sepp.scheduler.JobError

system： VirtualBox Graphical Version 7.1.0 r164728 (Qt6.5.3) PRETTY_NAME="Debian GNU/Linux 12 (bookworm)"

General Name. debian Operating System: Debian (64-bit) Base Memory. 18219 MB Processors: 8

command： picrust2_pipeline.py -s rep-seqs-no-mito_chloro.fasta -i feature-table.biom -o picrust2_output --placement_tool sepp --stratified --processes 4

Details

Error running this command: place_seqs.py --study_fasta rep-seqs-no-mito_chloro.fasta --ref_dir /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree picrust2_output/out.tre --processes 4 --intermediate picrust2_output/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool sepp

Standard error of the above failed command:

Error running this command: run_sepp.py --tree /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 4 --molecule dna --outdir picrust2_output/intermediate/place_seqs/sepp_out -seed 297834 --alignment /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment picrust2_output/intermediate/place_seqs/study_seqs_filtered.fasta

Standard error of the [10:48:02] config.py (line 349): [10:48:02] algorithm.py (line 258): [10:48:02] algorithm.py (line 265): [10:48:04] algorithm.py (line 238): [10:48:06] exhaustive.py (line 350): [10:48:08] exhaustive.py (line 397): [10:48:08] filemgr.py (line 129): [10:48:08] exhaustive.py (line 412): [10:48:08] jobs.py (line 131): [10:48:08] jobs.py (line 131): [10:48:08] jobs.py (line 131): [10:48:08] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:09] jobs.py (line 131): [10:48:34] jobs.py (line 131): [10:48:34] jobs.py (line 131): [10:48:34] jobs.py (line 131): [10:48:34] jobs.py (line 131): [10:48:58] jobs.py (line 131): [10:48:58] jobs.py (line 131): [10:48:58] jobs.py (line 131): [10:48:59] jobs.py (line 131): [10:49:22] jobs.py (line 131): [10:49:22] jobs.py (line 131): [10:49:22] jobs.py (line 131): [10:49:24] jobs.py (line 131): [10:49:44] jobs.py (line 131): [10:49:45] jobs.py (line 131): [10:49:45] jobs.py (line 131): [10:49:46] jobs.py (line 131): [10:49:46] exhaustive.py (line 80): [10:49:46] exhaustive.py (line 151): [10:49:46] jobs.py (line 131): [10:49:46] exhaustive.py (line 151): [10:49:46] alignment.py (line 556): [10:49:46] jobs.py (line 131): [10:49:46] exhaustive.py (line 151): [10:49:46] alignment.py (line 556): [10:49:46] jobs.py (line 131): [10:49:46] exhaustive.py (line 151): [10:49:46] alignment.py (line 556): [10:49:48] jobs.py (line 131): [10:49:48] exhaustive.py (line 151): [10:49:48] alignment.py (line 556): [10:49:48] exhaustive.py (line 151): [10:49:48] jobs.py (line 131): [10:49:48] exhaustive.py (line 151): [10:49:48] alignment.py (line 556): [10:49:50] jobs.py (line 131): [10:49:50] exhaustive.py (line 151): [10:49:50] alignment.py (line 556): [10:49:51] jobs.py (line 131): [10:49:51] exhaustive.py (line 151): [10:49:51] alignment.py (line 556): [10:49:57] jobs.py (line 131): [10:49:57] exhaustive.py (line 151): [10:49:57] alignment.py (line 556): [10:50:01] jobs.py (line 131): [10:50:01] exhaustive.py (line 151): [10:50:01] alignment.py (line 556): [10:50:05] jobs.py (line 131): [10:50:05] exhaustive.py (line 151): [10:50:05] alignment.py (line 556): [10:50:05] exhaustive.py (line 151): [10:50:07] jobs.py (line 131): [10:50:07] exhaustive.py (line 151): [10:50:07] alignment.py (line 556): [10:50:13] jobs.py (line 131): [10:50:13] exhaustive.py (line 151): [10:50:13] alignment.py (line 556): [10:50:18] jobs.py (line 131): [10:50:18] exhaustive.py (line 151): [10:50:18] alignment.py (line 556): multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/jxi/miniconda result = (True, func(*args, **kwds)) File "/home/jxi/miniconda return self.run() File "/home/jxi/miniconda raise JobError("\n".join([ sepp.scheduler.JobError: /home/jxi/miniconda3/envs/picr No error messages available """ above failed command: INFO: Seed number: 297834 INFO: Reading input alignment: <_io.TextIOWrapper name='/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna' mode='r' encoding='UTF-8'> INFO: Reading input tree: <_io.TextIOWrapper name='/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre' mode='r' encoding='UTF-8'> INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000 INFO: Breaking into 16 placement subsets. INFO: Breaking into 16 alignment subsets. INFO: Root temp directory built: /tmp/sepp/output.my73ijpt INFO: Breaking each alignment subset into 1 fragment chunks. INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_0/A_0_0/hmmbuild.input.u9gypea6.