pplacer or similar placement issue

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Ian Blixt

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Feb 18, 2025, 8:28:40 AMFeb 18

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Hello!

I'm a new picrust user and can't seem to get it working. I've tried running the pipeline code with epa-ng and sepp, and get the error messages below. The hmmalign.fasta files are both made correctly (ref_seqs_hmmalign.fasta and study_seqs_hmmalign.fasta) and contain sequence data. Unless I'm mistaken, it looks like the error is coming from pplacer, or placement in general, when trying to align the two sequence files. So, no out.tre file is created and the rest of the pipeline falls over.

I see a few other similar issues on this page, but those seem to be having poor alignments, while I'm having no alignments at all. Please help!

#==============

# EPA-NG

#==============

(picrust2) ianblixt@LAPTOP-7H5PH6LR:~/piecrust_data$ picrust2_pipeline.py -s /home/ianblixt/piecrust_data/ASVs_rep.fasta -i /home/ianblixt/piecrust_data/asv_counts.txt -o /home/ianblixt/piecrust_data/picrust2_out -p 4 --verbose
1571 of 1571 sequence ids overlap between input table and FASTA.

Placing sequences onto reference tree
place_seqs.py --study_fasta /home/ianblixt/piecrust_data/ASVs_rep.fasta --ref_dir /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree /home/ianblixt/piecrust_data/picrust2_out/out.tre --processes 4 --intermediate /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool epa-ng --verbose

Error running this command:
place_seqs.py --study_fasta /home/ianblixt/piecrust_data/ASVs_rep.fasta --ref_dir /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree /home/ianblixt/piecrust_data/picrust2_out/out.tre --processes 4 --intermediate /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool epa-ng --verbose

Standard output of the above failed command:

Standard error of the above failed command:
hmmalign --trim --dna --mapali /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/query_align.stockholm /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm /home/ianblixt/piecrust_data/ASVs_rep.fasta

Raw input sequences ranged in length from 379 to 430

epa-ng --tree /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/study_seqs_hmmalign.fasta --chunk-size 5000 -T 4 -m /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/epa_out --filter-acc-lwr 0.99 --filter-max 100

Error running this command:
epa-ng --tree /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --ref-msa /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/ref_seqs_hmmalign.fasta --query /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/study_seqs_hmmalign.fasta --chunk-size 5000 -T 4 -m /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model -w /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/epa_out --filter-acc-lwr 0.99 --filter-max 100

Standard output of the above failed command:
INFO Selected: Output dir: /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/epa_out/
INFO Selected: Query file: /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/study_seqs_hmmalign.fasta
INFO Selected: Tree file: /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre
INFO Selected: Reference MSA: /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/ref_seqs_hmmalign.fasta
INFO Selected: Filtering by accumulated threshold: 0.99
INFO Selected: Maximum number of placements per query: 100
INFO Selected: Automatic switching of use of per rate scalers
INFO Selected: Preserving the root of the input tree
INFO Selected: Specified model file: /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.model
INFO Selected: Reading queries in chunks of: 5000
INFO Selected: Using threads: 4
INFO ______ ____ ___ _ __ ______
/ ____// __ \ / | / | / // ____/
/ __/ / /_/ // /| | ______ / |/ // / __
/ /___ / ____// ___ |/_____// /| // /_/ /
/_____//_/ /_/ |_| /_/ |_/ \____/ (v0.3.8)

#=============================

# SEPP

#=============================

(picrust2) ianblixt@LAPTOP-7H5PH6LR:~/piecrust_data$ picrust2_pipeline.py -s /home/ianblixt/piecrust_data/ASVs_rep.fasta -i /home/ianblixt/piecrust_data/asv_counts.txt -o /home/ianblixt/piecrust_data/picrust2_out -p 4 --verbose -t sepp
1571 of 1571 sequence ids overlap between input table and FASTA.

Placing sequences onto reference tree
place_seqs.py --study_fasta /home/ianblixt/piecrust_data/ASVs_rep.fasta --ref_dir /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree /home/ianblixt/piecrust_data/picrust2_out/out.tre --processes 4 --intermediate /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool sepp --verbose

Error running this command:
place_seqs.py --study_fasta /home/ianblixt/piecrust_data/ASVs_rep.fasta --ref_dir /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree /home/ianblixt/piecrust_data/picrust2_out/out.tre --processes 4 --intermediate /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool sepp --verbose

Standard output of the above failed command:

Standard error of the above failed command:
hmmalign --trim --dna --mapali /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/query_align.stockholm /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm /home/ianblixt/piecrust_data/ASVs_rep.fasta

Raw input sequences ranged in length from 379 to 430

run_sepp.py --tree /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 4 --molecule dna --outdir /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/sepp_out -seed 297834 --alignment /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/study_seqs_filtered.fasta

