Picrust2 tutorial error on WSL2

[LeandroD94]

Hi, I need to use Picrust2 with sepp method but I'm getting an error during the tutorial. I'm using Picrust2-2021.2 (qiime 2021.2 plugin) on a Windows 10 with WSL2 and Ubuntu shell. If I use Qiime2021.4 then I can't install Picrust2. Below I copy the error message. Can you help me, please?

Error running this command:
place_seqs.py --study_fasta /tmp/tmph2815mng/seqs.fna --ref_dir /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree /tmp/tmph2815mng/picrust2_out/out.tre --processes 4 --intermediate /tmp/tmph2815mng/picrust2_out/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool sepp

Standard output of the above failed command:
['run_sepp.py', '--tree', '/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre', '--raxml', '/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info', '--cpu', '4', '--molecule', 'dna', '--outdir', '/tmp/tmph2815mng/picrust2_out/intermediate/place_seqs/sepp_out', '-seed', '297834', '--alignment', '/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna', '--fragment', '/tmp/tmph2815mng/picrust2_out/intermediate/place_seqs/study_seqs_filtered.fasta']

Standard error of the above failed command:

Error running this command:
run_sepp.py --tree /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 4 --molecule dna --outdir /tmp/tmph2815mng/picrust2_out/intermediate/place_seqs/sepp_out -seed 297834 --alignment /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmph2815mng/picrust2_out/intermediate/place_seqs/study_seqs_filtered.fasta