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_1/A_1_0/hmmbuild.input.t9y7cl22.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_3/A_3_0/hmmbuild.input.6zm73ohc.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_2/A_2_0/hmmbuild.input.d696izec.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_4/A_4_0/hmmbuild.input.h_im6jjg.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_5/A_5_0/hmmbuild.input.qjqti0dx.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_7/A_7_0/hmmbuild.input.d4ol9dwk.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_6/A_6_0/hmmbuild.input.w24rklok.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_8/A_8_0/hmmbuild.input.n441xct3.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_9/A_9_0/hmmbuild.input.r7qa71s5.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_10/A_10_0/hmmbuild.input.083qwvjd.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_11/A_11_0/hmmbuild.input.nkfcrtbi.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_12/A_12_0/hmmbuild.input.ymbufo9n.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_13/A_13_0/hmmbuild.input.hr_y60o5.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_14/A_14_0/hmmbuild.input.yy3inj2a.fasta INFO: Finished hmmbuild Job with input: /tmp/sepp/output.my73ijpt/root/P_15/A_150/hmmbuild.input.e7mua40.fasta INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_1/A_1_0/hmmbuild.model.03675moj, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.18m52aj7 INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_0/A_0_0/hmmbuild.model.egif4a1j, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.auxdqakf INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_2/A_2_0/hmmbuild.model.pnaqxijg, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_2/A_2_0/FC_2_0_0/hmmsearch.results.xm4ozu5m INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_3/A_3_0/hmmbuild.model.zhmdxjx2, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.qo0ts6a7 INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_5/A_5_0/hmmbuild.model.vdw0544f, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.ofxviqnd INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_4/A_4_0/hmmbuild.model.txi92yxm, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.4d8nbfd5 INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_7/A_7_0/hmmbuild.model.hz8p5wq3, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.q3_mhmje INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_6/A_6_0/hmmbuild.model.wxoxzg0s, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.tlcvzjo9 INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_8/A_8_0/hmmbuild.model.80y52_vl, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.ynl8y_pm INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_9/A_9_0/hmmbuild.model.ry38twis, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.p4b2gc87 INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_10/A_10_0/hmmbuild.model.x6ejkas2, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.xx0w3w59 INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_11/A_11_0/hmmbuild.model.9qgtk30v, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.1iyj9scr INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_12/A_12_0/hmmbuild.model.5xuxy76l, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.4wyf7gyv INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_13/A_13_0/hmmbuild.model.kvqk_3d9, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.vy8jqr3o INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_14/A_14_0/hmmbuild.model.ngpixf_5, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.7w_swt63 INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.my73ijpt/root/P_15/A_15_0/hmmbuild.model.82y12h7l, fragments:/tmp/sepp/output.my73ijpt/fragment_chunks/fragment_chunk_0b666m8qf.