf8, zu_ZA.utf8
Traceback (most recent call last):
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 696, in main
    _verify_python3_env()
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/lib/python3.6/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, ayc_PE.utf8, az_AZ.utf8, be_BY.utf8, bem_ZM.utf8, ber_DZ.utf8, ber_MA.utf8, bg_BG.utf8, bho_IN.utf8, bn_BD.utf8, bn_IN.utf8, bo_CN.utf8, bo_IN.utf8, br_FR.utf8, brx_IN.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, doi_IN.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_ZM.utf8, en_ZW.utf8, es_AR.utf8, es_BO.utf8, es_CL.utf8, es_CO.utf8, es_CR.utf8, es_CU.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, ff_SN.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, ia_FR.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, lb_LU.utf8, lg_UG.utf8, li_BE.utf8, li_NL.utf8, lij_IT.utf8, lo_LA.utf8, lt_LT.utf8, lv_LV.utf8, mag_IN.utf8, mai_IN.utf8, mg_MG.utf8, mhr_RU.utf8, mi_NZ.utf8, mk_MK.utf8, ml_IN.utf8, mn_MN.utf8, mni_IN.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, nhn_MX.utf8, niu_NU.utf8, niu_NZ.utf8, nl_AW.utf8, nl_BE.utf8, nl_NL.utf8, nn_NO.utf8, nr_ZA.utf8, nso_ZA.utf8, oc_FR.utf8, om_ET.utf8, om_KE.utf8, or_IN.utf8, os_RU.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, sat_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, sw_KE.utf8, sw_TZ.utf8, szl_PL.utf8, ta_IN.utf8, ta_LK.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, unm_US.utf8, ur_IN.utf8, ur_PK.utf8, ve_ZA.utf8, vi_VN.utf8, wa_BE.utf8, wae_CH.utf8, wal_ET.utf8, wo_SN.utf8, xh_ZA.utf8, yi_US.utf8, yo_NG.utf8, yue_HK.utf8, zh_CN.utf8, zh_HK.utf8, zh_SG.utf8, zh_TW.utf8, zu_ZA.utf8
Traceback (most recent call last):
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/lib/python3.6/site-packages/click/core.py", line 696, in main
    _verify_python3_env()
  File "/sw/hprc/sw/Anaconda/3-5.0.0.1/envs/qiime2-2019.10/lib/python3.6/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, ayc_PE.utf8, az_AZ.utf8, be_BY.utf8, bem_ZM.utf8, ber_DZ.utf8, ber_MA.utf8, bg_BG.utf8, bho_IN.utf8, bn_BD.utf8, bn_IN.utf8, bo_CN.utf8, bo_IN.utf8, br_FR.utf8, brx_IN.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, doi_IN.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_ZM.utf8, en_ZW.utf8, es_AR.utf8, es_BO.utf8, es_CL.utf8, es_CO.utf8, es_CR.utf8, es_CU.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, ff_SN.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, ia_FR.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, lb_LU.utf8, lg_UG.utf8, li_BE.utf8, li_NL.utf8, lij_IT.utf8, lo_LA.utf8, lt_LT.utf8, lv_LV.utf8, mag_IN.utf8, mai_IN.utf8, mg_MG.utf8, mhr_RU.utf8, mi_NZ.utf8, mk_MK.utf8, ml_IN.utf8, mn_MN.utf8, mni_IN.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, nhn_MX.utf8, niu_NU.utf8, niu_NZ.utf8, nl_AW.utf8, nl_BE.utf8, nl_NL.utf8, nn_NO.utf8, nr_ZA.utf8, nso_ZA.utf8, oc_FR.utf8, om_ET.utf8, om_KE.utf8, or_IN.utf8, os_RU.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, sat_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, sw_KE.utf8, sw_TZ.utf8, szl_PL.utf8, ta_IN.utf8, ta_LK.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, unm_US.utf8, ur_IN.utf8, ur_PK.utf8, ve_ZA.utf8, vi_VN.utf8, wa_BE.utf8, wae_CH.utf8, wal_ET.utf8, wo_SN.utf8, xh_ZA.utf8, yi_US.utf8, yo_NG.utf8, yue_HK.utf8, zh_CN.utf8, zh_HK.utf8, zh_SG.utf8, zh_TW.utf8, zu_ZA.utf8
/var/spool/slurmd/job3711623/slurm_script: line 34: warning: here-document at line 31 delimited by end-of-file (wanted `CITATION')
2

Hi @smurray4!

This is an environment and encoding issue, and the error itself is coming from a tool called click that q2cli uses. There is a helpful little snippet in the middle of all of that madness:

Please check out the link there for more detail (in particular, check out the section titled "Python 3 Surrogate Handling"). It might be helpful to get your sysadmin involved, too.

Keep us posted!

3

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