Error running this command:
run_sepp.py --tree /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 4 --molecule dna --outdir /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/sepp_out -seed 297834 --alignment /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /home/ianblixt/piecrust_data/picrust2_out/intermediate/place_seqs/study_seqs_filtered.fasta

Standard error of the above failed command:
[17:35:46] config.py (line 370): INFO: Seed number: 297834
[17:35:46] algorithm.py (line 267): INFO: Reading input alignment: <_io.TextIOWrapper name='/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna' mode='r' encoding='UTF-8'>
[17:35:46] algorithm.py (line 274): INFO: Reading input tree: <_io.TextIOWrapper name='/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre' mode='r' encoding='UTF-8'>
[17:35:48] algorithm.py (line 247): INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000
[17:35:52] exhaustive.py (line 351): INFO: Breaking into 16 placement subsets.
[17:35:53] exhaustive.py (line 398): INFO: Breaking into 16 alignment subsets.
[17:35:53] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/output.o5n1_s57
[17:35:53] exhaustive.py (line 413): INFO: Breaking each alignment subset into 1 fragment chunks.
[17:35:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_1/A_1_0/hmmbuild.input.ovpdryhb.fasta
[17:35:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_0/A_0_0/hmmbuild.input.kao5nl85.fasta
[17:35:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_3/A_3_0/hmmbuild.input.786c2_zo.fasta
[17:35:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_2/A_2_0/hmmbuild.input.ingk3610.fasta
[17:35:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_4/A_4_0/hmmbuild.input.auv2f5f5.fasta
[17:35:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_5/A_5_0/hmmbuild.input.l_s6klua.fasta
[17:35:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_7/A_7_0/hmmbuild.input.0n991yg8.fasta
[17:35:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_6/A_6_0/hmmbuild.input.aablk8nw.fasta
[17:35:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_8/A_8_0/hmmbuild.input.gheqmem1.fasta
[17:35:59] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_10/A_10_0/hmmbuild.input.nlq0ak48.fasta
[17:35:59] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_9/A_9_0/hmmbuild.input.rc65k5t8.fasta
[17:35:59] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_11/A_11_0/hmmbuild.input.v47oqg2w.fasta
[17:35:59] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_12/A_12_0/hmmbuild.input.2hlorj5b.fasta
[17:35:59] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_13/A_13_0/hmmbuild.input.j4q4gify.fasta
[17:35:59] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_14/A_14_0/hmmbuild.input.ur66u0a1.fasta
[17:35:59] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.o5n1_s57/root/P_15/A_15_0/hmmbuild.input.lxk0nfoi.fasta
[17:36:35] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_1/A_1_0/hmmbuild.model.d47ql11b, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.kahbeqb3
[17:36:35] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_2/A_2_0/hmmbuild.model.jb0w4l1h, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_2/A_2_0/FC_2_0_0/hmmsearch.results.d23_f6nl
[17:36:35] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_3/A_3_0/hmmbuild.model.395ocnie, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.p65me0yc
[17:36:36] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_0/A_0_0/hmmbuild.model.kjk_xmi8, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.n5mct8z6
[17:37:09] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_4/A_4_0/hmmbuild.model.qtzqw7yk, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.g0mxvbdy
[17:37:10] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_7/A_7_0/hmmbuild.model.gqr4b3u0, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.x2jxrmgp
[17:37:10] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_5/A_5_0/hmmbuild.model.kh0s4g1a, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.p0hoc3oc
[17:37:10] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_6/A_6_0/hmmbuild.model.6er2wf_5, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.guthfoxz
[17:37:42] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_8/A_8_0/hmmbuild.model.bbe6wc6n, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.y94f47dp
[17:37:42] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_10/A_10_0/hmmbuild.model.jbyps1hb, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.za3ciwkv
[17:37:43] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_9/A_9_0/hmmbuild.model.f7juswv9, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.kuopjme1
[17:37:44] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_11/A_11_0/hmmbuild.model.t3v302di, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.1op_2t6e
[17:38:16] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_12/A_12_0/hmmbuild.model.631i1tox, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.o1q42nqe
[17:38:17] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_13/A_13_0/hmmbuild.model.rws1m56m, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.l75cs7fj
[17:38:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_14/A_14_0/hmmbuild.model.17eac4q6, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.loes5koe
[17:38:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_15/A_15_0/hmmbuild.model.5qss3tuu, fragments:/tmp/sepp/output.o5n1_s57/fragment_chunks/fragment_chunk_08eibhnfw.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.o5n1_s57/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.os4rykfx
[17:38:18] exhaustive.py (line 81): WARNING: Fragments [] are not scored against any subset
[17:38:18] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_0/A_0_0/hmmbuild.model.kjk_xmi8, fragments:/tmp/sepp/output.o5n1_s57/root/P_0/A_0_0/FC_0_0_0/hmmalign.frag.vyqxzv28.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_0/A_0_0/hmmbuild.input.kao5nl85.fasta
[17:38:18] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_0.
[17:38:18] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_0/A_0_0/FC_0_0_0/hmmalign.results.8hbi9b8b) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_0/A_0_0/hmmbuild.input.kao5nl85.fasta).
[17:38:18] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_3/A_3_0/hmmbuild.model.395ocnie, fragments:/tmp/sepp/output.o5n1_s57/root/P_3/A_3_0/FC_3_0_0/hmmalign.frag.0_imx426.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_3/A_3_0/hmmbuild.input.786c2_zo.fasta
[17:38:18] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_3.