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.my73ijpt/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.01f7zhxg WARNING: Fragments [] are not scored against any subset INFO: Merging sub-alignments for placement problem : P_0. INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_3/A_3_0/hmmbuild.model.zhmdxjx2, fragments:/tmp/sepp/output.my73ijpt/root/P_3/A_3_0/FC_3_0_0/hmmalign.frag.m_q796em.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_3/A_3_0/hmmbuild.input.6zm73ohc.fasta INFO: Merging sub-alignments for placement problem : P_3. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_3/A_3_0/FC_3_0_0/hmmalign.results.jlheqy85) into base alignment (/tmp/sepp/output.my73ijpt/root/P_3/A_3_0/hmmbuild.input.6zm73ohc.fasta). INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_1/A_1_0/hmmbuild.model.03675moj, fragments:/tmp/sepp/output.my73ijpt/root/P_1/A_1_0/FC_1_0_0/hmmalign.frag.jw28d0ib.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_1/A_1_0/hmmbuild.input.t9y7cl22.fasta INFO: Merging sub-alignments for placement problem : P_1. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_1/A_1_0/FC_1_0_0/hmmalign.results.86yfvm2j) into base alignment (/tmp/sepp/output.my73ijpt/root/P_1/A_1_0/hmmbuild.input.t9y7cl22.fasta). INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_4/A_4_0/hmmbuild.model.txi92yxm, fragments:/tmp/sepp/output.my73ijpt/root/P_4/A_4_0/FC_4_0_0/hmmalign.frag.qhqu4_qj.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_4/A_4_0/hmmbuild.input.h_im6jjg.fasta INFO: Merging sub-alignments for placement problem : P_4. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_4/A_4_0/FC_4_0_0/hmmalign.results.5uftmh6p) into base alignment (/tmp/sepp/output.my73ijpt/root/P_4/A_4_0/hmmbuild.input.h_im6jjg.fasta). INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_2/A_2_0/hmmbuild.model.pnaqxijg, fragments:/tmp/sepp/output.my73ijpt/root/P_2/A_2_0/FC_2_0_0/hmmalign.frag.nxue6s7s.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_2/A_2_0/hmmbuild.input.d696izec.fasta INFO: Merging sub-alignments for placement problem : P_2. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_2/A_2_0/FC_2_0_0/hmmalign.results.2ajanlew) into base alignment (/tmp/sepp/output.my73ijpt/root/P_2/A_2_0/hmmbuild.input.d696izec.fasta). INFO: Merging sub-alignments for placement problem : P_8. INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_9/A_9_0/hmmbuild.model.ry38twis, fragments:/tmp/sepp/output.my73ijpt/root/P_9/A_9_0/FC_9_0_0/hmmalign.frag.guqrkstd.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_9/A_9_0/hmmbuild.input.r7qa71s5.fasta INFO: Merging sub-alignments for placement problem : P_9. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_9/A_9_0/FC_9_0_0/hmmalign.results.dt4qpdlu) into base alignment (/tmp/sepp/output.my73ijpt/root/P_9/A_9_0/hmmbuild.input.r7qa71s5.fasta). INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_5/A_5_0/hmmbuild.model.vdw0544f, fragments:/tmp/sepp/output.my73ijpt/root/P_5/A_5_0/FC_5_0_0/hmmalign.frag.19zls7e5.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_5/A_5_0/hmmbuild.input.qjqti0dx.fasta INFO: Merging sub-alignments for placement problem : P_5. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_5/A_5_0/FC_5_0_0/hmmalign.results.ptw5tysi) into base alignment (/tmp/sepp/output.my73ijpt/root/P_5/A_5_0/hmmbuild.input.qjqti0dx.fasta). INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_10/A_10_0/hmmbuild.model.x6ejkas2, fragments:/tmp/sepp/output.my73ijpt/root/P_10/A_10_0/FC_10_0_0/hmmalign.frag.nfl0mk91.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_10/A_10_0/hmmbuild.input.083qwvjd.fasta INFO: Merging sub-alignments for placement problem : P_10. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_10/A_10_0/FC_10_0_0/hmmalign.results.k70qejvi) into base alignment (/tmp/sepp/output.my73ijpt/root/P_10/A_10_0/hmmbuild.input.083qwvjd.fasta). INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_11/A_11_0/hmmbuild.model.9qgtk30v, fragments:/tmp/sepp/output.my73ijpt/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.u7ti0l9s.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_11/A_11_0/hmmbuild.input.nkfcrtbi.fasta INFO: Merging sub-alignments for placement problem : P_11. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.y12pr095) into base alignment (/tmp/sepp/output.my73ijpt/root/P_11/A_11_0/hmmbuild.input.nkfcrtbi.fasta). INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_7/A_7_0/hmmbuild.model.hz8p5wq3, fragments:/tmp/sepp/output.my73ijpt/root/P_7/A_7_0/FC_7_0_0/hmmalign.frag.njq2sma4.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_7/A_7_0/hmmbuild.input.d4ol9dwk.fasta INFO: Merging sub-alignments for placement problem : P_7. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_7/A_7_0/FC_7_0_0/hmmalign.results.i_oo69xa) into base alignment (/tmp/sepp/output.my73ijpt/root/P_7/A_7_0/hmmbuild.input.d4ol9dwk.fasta). INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_12/A_12_0/hmmbuild.model.5xuxy76l, fragments:/tmp/sepp/output.my73ijpt/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.0pzj7b27.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_12/A_12_0/hmmbuild.input.ymbufo9n.fasta INFO: Merging sub-alignments for placement problem : P_12. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_12/A_12_0/FC_12_0_0/hmmalign.results.tyd8d4p4) into base alignment (/tmp/sepp/output.my73ijpt/root/P_12/A_12_0/hmmbuild.input.ymbufo9n.fasta). INFO: Merging sub-alignments for placement problem : P_15. INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_6/A_6_0/hmmbuild.model.wxoxzg0s, fragments:/tmp/sepp/output.my73ijpt/root/P_6/A_6_0/FC_6_0_0/hmmalign.frag.fcq3xik8.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_6/A_6_0/hmmbuild.input.w24rklok.fasta INFO: Merging sub-alignments for placement problem : P_6. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_6/A_6_0/FC_6_0_0/hmmalign.results.wg5edkog) into base alignment (/tmp/sepp/output.my73ijpt/root/P_6/A_6_0/hmmbuild.input.w24rklok.fasta). INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_14/A_14_0/hmmbuild.model.ngpixf_5, fragments:/tmp/sepp/output.my73ijpt/root/P_14/A_14_0/FC_14_0_0/hmmalign.frag.xei2po41.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_14/A_14_0/hmmbuild.input.yy3inj2a.fasta INFO: Merging sub-alignments for placement problem : P_14. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_14/A_14_0/FC_14_0_0/hmmalign.results.i3s2lmp8) into base alignment (/tmp/sepp/output.my73ijpt/root/P_14/A_14_0/hmmbuild.input.yy3inj2a.fasta). INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.my73ijpt/root/P_13/A_13_0/hmmbuild.model.kvqk_3d9, fragments:/tmp/sepp/output.my73ijpt/root/P_13/A_13_0/FC_13_0_0/hmmalign.frag.rwnxbgm6.fasta, trim:False, base_alignment:/tmp/sepp/output.my73ijpt/root/P_13/A_13_0/hmmbuild.input.hr_y60o5.fasta INFO: Merging sub-alignments for placement problem : P_13. INFO: Merging extension sto file (/tmp/sepp/output.my73ijpt/root/P_13/A_13_0/FC_13_0_0/hmmalign.results.puz19c_o) into base alignment (/tmp/sepp/output.my73ijpt/root/P_13/A_13_0/hmmbuild.input.hr_y60o5.fasta). 3/envs/picrust2/lib/python3.8/multiprocessing/pool.py", line 125, in worker 3/envs/picrust2/lib/python3.8/site-packages/sepp/scheduler.py", line 74, in call 3/envs/picrust2/lib/python3.8/site-packages/sepp/jobs.py", line 150, in run The following execution failed: ust2/bin/pplacer --out-dir /tmp/sepp/output.my73ijpt/root/P_3 -j 1 -r /tmp/sepp/output.my73ijpt/root/P_3/pplacer.backbone.k2iahk9r.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.my73ijpt/root/P_3/pplacer.tree.k2itbc46.tre --groups 10 /tmp/sepp/output.my73ijpt/root/P_3/pplacer.extended.0.9vbie6r9.fasta