Standard error of the above failed command:
[19:24:57] config.py (line 349): INFO: Seed number: 297834
[19:24:57] algorithm.py (line 259): INFO: Reading input alignment: <io.TextIOWrapper name='/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna' mode='r' encoding='UTF-8'>
[19:24:57] algorithm.py (line 265): INFO: Reading input tree: <io.TextIOWrapper name='/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre' mode='r' encoding='UTF-8'>
[19:24:59] algorithm.py (line 240): INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000
[19:25:02] exhaustive.py (line 351): INFO: Breaking into 16 placement subsets.
[19:25:04] exhaustive.py (line 398): INFO: Breaking into 16 alignment subsets.
[19:25:04] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/output.h1c8yids
[19:25:04] exhaustive.py (line 413): INFO: Breaking each alignment subset into 1 fragment chunks.
[19:25:05] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_1/A_1_0/hmmbuild.input.x__sopk9.fasta
[19:25:05] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_0/A_0_0/hmmbuild.input.x018948c.fasta
[19:25:05] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_3/A_3_0/hmmbuild.input.j5oedk43.fasta
[19:25:05] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_2/A_2_0/hmmbuild.input.i6orc2pe.fasta
[19:25:05] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_4/A_4_0/hmmbuild.input.6mt8fpyr.fasta
[19:25:06] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_5/A_5_0/hmmbuild.input.u0zient.fasta
[19:25:06] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_7/A_7_0/hmmbuild.input.76mb9mi8.fasta
[19:25:06] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_6/A_6_0/hmmbuild.input.tpuk93pa.fasta
[19:25:06] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_8/A_8_0/hmmbuild.input.ie3y7aq9.fasta
[19:25:06] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_9/A_9_0/hmmbuild.input.yybrqk3m.fasta
[19:25:06] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_10/A_10_0/hmmbuild.input.5edcco_0.fasta
[19:25:06] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_11/A_11_0/hmmbuild.input.uanye6rb.fasta
[19:25:07] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_12/A_12_0/hmmbuild.input.0fa39m20.fasta
[19:25:07] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_13/A_13_0/hmmbuild.input.ow5bc9zx.fasta
[19:25:07] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_14/A_14_0/hmmbuild.input.f71l8tpr.fasta
[19:25:07] jobs.py (line 132): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.h1c8yids/root/P_15/A_15_0/hmmbuild.input.yecdi373.fasta
[19:25:15] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_1/A_1_0/hmmbuild.model.zc7hxh83, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.wpwv9hyk
[19:25:15] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_0/A_0_0/hmmbuild.model.u60euv2w, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.51geonoo
[19:25:15] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_2/A_2_0/hmmbuild.model.v2fna7th, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_2/A_2_0/FC_2_0_0/hmmsearch.results.va62mtvc
[19:25:15] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_3/A_3_0/hmmbuild.model.v2li2i2t, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.6lswlc10
[19:25:23] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_4/A_4_0/hmmbuild.model.gux98azw, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.rrdgn569
[19:25:23] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_5/A_5_0/hmmbuild.model.a695y2qg, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.ksdg7hib
[19:25:23] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_7/A_7_0/hmmbuild.model.irkkilur, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.wup3ute9
[19:25:23] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_6/A_6_0/hmmbuild.model.zdbizu7o, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.7wwv9ix7
[19:25:31] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_8/A_8_0/hmmbuild.model.kvjqnz81, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.vz9uqt2
[19:25:31] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_9/A_9_0/hmmbuild.model.84otab50, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.21hiwzwn
[19:25:32] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_10/A_10_0/hmmbuild.model.66rj6oi_, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.u6j9238r
[19:25:32] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_11/A_11_0/hmmbuild.model.zlg7hyhe, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.sy45npmr
[19:25:39] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_12/A_12_0/hmmbuild.model.rmx7_4rn, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.s1x85drh
[19:25:40] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_13/A_13_0/hmmbuild.model.o9ee7yrk, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.wf6779hy
[19:25:40] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_14/A_14_0/hmmbuild.model.e6aixph_, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.6tokd_of
[19:25:40] jobs.py (line 132): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.h1c8yids/root/P_15/A_15_0/hmmbuild.model.p909vvrc, fragments:/tmp/sepp/output.h1c8yids/fragment_chunks/fragment_chunk_0z05p13cy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.h1c8yids/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.498qf5aq
[19:25:40] exhaustive.py (line 81): WARNING: Fragments [] are not scored against any subset
[19:25:40] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_0.
[19:25:40] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_3/A_3_0/hmmbuild.model.v2li2i2t, fragments:/tmp/sepp/output.h1c8yids/root/P_3/A_3_0/FC_3_0_0/hmmalign.frag.p88p__m9.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_3/A_3_0/hmmbuild.input.j5oedk43.fasta