[17:38:18] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_3/A_3_0/FC_3_0_0/hmmalign.results.wpqgrhkp) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_3/A_3_0/hmmbuild.input.786c2_zo.fasta).
[17:38:18] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_2/A_2_0/hmmbuild.model.jb0w4l1h, fragments:/tmp/sepp/output.o5n1_s57/root/P_2/A_2_0/FC_2_0_0/hmmalign.frag.52inynd7.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_2/A_2_0/hmmbuild.input.ingk3610.fasta
[17:38:18] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_2.
[17:38:18] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_2/A_2_0/FC_2_0_0/hmmalign.results.kb5tyle8) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_2/A_2_0/hmmbuild.input.ingk3610.fasta).
[17:38:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_1/A_1_0/hmmbuild.model.d47ql11b, fragments:/tmp/sepp/output.o5n1_s57/root/P_1/A_1_0/FC_1_0_0/hmmalign.frag.nwaec8e4.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_1/A_1_0/hmmbuild.input.ovpdryhb.fasta
[17:38:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_1.
[17:38:19] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_1/A_1_0/FC_1_0_0/hmmalign.results._o2f5zcx) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_1/A_1_0/hmmbuild.input.ovpdryhb.fasta).
[17:38:20] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_5/A_5_0/hmmbuild.model.kh0s4g1a, fragments:/tmp/sepp/output.o5n1_s57/root/P_5/A_5_0/FC_5_0_0/hmmalign.frag.ciy3hs2n.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_5/A_5_0/hmmbuild.input.l_s6klua.fasta
[17:38:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_5.
[17:38:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_5/A_5_0/FC_5_0_0/hmmalign.results.bb1_096s) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_5/A_5_0/hmmbuild.input.l_s6klua.fasta).
[17:38:20] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_8/A_8_0/hmmbuild.model.bbe6wc6n, fragments:/tmp/sepp/output.o5n1_s57/root/P_8/A_8_0/FC_8_0_0/hmmalign.frag.m61f8r10.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_8/A_8_0/hmmbuild.input.gheqmem1.fasta
[17:38:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_8.
[17:38:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_8/A_8_0/FC_8_0_0/hmmalign.results.fmmz5fs5) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_8/A_8_0/hmmbuild.input.gheqmem1.fasta).
[17:38:20] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_7/A_7_0/hmmbuild.model.gqr4b3u0, fragments:/tmp/sepp/output.o5n1_s57/root/P_7/A_7_0/FC_7_0_0/hmmalign.frag.i06vhk0k.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_7/A_7_0/hmmbuild.input.0n991yg8.fasta
[17:38:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_7.
[17:38:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_7/A_7_0/FC_7_0_0/hmmalign.results.erfq67mp) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_7/A_7_0/hmmbuild.input.0n991yg8.fasta).
[17:38:21] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_10/A_10_0/hmmbuild.model.jbyps1hb, fragments:/tmp/sepp/output.o5n1_s57/root/P_10/A_10_0/FC_10_0_0/hmmalign.frag.sbyoir3v.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_10/A_10_0/hmmbuild.input.nlq0ak48.fasta
[17:38:21] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_10.
[17:38:21] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_10/A_10_0/FC_10_0_0/hmmalign.results.9tbuojk1) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_10/A_10_0/hmmbuild.input.nlq0ak48.fasta).
[17:38:21] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_9/A_9_0/hmmbuild.model.f7juswv9, fragments:/tmp/sepp/output.o5n1_s57/root/P_9/A_9_0/FC_9_0_0/hmmalign.frag.lqdyzwe5.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_9/A_9_0/hmmbuild.input.rc65k5t8.fasta
[17:38:21] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_9.
[17:38:21] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_9/A_9_0/FC_9_0_0/hmmalign.results.4wtptd4j) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_9/A_9_0/hmmbuild.input.rc65k5t8.fasta).
[17:38:21] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_6/A_6_0/hmmbuild.model.6er2wf_5, fragments:/tmp/sepp/output.o5n1_s57/root/P_6/A_6_0/FC_6_0_0/hmmalign.frag.8a2e8qxi.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_6/A_6_0/hmmbuild.input.aablk8nw.fasta
[17:38:21] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_6.
[17:38:21] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_6/A_6_0/FC_6_0_0/hmmalign.results.zd_dmrn6) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_6/A_6_0/hmmbuild.input.aablk8nw.fasta).
[17:38:21] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_4/A_4_0/hmmbuild.model.qtzqw7yk, fragments:/tmp/sepp/output.o5n1_s57/root/P_4/A_4_0/FC_4_0_0/hmmalign.frag.87fi1358.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_4/A_4_0/hmmbuild.input.auv2f5f5.fasta
[17:38:21] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_4.
[17:38:21] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_4/A_4_0/FC_4_0_0/hmmalign.results.7mgrqs4n) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_4/A_4_0/hmmbuild.input.auv2f5f5.fasta).
[17:38:23] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_13/A_13_0/hmmbuild.model.rws1m56m, fragments:/tmp/sepp/output.o5n1_s57/root/P_13/A_13_0/FC_13_0_0/hmmalign.frag.gbvo0lyf.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_13/A_13_0/hmmbuild.input.j4q4gify.fasta
[17:38:23] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_13.
[17:38:23] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_13/A_13_0/FC_13_0_0/hmmalign.results.9o1e0ie9) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_13/A_13_0/hmmbuild.input.j4q4gify.fasta).
[17:38:23] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_14/A_14_0/hmmbuild.model.17eac4q6, fragments:/tmp/sepp/output.o5n1_s57/root/P_14/A_14_0/FC_14_0_0/hmmalign.frag.je00dy94.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_14/A_14_0/hmmbuild.input.ur66u0a1.fasta
[17:38:23] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_15/A_15_0/hmmbuild.model.5qss3tuu, fragments:/tmp/sepp/output.o5n1_s57/root/P_15/A_15_0/FC_15_0_0/hmmalign.frag.sf3vcd7h.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_15/A_15_0/hmmbuild.input.lxk0nfoi.fasta
[17:38:23] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_14.
[17:38:23] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_14/A_14_0/FC_14_0_0/hmmalign.results.9d3f0f_w) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_14/A_14_0/hmmbuild.input.ur66u0a1.fasta).