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

Traceback (most recent call last): File "/home/jxi/miniconda3/envs/picrust2/bin/run_sepp.py", line 26, in ExhaustiveAlgorithm().run() File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/algorithm.py", line 174, in run if (not JobPool().wait_for_all_jobs()): File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/scheduler.py", line 382, in wait_for_all_jobs result.get() File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value sepp.scheduler.JobError: The following execution failed: /home/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.my73ijpt/root/P_3 -j 1 -r /tmp/sepp/output.my73ijpt/root/P_3/pplacer.backbone.k2iahk9r.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.my73ijpt/root/P_3/pplacer.tree.k2itbc46.tre --groups 10 /tmp/sepp/output.my73ijpt/root/P_3/pplacer.extended.0.9vbie6r9.fasta No error messages available Traceback (most recent call last): File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.my73ijpt/root/P_14 -j 1 -r /tmp/sepp/output.my73ijpt/root/P_14/pplacer.backbone.wszkf_yr.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.my73ijpt/root/P_14/pplacer.tree.x7nnvmhu.tre --groups 10 /tmp/sepp/output.my73ijpt/root/P_14/pplacer.extended.0.6w97ptki.fasta No error messages available

Is there anyone please help how to fix this problem? And I run the same command in WSL2 with Ubuntu 22.04.3 LTS also giving errors:

picrust2_pipeline.py \ -s rep-seqs-no-mito_chloro.fasta \ -i feature-table.biom \ -o picrust2_output \ --placement_tool sepp \ --stratified \ --processes 4

Error running this command: place_seqs.py --study_fasta rep-seqs-no-mito_chloro.fasta --ref_dir /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree picrust2_output/out.tre --processes 4 --intermediate picrust2_output/intermediate/place_seqs --min_align 0.8 --chunk_size 5000 --placement_tool sepp

Standard error of the above failed command:

Error running this command: run_sepp.py --tree /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 4 --molecule dna --outdir picrust2_output/intermediate/place_seqs/sepp_out -seed 297834 --alignment /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment picrust2_output/intermediate/place_seqs/study_seqs_filtered.fasta