[19:25:40] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_1/A_1_0/hmmbuild.model.zc7hxh83, fragments:/tmp/sepp/output.h1c8yids/root/P_1/A_1_0/FC_1_0_0/hmmalign.frag.ynqahs52.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_1/A_1_0/hmmbuild.input.x__sopk9.fasta
[19:25:40] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_3.
[19:25:40] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_3/A_3_0/FC_3_0_0/hmmalign.results.4vz3oftm) into base alignment (/tmp/sepp/output.h1c8yids/root/P_3/A_3_0/hmmbuild.input.j5oedk43.fasta).
[19:25:40] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_4/A_4_0/hmmbuild.model.gux98azw, fragments:/tmp/sepp/output.h1c8yids/root/P_4/A_4_0/FC_4_0_0/hmmalign.frag.7a5bbqqc.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_4/A_4_0/hmmbuild.input.6mt8fpyr.fasta
[19:25:40] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_1.
[19:25:40] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_1/A_1_0/FC_1_0_0/hmmalign.results.qbymx47) into base alignment (/tmp/sepp/output.h1c8yids/root/P_1/A_1_0/hmmbuild.input.x__sopk9.fasta).
[19:25:40] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_5/A_5_0/hmmbuild.model.a695y2qg, fragments:/tmp/sepp/output.h1c8yids/root/P_5/A_5_0/FC_5_0_0/hmmalign.frag.86ph6pme.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_5/A_5_0/hmmbuild.input.u0zient.fasta
[19:25:40] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_4.
[19:25:40] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_4/A_4_0/FC_4_0_0/hmmalign.results.e1p3cl35) into base alignment (/tmp/sepp/output.h1c8yids/root/P_4/A_4_0/hmmbuild.input.6mt8fpyr.fasta).
[19:25:40] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_5.
[19:25:40] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_5/A_5_0/FC_5_0_0/hmmalign.results.8fymlpoq) into base alignment (/tmp/sepp/output.h1c8yids/root/P_5/A_5_0/hmmbuild.input.u0zient_.fasta).
[19:25:40] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_6/A_6_0/hmmbuild.model.zdbizu7o, fragments:/tmp/sepp/output.h1c8yids/root/P_6/A_6_0/FC_6_0_0/hmmalign.frag.kw6rlk7_.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_6/A_6_0/hmmbuild.input.tpuk93pa.fasta
[19:25:40] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_8.
[19:25:40] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_9.
[19:25:40] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_2/A_2_0/hmmbuild.model.v2fna7th, fragments:/tmp/sepp/output.h1c8yids/root/P_2/A_2_0/FC_2_0_0/hmmalign.frag.f3hmq5bh.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_2/A_2_0/hmmbuild.input.i6orc2pe.fasta
[19:25:40] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_6.
[19:25:40] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_6/A_6_0/FC_6_0_0/hmmalign.results.gb_nn2nm) into base alignment (/tmp/sepp/output.h1c8yids/root/P_6/A_6_0/hmmbuild.input.tpuk93pa.fasta).
[19:25:40] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_2.
[19:25:40] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_2/A_2_0/FC_2_0_0/hmmalign.results.77t12ijx) into base alignment (/tmp/sepp/output.h1c8yids/root/P_2/A_2_0/hmmbuild.input.i6orc2pe.fasta).
[19:25:40] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_7/A_7_0/hmmbuild.model.irkkilur, fragments:/tmp/sepp/output.h1c8yids/root/P_7/A_7_0/FC_7_0_0/hmmalign.frag.p06ekhsc.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_7/A_7_0/hmmbuild.input.76mb9mi8.fasta
[19:25:40] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_7.
[19:25:40] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_7/A_7_0/FC_7_0_0/hmmalign.results.r7k73l1e) into base alignment (/tmp/sepp/output.h1c8yids/root/P_7/A_7_0/hmmbuild.input.76mb9mi8.fasta).
[19:25:41] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_10/A_10_0/hmmbuild.model.66rj6oi_, fragments:/tmp/sepp/output.h1c8yids/root/P_10/A_10_0/FC_10_0_0/hmmalign.frag.7cmeoe6x.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_10/A_10_0/hmmbuild.input.5edcco_0.fasta
[19:25:41] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_10.
[19:25:41] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_10/A_10_0/FC_10_0_0/hmmalign.results.ijm19e63) into base alignment (/tmp/sepp/output.h1c8yids/root/P_10/A_10_0/hmmbuild.input.5edcco_0.fasta).
[19:25:41] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_14.
[19:25:41] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_15/A_15_0/hmmbuild.model.p909vvrc, fragments:/tmp/sepp/output.h1c8yids/root/P_15/A_15_0/FC_15_0_0/hmmalign.frag.lcx1l9my.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_15/A_15_0/hmmbuild.input.yecdi373.fasta
[19:25:41] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_15.
[19:25:41] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_15/A_15_0/FC_15_0_0/hmmalign.results.iee_iyff) into base alignment (/tmp/sepp/output.h1c8yids/root/P_15/A_15_0/hmmbuild.input.yecdi373.fasta).
[19:25:41] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_13/A_13_0/hmmbuild.model.o9ee7yrk, fragments:/tmp/sepp/output.h1c8yids/root/P_13/A_13_0/FC_13_0_0/hmmalign.frag.jul_zdgu.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_13/A_13_0/hmmbuild.input.ow5bc9zx.fasta
[19:25:41] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_13.
[19:25:41] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_13/A_13_0/FC_13_0_0/hmmalign.results.tmd2tyu1) into base alignment (/tmp/sepp/output.h1c8yids/root/P_13/A_13_0/hmmbuild.input.ow5bc9zx.fasta).
[19:25:48] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_12/A_12_0/hmmbuild.model.rmx7_4rn, fragments:/tmp/sepp/output.h1c8yids/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.of9cm3uj.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_12/A_12_0/hmmbuild.input.0fa39m20.fasta
[19:25:48] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_12.