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_0 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_0/pplacer.backbone.9qq_1lrq.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_0/pplacer.tree.pre9h_il.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_0/pplacer.extended.0.616idlga.fasta
No error messages available
[17:38:23] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_15.
[17:38:23] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_15/A_15_0/FC_15_0_0/hmmalign.results.nqu1vcpa) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_15/A_15_0/hmmbuild.input.lxk0nfoi.fasta).
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_3 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_3/pplacer.backbone.dudsgs6h.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_3/pplacer.tree.5mh0y6nj.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_3/pplacer.extended.0.boq4u4ty.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_2 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_2/pplacer.backbone.75c7r4bd.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_2/pplacer.tree.uzphvbqo.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_2/pplacer.extended.0.ujcal5d2.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_1 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_1/pplacer.backbone.wgpjdwsb.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_1/pplacer.tree.fzjrxzzg.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_1/pplacer.extended.0.upqdosi_.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_5 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_5/pplacer.backbone.8ly8qeb_.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_5/pplacer.tree.xnumzo_7.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_5/pplacer.extended.0.tdn0qu_n.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_8 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_8/pplacer.backbone.e2gmq7r3.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_8/pplacer.tree.1_hr0qlh.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_8/pplacer.extended.0.tqfn1119.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_7 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_7/pplacer.backbone.19264h5w.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_7/pplacer.tree.51zhmt85.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_7/pplacer.extended.0.52w5kn96.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_10 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_10/pplacer.backbone.o7b04v6f.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_10/pplacer.tree.tpnxx_oi.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_10/pplacer.extended.0.a4lmtvl_.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_9 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_9/pplacer.backbone.xlw54qmz.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_9/pplacer.tree.rbkvmb_p.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_9/pplacer.extended.0.8t2yhq_h.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_6 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_6/pplacer.backbone.8lt0nzo4.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_6/pplacer.tree.l4rn35e6.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_6/pplacer.extended.0.pb1cg6y5.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_4 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_4/pplacer.backbone.hgd2owol.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_4/pplacer.tree.60orasoh.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_4/pplacer.extended.0.emdn30eu.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_13 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_13/pplacer.backbone.9tn2mvj5.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_13/pplacer.tree.axibv171.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_13/pplacer.extended.0.eutgx2ng.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_14 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_14/pplacer.backbone.uudlnh3s.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_14/pplacer.tree.aky_reey.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_14/pplacer.extended.0.94v_rg8g.fasta
No error messages available
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_15 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_15/pplacer.backbone.9g3ct_jw.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_15/pplacer.tree.f6nudgfl.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_15/pplacer.extended.0._yw_67a2.fasta
No error messages available
[17:38:26] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_12/A_12_0/hmmbuild.model.631i1tox, fragments:/tmp/sepp/output.o5n1_s57/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.zi22_0qb.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_12/A_12_0/hmmbuild.input.2hlorj5b.fasta
[17:38:26] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_12.
[17:38:26] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_12/A_12_0/FC_12_0_0/hmmalign.results.oiv4a_c6) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_12/A_12_0/hmmbuild.input.2hlorj5b.fasta).
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_12 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_12/pplacer.backbone.dahvyafc.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_12/pplacer.tree.ceg8lldj.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_12/pplacer.extended.0.xyoy8osr.fasta
No error messages available
[17:38:27] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.o5n1_s57/root/P_11/A_11_0/hmmbuild.model.t3v302di, fragments:/tmp/sepp/output.o5n1_s57/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.fweixko_.fasta, trim:False, base_alignment:/tmp/sepp/output.o5n1_s57/root/P_11/A_11_0/hmmbuild.input.v47oqg2w.fasta
[17:38:27] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_11.
[17:38:27] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.o5n1_s57/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.xj6j_ruj) into base alignment (/tmp/sepp/output.o5n1_s57/root/P_11/A_11_0/hmmbuild.input.v47oqg2w.fasta).
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/scheduler.py", line 74, in __call__
return self.run()
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run
raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_0 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_0/pplacer.backbone.9qq_1lrq.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_0/pplacer.tree.pre9h_il.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_0/pplacer.extended.0.616idlga.fasta
No error messages available
"""