Standard error of the above failed command: [09:12:51] config.py (line 370): INFO: Seed number: 297834 [09:12:51] algorithm.py (line 267): INFO: Reading input alignment: <_io.TextIOWrapper name='/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna' mode='r' encoding='UTF-8'> [09:12:51] algorithm.py (line 274): INFO: Reading input tree: <_io.TextIOWrapper name='/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre' mode='r' encoding='UTF-8'> [09:12:53] algorithm.py (line 247): INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000 [09:12:55] exhaustive.py (line 351): INFO: Breaking into 16 placement subsets. [09:12:57] exhaustive.py (line 398): INFO: Breaking into 16 alignment subsets. [09:12:57] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/output.zghtxx09 [09:12:57] exhaustive.py (line 413): INFO: Breaking each alignment subset into 1 fragment chunks. [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_0/A_0_0/hmmbuild.input.uvk7mqbh.fasta [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_1/A_1_0/hmmbuild.input.lidz5zq3.fasta [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_2/A_2_0/hmmbuild.input.plifpayy.fasta [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_3/A_3_0/hmmbuild.input.u06dc6sq.fasta [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_4/A_4_0/hmmbuild.input.1okf53pn.fasta [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_5/A_5_0/hmmbuild.input.7ey4_6je.fasta [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_7/A_7_0/hmmbuild.input.drco0mu6.fasta [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_6/A_6_0/hmmbuild.input.bwcopfxa.fasta [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_8/A_8_0/hmmbuild.input.v5bw12xu.fasta [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_9/A_9_0/hmmbuild.input.wrc0lak4.fasta [09:13:00] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_10/A_10_0/hmmbuild.input.bgtfg09u.fasta [09:13:01] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_11/A_11_0/hmmbuild.input.fo3u8os7.fasta [09:13:01] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_12/A_12_0/hmmbuild.input.bloseifa.fasta [09:13:01] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_13/A_13_0/hmmbuild.input.rio7dlv5.fasta [09:13:01] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_14/A_14_0/hmmbuild.input._ba6klh3.fasta [09:13:01] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.zghtxx09/root/P_15/A_15_0/hmmbuild.input.rrjy8m5q.fasta [09:13:32] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_0/A_0_0/hmmbuild.model.eaqic56x, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results._2w3jx5c [09:13:33] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_1/A_1_0/hmmbuild.model.mtchs3fq, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.r1xcab10 [09:13:33] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_2/A_2_0/hmmbuild.model.suxtu5i1, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_2/A_2_0/FC_2_0_0/hmmsearch.results.fw3h2qe7 [09:13:33] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_3/A_3_0/hmmbuild.model.zud_i1wh, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.8n5brlm1 [09:14:03] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_5/A_5_0/hmmbuild.model.0n4woyhn, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.v7jraif0 [09:14:04] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_4/A_4_0/hmmbuild.model.v80damo4, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.tmv_z_jf [09:14:04] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_7/A_7_0/hmmbuild.model.g02l8sl2, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.02qt2qte [09:14:04] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_6/A_60/hmmbuild.model.u55lkuy, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.fcq2zcph [09:14:37] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_8/A_8_0/hmmbuild.model.olq76dl7, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.jx6wwqnh [09:14:37] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_9/A_9_0/hmmbuild.model.qfib1hh4, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.7_hrux0f [09:14:37] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_10/A_10_0/hmmbuild.model.3lgqvblo, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.5ldpdukw [09:14:38] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_11/A_11_0/hmmbuild.model.nif8jn, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.34zuzf42 [09:15:14] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_12/A_12_0/hmmbuild.model.u667t07e, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.b8r6o3r5 [09:15:15] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_13/A_13_0/hmmbuild.model.1igvzrzs, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.ujb2815v [09:15:15] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_14/A_14_0/hmmbuild.model.pkhvm3vw, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.gu4xm82d [09:15:15] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.zghtxx09/root/P_15/A_15_0/hmmbuild.model.lc1swuig, fragments:/tmp/sepp/output.zghtxx09/fragment_chunks/fragment_chunk_0dpxtwtc3.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.zghtxx09/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.yvz7_1k8 [09:15:15] exhaustive.py (line 81): WARNING: Fragments [] are not scored against any subset [09:15:15] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_0. [09:15:16] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_3/A_3_0/hmmbuild.model.zud_i1wh, fragments:/tmp/sepp/output.zghtxx09/root/P_3/A_3_0/FC_3_0_0/hmmalign.frag.4zo3f0sb.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_3/A_3_0/hmmbuild.input.u06dc6sq.fasta [09:15:16] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_3. [09:15:16] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_3/A_3_0/FC_3_0_0/hmmalign.results.oj9m1z0a) into base alignment (/tmp/sepp/output.zghtxx09/root/P_3/A_3_0/hmmbuild.input.u06dc6sq.fasta). [09:15:16] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_1/A_1_0/hmmbuild.model.mtchs3fq, fragments:/tmp/sepp/output.zghtxx09/root/P_1/A_1_0/FC_1_0_0/hmmalign.frag.tznld7o2.