[19:25:48] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_12/A_12_0/FC_12_0_0/hmmalign.results.5ckahzu_) into base alignment (/tmp/sepp/output.h1c8yids/root/P_12/A_12_0/hmmbuild.input.0fa39m20.fasta).
[19:25:48] jobs.py (line 132): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.h1c8yids/root/P_11/A_11_0/hmmbuild.model.zlg7hyhe, fragments:/tmp/sepp/output.h1c8yids/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.dv99zukh.fasta, trim:False, base_alignment:/tmp/sepp/output.h1c8yids/root/P_11/A_11_0/hmmbuild.input.uanye6rb.fasta
[19:25:48] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_11.
[19:25:48] alignment.py (line 558): INFO: Merging extension sto file (/tmp/sepp/output.h1c8yids/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.0nrykou6) into base alignment (/tmp/sepp/output.h1c8yids/root/P_11/A_11_0/hmmbuild.input.uanye6rb.fasta).
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_3 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_3/pplacer.backbone.6iir7ttx.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_3/pplacer.tree.3t9wv7eh.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_3/pplacer.extended.0.vm2ugnti.fasta
No error messages available
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_1 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_1/pplacer.backbone.rpzu5m0a.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_1/pplacer.tree.26lflrp4.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_1/pplacer.extended.0.km7zfq.fasta
No error messages available
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_4 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_4/pplacer.backbone.x6tsms2l.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_4/pplacer.tree.i4bqgxm9.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_4/pplacer.extended.0.4un1zl8y.fasta
No error messages available
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_5 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_5/pplacer.backbone.iqjqgu20.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_5/pplacer.tree.f7_92f97.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_5/pplacer.extended.0.sxf0ru3a.fasta
No error messages available
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_6 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_6/pplacer.backbone.rysnjue6.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_6/pplacer.tree.nktceosi.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_6/pplacer.extended.0.5_jw77sq.fasta
No error messages available
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_2 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_2/pplacer.backbone.pk5p_5ii.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_2/pplacer.tree.iijpo3mq.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_2/pplacer.extended.0.8zxalp86.fasta
No error messages available
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_7 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_7/pplacer.backbone.rysskbqd.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_7/pplacer.tree.hvio14za.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_7/pplacer.extended.0.igbul3yg.fasta
No error messages available
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_10 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_10/pplacer.backbone.y940okz3.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_10/pplacer.tree.74_ny8hr.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_10/pplacer.extended.0.yo85ud4w.fasta
No error messages available
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_15 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_15/pplacer.backbone.bfz6aohb.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_15/pplacer.tree.cbs8vejp.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_15/pplacer.extended.0.4qfthufp.fasta
No error messages available
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_12 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_12/pplacer.backbone.24j0tcfg.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_12/pplacer.tree.htonnwfk.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_12/pplacer.extended.0.maik2nsz.fasta
No error messages available
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/scheduler.py", line 74, in call
return self.run()
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/jobs.py", line 154, in run
if self.read_stderr() else 'No error messages available']))
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_3 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_3/pplacer.backbone.6iir7ttx.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_3/pplacer.tree.3t9wv7eh.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_3/pplacer.extended.0.vm2ugnti.fasta
No error messages available
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/leand/miniconda3/envs/qiime2-2021.2/bin/run_sepp.py", line 26, in
ExhaustiveAlgorithm().run()
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/algorithm.py", line 174, in run
if (not JobPool().wait_for_all_jobs()):
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/sepp/scheduler.py", line 382, in wait_for_all_jobs
result.get()
File "/home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
sepp.scheduler.JobError: The following execution failed:
/home/leand/miniconda3/envs/qiime2-2021.2/bin/pplacer --out-dir /tmp/sepp/output.h1c8yids/root/P_3 -j 1 -r /tmp/sepp/output.h1c8yids/root/P_3/pplacer.backbone.6iir7ttx.fasta -s /home/leand/miniconda3/envs/qiime2-2021.2/lib/python3.6/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.h1c8yids/root/P_3/pplacer.tree.3t9wv7eh.tre --groups 10 /tmp/sepp/output.h1c8yids/root/P_3/pplacer.extended.0.vm2ugnti.fasta
No error messages available