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

Traceback (most recent call last):
File "/home/ianblixt/.local/share/mamba/envs/picrust2/bin/run_sepp.py", line 26, in <module>
ExhaustiveAlgorithm().run()
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/algorithm.py", line 175, in run
if not JobPool().wait_for_all_jobs():
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/sepp/scheduler.py", line 383, in wait_for_all_jobs
result.get()
File "/home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/multiprocessing/pool.py", line 771, in get
raise self._value
sepp.scheduler.JobError: The following execution failed:
/home/ianblixt/.local/share/mamba/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.o5n1_s57/root/P_0 -j 1 -r /tmp/sepp/output.o5n1_s57/root/P_0/pplacer.backbone.9qq_1lrq.fasta -s /home/ianblixt/.local/share/mamba/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.o5n1_s57/root/P_0/pplacer.tree.pre9h_il.tre --groups 10 /tmp/sepp/output.o5n1_s57/root/P_0/pplacer.extended.0.616idlga.fasta
No error messages available

Robyn Wright

unread,

Feb 18, 2025, 8:49:23 AMFeb 18

to picrust-users

Hi there,

A couple of questions:

1. What kind of computer are you trying to run PICRUSt2 on? (How much RAM, which OS, etc)

2. Could you try running one of the commands on the tutorial dataset? This is very small, and if it works, it would suggest a memory issue. Try running this:
wget http://kronos.pharmacology.dal.ca/public_files/picrust/picrust2_tutorial_files/chemerin_16S.zip unzip chemerin_16S.zip cd chemerin_16S

place_seqs.py -s seqs.fna -o out.tre -p 1 --intermediate intermediate/place_seqs

Thanks,

Robyn

Ian Blixt

unread,

Feb 20, 2025, 7:17:27 AMFeb 20

to picrust-users

Hi Robyn,

Sorry for the delayed response. I was trying to run this on my personal laptop, but I've now switched to running this on my university's Linux server. That seems to have sorted out whatever issue was going on.

Thank you for the help anyway :)

Cheers,

Ian

Robyn Wright

unread,

Feb 21, 2025, 7:38:54 AMFeb 21

to picrust-users

Glad it's all working now and no problem! I imagine that it was a memory issue in that case.

Robyn

Bhavuk Nccs Lab3

unread,

Feb 25, 2025, 9:31:09 AMFeb 25

to picrust-users

Hello!

I am also trying to install and run the picrust2 in wsl ubuntu 24.04 and getteing same error, how i can resolve that.

Running the pytest gave this error below.

picrust2-2.6.0$ pytest
====================================================== test session starts ======================================================
platform linux -- Python 3.10.16, pytest-8.3.4, pluggy-1.5.0
rootdir: /home/bhavukgamer/picrust2-2.6.0
configfile: pyproject.toml
plugins: cov-6.0.0
collected 61 items

tests/test_hsp.py ........ [ 13%]
tests/test_metagenome_pipeline.py ............... [ 37%]
tests/test_pathway_pipeline.py .... [ 44%]
tests/test_place_seqs.py ........F [ 59%]
tests/test_util.py .................... [ 91%]
tests/test_workflow.py ..... [100%]

=========================================================== FAILURES ============================================================
______________________________________ place_seqs_tests.test_run_place_seqs_pipeline_sepp _______________________________________
self = <tests.test_place_seqs.place_seqs_tests testMethod=test_run_place_seqs_pipeline_sepp>

def test_run_place_seqs_pipeline_sepp(self):
'''Basic test of full place seqs pipeline with SEPP. Just run to
see if any errors occur'''
with TemporaryDirectory() as temp_dir:
tmp_tree = path.join(temp_dir, "out.tre")