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_1/A_1_0/hmmbuild.input.lidz5zq3.fasta [09:15:16] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_1. [09:15:16] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_1/A_1_0/FC_1_0_0/hmmalign.results.npzzj9_7) into base alignment (/tmp/sepp/output.zghtxx09/root/P_1/A_1_0/hmmbuild.input.lidz5zq3.fasta). [09:15:16] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_4/A_4_0/hmmbuild.model.v80damo4, fragments:/tmp/sepp/output.zghtxx09/root/P_4/A_4_0/FC_4_0_0/hmmalign.frag.u1f_22cb.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_4/A_4_0/hmmbuild.input.1okf53pn.fasta [09:15:16] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_4. [09:15:16] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_4/A_4_0/FC_4_0_0/hmmalign.results.dahqlsbx) into base alignment (/tmp/sepp/output.zghtxx09/root/P_4/A_4_0/hmmbuild.input.1okf53pn.fasta). [09:15:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_2/A_2_0/hmmbuild.model.suxtu5i1, fragments:/tmp/sepp/output.zghtxx09/root/P_2/A_2_0/FC_2_0_0/hmmalign.frag.wnope8nr.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_2/A_2_0/hmmbuild.input.plifpayy.fasta [09:15:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_2. [09:15:19] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_2/A_2_0/FC_2_0_0/hmmalign.results.wv56u8dm) into base alignment (/tmp/sepp/output.zghtxx09/root/P_2/A_2_0/hmmbuild.input.plifpayy.fasta). [09:15:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_8. [09:15:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_9/A_9_0/hmmbuild.model.qfib1hh4, fragments:/tmp/sepp/output.zghtxx09/root/P_9/A_9_0/FC_9_0_0/hmmalign.frag.etmd01ro.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_9/A_9_0/hmmbuild.input.wrc0lak4.fasta [09:15:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_9. [09:15:19] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_9/A_9_0/FC_9_0_0/hmmalign.results.e3oiq_qb) into base alignment (/tmp/sepp/output.zghtxx09/root/P_9/A_9_0/hmmbuild.input.wrc0lak4.fasta). [09:15:21] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_5/A_5_0/hmmbuild.model.0n4woyhn, fragments:/tmp/sepp/output.zghtxx09/root/P_5/A_5_0/FC_5_0_0/hmmalign.frag.mdxao8r4.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_5/A_5_0/hmmbuild.input.7ey4_6je.fasta [09:15:21] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_5. [09:15:21] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_5/A_5_0/FC_5_0_0/hmmalign.results.wq1l4ulz) into base alignment (/tmp/sepp/output.zghtxx09/root/P_5/A_5_0/hmmbuild.input.7ey4_6je.fasta). [09:15:23] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_10/A_10_0/hmmbuild.model.3lgqvblo, fragments:/tmp/sepp/output.zghtxx09/root/P_10/A_10_0/FC_10_0_0/hmmalign.frag.zhm2ay_2.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_10/A_10_0/hmmbuild.input.bgtfg09u.fasta [09:15:23] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_10. [09:15:23] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_10/A_10_0/FC_10_0_0/hmmalign.results.fhb0okdv) into base alignment (/tmp/sepp/output.zghtxx09/root/P_10/A_10_0/hmmbuild.input.bgtfg09u.fasta). [09:15:31] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_11/A_11_0/hmmbuild.model.nif8jn, fragments:/tmp/sepp/output.zghtxx09/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.qqkcif1u.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_11/A_11_0/hmmbuild.input.fo3u8os7.fasta [09:15:31] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_11. [09:15:31] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.fg9l9pyv) into base alignment (/tmp/sepp/output.zghtxx09/root/P_11/A_11_0/hmmbuild.input.fo3u8os7.fasta). [09:15:36] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_7/A_7_0/hmmbuild.model.g02l8sl2, fragments:/tmp/sepp/output.zghtxx09/root/P_7/A_7_0/FC_7_0_0/hmmalign.frag.s_4ncqxv.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_7/A_7_0/hmmbuild.input.drco0mu6.fasta [09:15:36] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_7. [09:15:36] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_7/A_7_0/FC_7_0_0/hmmalign.results.gvonxsbx) into base alignment (/tmp/sepp/output.zghtxx09/root/P_7/A_7_0/hmmbuild.input.drco0mu6.fasta). [09:15:42] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_12/A_12_0/hmmbuild.model.u667t07e, fragments:/tmp/sepp/output.zghtxx09/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.loozt_1p.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_12/A_12_0/hmmbuild.input.bloseifa.fasta [09:15:42] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_12. [09:15:42] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_12/A_12_0/FC_12_0_0/hmmalign.results.v7mb4wfr) into base alignment (/tmp/sepp/output.zghtxx09/root/P_12/A_12_0/hmmbuild.input.bloseifa.fasta). Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_3 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_3/pplacer.backbone.ix1qi2at.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_3/pplacer.tree.akrdfc_t.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_3/pplacer.extended.0.86xe71kn.fasta No error messages available Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_1 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_1/pplacer.backbone.dfynphnm.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_1/pplacer.tree.jafoex89.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_1/pplacer.extended.0.7zk0mi5i.fasta No error messages available Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_4 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_4/pplacer.backbone.tilcvafx.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_4/pplacer.tree.vnxxo0qe.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_4/pplacer.extended.0.a16px5.fasta No error messages available Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_2 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_2/pplacer.backbone.c9lw450t.