[gavinmdouglas]

Hi @LeandroD94,

Thanks for posting the error message, but it's not obvious to me what the problem is based on that. Could you post the full command you're running?

Thanks,

Gavin

[LeandroD94]

Hi Gavin, thank you for your quick feedback.
The command is the following:

cd /mnt/c//users/leand/Desktop/q2-picrust2_tutorial

qiime picrust2 full-pipeline --i-table mammal_biom.qza --i-seq mammal_seqs.qza --output-dir q2-picrust2_output --p-placement-tool sepp --p-threads 4 --p-hsp-method pic --p-max-nsti 2 --verbose

Trying to delete or change same argument (p-threads, --p-hsp-method ecc.) i get the error above.
I write same other detail, hoping that it's usefull:

1. i'm on an Intel core I7 processor with 12 GB RAM (extended);
2. even using QIIME2-PICRUST2 image on docker (only older QIIME2 version actually avaiable) I get the same error;
3. on a similar issue, I read that the other method (epa ng) worked but not for me (I need the Sepp method anyway because of my PC);
4. during installation of Picrust2 the "solving enviroment" with "current repodata.json" failed but it worked with repodata.json;
5. I have already tried to update every repository and package in conda enviroment but nothing changed.

Thank you!

[gavinmdouglas]

Hmm thanks for sharing all of those details. Unfortunately I don't know what else to suggest for you to try besides just reinstalling the conda environment and trying it again.

Since it's not clear how to further troubleshoot this problem you're having you might want to use an alternative metagenome prediction tool like Piphillin or Tax4Fun2 instead in order for your work to move forward.

[LeandroD94]

If it's possible I would like to continue working with PICRUST2 because it's specifically requested by my client. Indeed I tried reinstalling everything and try with PICRUST2 standalone (installation by souce) meanwhile. The pytest displayed the same error (error only on placeseqs.py script!). I attach the file with what appeared on prompt.

If it's still not clear how to resolve this then dont'worry. Thank you anyway.

Leandro

Errore di Picrust.txt

[LeandroD94]

I have found the issue! Reinstalling everything I got the same error of issue #182 (sepp not working on WSL) so I decided to try Picrust2 on a virtual machine (running Ubuntu) and it worked fine. I deduce that there is a wrong interaction between WSL and sepp, is it right?

Two questions: 1) there will be an update to resolve this? 2) how much RAM this SEPP method would require with larger dataset (around 50 samples)?

Thank you for you time, have a good work

Leandro

[gavinmdouglas]

Ah great, sorry I had forgotten about that previous issue - I'm glad your it's resolved for you now! :)

1. There wont be an update on the PICRUSt2 side for this as it's an issue with SEPP dependency.

2. In terms of RAM usage I believe SEPP should only use ~8GB of RAM at max, but I haven't experimented too much to know the limits. By the way, the number of samples wont directly affect the RAM usage anyway - it's only the total number of ASVs that matters.

Cheers,

Gavin