> place_seqs_pipeline(study_fasta=test_study_seqs,
ref_dir=default_ref_dir,
placement_tool="sepp",
out_tree=tmp_tree,
threads=1,
out_dir=temp_dir,
min_align=0.8,
chunk_size=5000,
verbose=True)

tests/test_place_seqs.py:160:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
picrust2/place_seqs.py:95: in place_seqs_pipeline
run_sepp(tree=tree,
picrust2/place_seqs.py:458: in run_sepp
system_call_check(sepp_command, print_command=print_cmds,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

cmd = ['run_sepp.py', '--tree', '/home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre', '--raxml', '/home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info', '--cpu', ...]
print_command = True, print_stdout = True, print_stderr = True

def system_call_check(cmd, print_command=False, print_stdout=False,
print_stderr=False):
'''Run system command and throw and error if return is not 0. Input command
can be a list containing the command or a string.'''

# Convert command to list if input as string.
if type(cmd) is str:
cmd = cmd.split()

# Print command out if option set.
if print_command:
print(" ".join(cmd), file=sys.stderr)

stdout_log = ""
stderr_log = ""

# Write stdout and stderr of command to temporary files.
# Only output the content of these files if the job fails.
with TemporaryDirectory() as temp_dir:

stdout_file = join(temp_dir, "stdout.txt")
stderr_file = join(temp_dir, "stderr.txt")

with open(stdout_file, "wb") as stdout_fh, \
open(stderr_file, "wb") as stderr_fh:

return_value = call(cmd, stdout=stdout_fh,
stderr=stderr_fh)

# Capture stdout and stderr.
with open(stdout_file, 'r') as stdout_fh:
stdout_log = stdout_fh.read()

with open(stderr_file, 'r') as stderr_fh:
stderr_log = stderr_fh.read()

# Exit with error if command did not finish successfully.
if return_value != 0:
print("\nError running this command:\n" + " ".join(cmd),
file=sys.stderr)

if stdout_log:
print("\nStandard output of the above failed command:\n" +
stdout_log, file=sys.stderr)

if stderr_log:
print("\nStandard error of the above failed command:\n" +
stderr_log, file=sys.stderr)

> sys.exit(1)
E SystemExit: 1

picrust2/util.py:299: SystemExit
----------------------------------------------------- Captured stdout call ------------------------------------------------------

----------------------------------------------------- Captured stderr call ------------------------------------------------------
hmmalign --trim --dna --mapali /home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /tmp/tmpdohhy290/query_align.stockholm /home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm /home/bhavukgamer/picrust2-2.6.0/tests/test_data/place_seqs/study_seqs_test.fasta

All raw input sequences were the same length (400)

run_sepp.py --tree /home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpdohhy290/sepp_out -seed 297834 --alignment /home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpdohhy290/study_seqs_filtered.fasta

Error running this command:
run_sepp.py --tree /home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmpdohhy290/sepp_out -seed 297834 --alignment /home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmpdohhy290/study_seqs_filtered.fasta

Standard output of the above failed command:

root_p='/home/bhavukgamer/miniconda3/envs/picrust2/share/sepp/sepp'

Standard error of the above failed command:

[21:38:12] config.py (line 371): INFO: Seed number: 297834
[21:38:12] algorithm.py (line 153): INFO: SEPP version 4.5.5 used with HMMER version 3.4
[21:38:12] algorithm.py (line 155): INFO: Will user HMMER located at /home/bhavukgamer/miniconda3/envs/picrust2/bin/hmmbuild
[21:38:12] algorithm.py (line 157): INFO: All options: Namespace(pplacer=Namespace(path='/home/bhavukgamer/miniconda3/envs/picrust2/bin/pplacer'), hmmalign=Namespace(path='/home/bhavukgamer/miniconda3/envs/picrust2/bin/hmmalign'), hmmsearch=Namespace(path='/home/bhavukgamer/miniconda3/envs/picrust2/bin/hmmsearch', piped='False', elim='10000', filters='True'), hmmbuild=Namespace(path='/home/bhavukgamer/miniconda3/envs/picrust2/bin/hmmbuild'), jsonmerger=Namespace(path='/home/bhavukgamer/miniconda3/envs/picrust2/bin/seppJsonMerger.jar'), exhaustive=Namespace(strategy='centroid', minsubsetsize='20', placementminsubsetsizefacotr='4', placer='pplacer', weight_placement_by_alignment='True'), alignment_size=None, placement_size=None, max_chunk_size=20000, distance=1, maxDiam=None, decomp_strategy='normal', tempdir='/tmp/sepp', remtemp=False, output='output', outdir='/tmp/tmpdohhy290/sepp_out', config_file=None, tree_file=<_io.TextIOWrapper name='/home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre' mode='r' encoding='UTF-8'>, info_file=<_io.TextIOWrapper name='/home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info' mode='r' encoding='UTF-8'>, alignment_file=<_io.TextIOWrapper name='/home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna' mode='r' encoding='UTF-8'>, fragment_file=<_io.TextIOWrapper name='/tmp/tmpdohhy290/study_seqs_filtered.fasta' mode='r' encoding='UTF-8'>, molecule='dna', ignore_overlap=False, cpu=1, checkpoint=<sepp.checkpointing.CheckPointManager object at 0x7fb1bdfa5330>, checkpoint_interval=3600, seed=297834)
[21:38:12] algorithm.py (line 284): INFO: Reading input alignment: <_io.TextIOWrapper name='/home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna' mode='r' encoding='UTF-8'>
[21:38:12] algorithm.py (line 288): INFO: Alignment has 20000 sequences and 1582 sites
[21:38:12] algorithm.py (line 293): INFO: Reading input tree: <_io.TextIOWrapper name='/home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre' mode='r' encoding='UTF-8'>
[21:38:13] algorithm.py (line 298): INFO: Tree has 20000 leaves
[21:38:13] algorithm.py (line 264): INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000
[21:38:15] exhaustive.py (line 352): INFO: Breaking into 16 placement subsets.
[21:38:15] exhaustive.py (line 399): INFO: Breaking into 16 alignment subsets.
[21:38:15] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/output.tnqtfqc7
[21:38:15] exhaustive.py (line 414): INFO: Breaking each alignment subset into 1 fragment chunks.
[21:38:17] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_0/A_0_0/hmmbuild.input.6bvu0pk5.fasta
[21:38:18] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_1/A_1_0/hmmbuild.input.5dur6zeq.fasta
[21:38:18] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_2/A_2_0/hmmbuild.input.d7rayxgx.fasta
[21:38:18] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_3/A_3_0/hmmbuild.input.fo31tuym.fasta
[21:38:18] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_4/A_4_0/hmmbuild.input.5dfria4_.fasta
[21:38:19] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_5/A_5_0/hmmbuild.input.hbhjg1cg.fasta
[21:38:19] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_6/A_6_0/hmmbuild.input.v4r6iau8.fasta
[21:38:19] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_7/A_7_0/hmmbuild.input.5sjjd17_.fasta
[21:38:19] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_8/A_8_0/hmmbuild.input.0buwwokw.fasta
[21:38:20] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_9/A_9_0/hmmbuild.input._kex8jm4.fasta
[21:38:20] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_10/A_10_0/hmmbuild.input.9jrtxbr3.fasta
[21:38:20] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_11/A_11_0/hmmbuild.input.__eomani.fasta
[21:38:20] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_12/A_12_0/hmmbuild.input.ix3bg1mo.fasta
[21:38:20] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_13/A_13_0/hmmbuild.input.gf_gu0r_.fasta
[21:38:21] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_14/A_14_0/hmmbuild.input.se1b_06_.fasta
[21:38:21] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.tnqtfqc7/root/P_15/A_15_0/hmmbuild.input.ptme_tvg.fasta
[21:38:21] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_0/A_0_0/hmmbuild.model.bb_6p8c7, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.gmxe0gfw
[21:38:21] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_1/A_1_0/hmmbuild.model.e7o8ztql, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.7pvcl_z0
[21:38:21] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_2/A_2_0/hmmbuild.model.6n1o_7ek, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_2/A_2_0/FC_2_0_0/hmmsearch.results.p_naohoa
[21:38:21] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_3/A_3_0/hmmbuild.model.30e8o9yn, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.gcz6wphc
[21:38:21] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_4/A_4_0/hmmbuild.model.mbxoa90h, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.irwzhy6v
[21:38:21] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_5/A_5_0/hmmbuild.model.jitr4shc, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.aoes4n13
[21:38:21] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_6/A_6_0/hmmbuild.model.vldsfvjf, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.7k7recim
[21:38:21] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_7/A_7_0/hmmbuild.model.uoqbu3mj, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.hjgqeuek
[21:38:21] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_8/A_8_0/hmmbuild.model.l7a5ztzz, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.qrabkv4o
[21:38:21] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_9/A_9_0/hmmbuild.model.1f5vqzgp, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.q6jr0cl7
[21:38:22] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_10/A_10_0/hmmbuild.model.agwiovrj, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.tvasrerz
[21:38:22] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_11/A_11_0/hmmbuild.model.tn0uf53j, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.odqqpab1
[21:38:22] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_12/A_12_0/hmmbuild.model.5_skvji5, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.a1v335zc
[21:38:22] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_13/A_13_0/hmmbuild.model.cdurb_gh, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.ycdxra86
[21:38:22] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_14/A_14_0/hmmbuild.model.q8pe6k5c, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.4j0ep2i3
[21:38:22] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_15/A_15_0/hmmbuild.model.c1o57uc5, fragments:/tmp/sepp/output.tnqtfqc7/fragment_chunks/fragment_chunk_0_6zlzvvy.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.tnqtfqc7/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.x2apnccq
[21:38:22] exhaustive.py (line 81): WARNING: Fragments [] are not scored against any subset
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_0.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_1.
[21:38:22] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_11/A_11_0/hmmbuild.model.tn0uf53j, fragments:/tmp/sepp/output.tnqtfqc7/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.bzj11fma.fasta, trim:False, base_alignment:/tmp/sepp/output.tnqtfqc7/root/P_11/A_11_0/hmmbuild.input.__eomani.fasta
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_2.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_3.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_4.
[21:38:22] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.tnqtfqc7/root/P_12/A_12_0/hmmbuild.model.5_skvji5, fragments:/tmp/sepp/output.tnqtfqc7/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.26_5n92z.fasta, trim:False, base_alignment:/tmp/sepp/output.tnqtfqc7/root/P_12/A_12_0/hmmbuild.input.ix3bg1mo.fasta
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_5.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_6.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_7.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_8.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_9.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_10.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_11.
[21:38:22] alignment.py (line 570): INFO: Merging extension sto file (/tmp/sepp/output.tnqtfqc7/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.m5cripm0) into base alignment (/tmp/sepp/output.tnqtfqc7/root/P_11/A_11_0/hmmbuild.input.__eomani.fasta).
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_12.
[21:38:22] alignment.py (line 570): INFO: Merging extension sto file (/tmp/sepp/output.tnqtfqc7/root/P_12/A_12_0/FC_12_0_0/hmmalign.results.2k6a8dbx) into base alignment (/tmp/sepp/output.tnqtfqc7/root/P_12/A_12_0/hmmbuild.input.ix3bg1mo.fasta).
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_13.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_14.
[21:38:22] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_15.
[21:38:24] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.tnqtfqc7/root/P_11/pplacer.backbone.qnt1uw11.fasta, tree_file:/tmp/sepp/output.tnqtfqc7/root/P_11/pplacer.tree.r7vrzxp0.tre, info_file:/home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.tnqtfqc7/root/P_11/pplacer.extended.0.rrdrdqi9.fasta, output:/tmp/sepp/output.tnqtfqc7/root/P_11/pplacer.extended.0.rrdrdqi9.jplace
[21:38:26] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.tnqtfqc7/root/P_12/pplacer.backbone.in7ru78v.fasta, tree_file:/tmp/sepp/output.tnqtfqc7/root/P_12/pplacer.tree.cdjbd8oa.tre, info_file:/home/bhavukgamer/picrust2-2.6.0/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.tnqtfqc7/root/P_12/pplacer.extended.0.8kxzzjsn.fasta, output:/tmp/sepp/output.tnqtfqc7/root/P_12/pplacer.extended.0.8kxzzjsn.jplace

Traceback (most recent call last):

File "/home/bhavukgamer/miniconda3/envs/picrust2/lib/python3.10/site-packages/sepp/jobs.py", line 150, in run

raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:

Traceback (most recent call last):

File "/home/bhavukgamer/miniconda3/envs/picrust2/bin/run_sepp.py", line 26, in <module>
ExhaustiveAlgorithm().run()
File "/home/bhavukgamer/miniconda3/envs/picrust2/lib/python3.10/site-packages/sepp/algorithm.py", line 205, in run
self.merge_results()
File "/home/bhavukgamer/miniconda3/envs/picrust2/lib/python3.10/site-packages/sepp/exhaustive.py", line 292, in merge_results
mergeJsonJob.run()
File "/home/bhavukgamer/miniconda3/envs/picrust2/lib/python3.10/site-packages/sepp/jobs.py", line 150, in run

raise JobError("\n".join([
sepp.scheduler.JobError: The following execution failed:

java -jar /home/bhavukgamer/miniconda3/envs/picrust2/bin/seppJsonMerger.jar - - /tmp/tmpdohhy290/sepp_out/output_placement.json
json locations: [/tmp/sepp/output.tnqtfqc7/root/P_11/pplacer.extended.0.rrdrdqi9.jplace, /tmp/sepp/output.tnqtfqc7/root/P_12/pplacer.extended.0.8kxzzjsn.jplace]
Exception in thread "main" java.lang.NumberFormatException: Cannot parse null string
at java.base/java.lang.Integer.parseInt(Integer.java:550)
at java.base/java.lang.Integer.<init>(Integer.java:1065)
at phylolab.taxonamic.PPlacerJSONMerger.relabelJson(PPlacerJSONMerger.java:172)
at phylolab.taxonamic.PPlacerJSONMerger.main(PPlacerJSONMerger.java:288)

==================================================== short test summary info ====================================================
FAILED tests/test_place_seqs.py::place_seqs_tests::test_run_place_seqs_pipeline_sepp - SystemExit: 1
============================================ 1 failed, 60 passed in 75.30s (0:01:15) ============================================

Robyn Wright

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Feb 25, 2025, 9:38:30 AMFeb 25

to picrust-users

Hi,

Could you give details on how you installed PICRUSt2 please?

Thanks,

Robyn

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