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_2/pplacer.tree.gh7tjru4.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_2/pplacer.extended.0.tljt2uuj.fasta No error messages available [09:15:42] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_15. Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_9 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_9/pplacer.backbone.evkj4hji.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_9/pplacer.tree.67rkm2gx.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_9/pplacer.extended.0.h8awwpfw.fasta No error messages available Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_5 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_5/pplacer.backbone.lb7w17z5.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_5/pplacer.tree.pwqqz8hs.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_5/pplacer.extended.0.6i1_iu2u.fasta No error messages available Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_10 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_10/pplacer.backbone.d842jfht.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_10/pplacer.tree.bmasscbf.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_10/pplacer.extended.0.6fut4bj3.fasta No error messages available Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_11 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_11/pplacer.backbone.o1eydp1r.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_11/pplacer.tree.rz1t6piq.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_11/pplacer.extended.0.eq91_ass.fasta No error messages available Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_7 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_7/pplacer.backbone.m6zgszed.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_7/pplacer.tree.j6urbg3w.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_7/pplacer.extended.0.hr_cki_i.fasta No error messages available Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_12 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_12/pplacer.backbone.nx5dja1d.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_12/pplacer.tree.gjtsl1zd.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_12/pplacer.extended.0.jz16a1np.fasta No error messages available [09:15:44] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_6/A_60/hmmbuild.model.u55lkuy, fragments:/tmp/sepp/output.zghtxx09/root/P_6/A_6_0/FC_6_0_0/hmmalign.frag.2irs4esx.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_6/A_6_0/hmmbuild.input.bwcopfxa.fasta [09:15:44] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_6. [09:15:44] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_6/A_6_0/FC_6_00/hmmalign.results.dqso39u) into base alignment (/tmp/sepp/output.zghtxx09/root/P_6/A_6_0/hmmbuild.input.bwcopfxa.fasta). Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_6 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_6/pplacer.backbone.5oznsfpd.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_6/pplacer.tree.8qjazy3b.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_6/pplacer.extended.0.etzlf0jk.fasta No error messages available [09:15:51] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_14/A_14_0/hmmbuild.model.pkhvm3vw, fragments:/tmp/sepp/output.zghtxx09/root/P_14/A_14_0/FC_14_0_0/hmmalign.frag.7j129a5d.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_14/A_14_0/hmmbuild.input._ba6klh3.fasta [09:15:51] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_14. [09:15:51] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_14/A_14_0/FC_14_0_0/hmmalign.results.1idsmyy0) into base alignment (/tmp/sepp/output.zghtxx09/root/P_14/A_14_0/hmmbuild.input._ba6klh3.fasta). Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_14 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_14/pplacer.backbone.ozlqaxuj.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_14/pplacer.tree.5xnvfh07.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_14/pplacer.extended.0.r8s9wf7c.fasta No error messages available [09:15:56] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.zghtxx09/root/P_13/A_13_0/hmmbuild.model.1igvzrzs, fragments:/tmp/sepp/output.zghtxx09/root/P_13/A_13_0/FC_13_0_0/hmmalign.frag.wflov8jo.fasta, trim:False, base_alignment:/tmp/sepp/output.zghtxx09/root/P_13/A_13_0/hmmbuild.input.rio7dlv5.fasta [09:15:56] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_13. [09:15:56] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.zghtxx09/root/P_13/A_13_0/FC_13_0_0/hmmalign.results.86p5r4tm) into base alignment (/tmp/sepp/output.zghtxx09/root/P_13/A_13_0/hmmbuild.input.rio7dlv5.fasta). multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/scheduler.py", line 74, in call return self.run() File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_3 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_3/pplacer.backbone.ix1qi2at.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_3/pplacer.tree.akrdfc_t.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_3/pplacer.extended.0.86xe71kn.fasta No error messages available """

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

Traceback (most recent call last): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/run_sepp.py", line 26, in ExhaustiveAlgorithm().run() File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/algorithm.py", line 175, in run if not JobPool().wait_for_all_jobs(): File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/scheduler.py", line 383, in wait_for_all_jobs result.get() File "/home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/multiprocessing/pool.py", line 771, in get raise self._value sepp.scheduler.JobError: The following execution failed: /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/bin/pplacer --out-dir /tmp/sepp/output.zghtxx09/root/P_3 -j 1 -r /tmp/sepp/output.zghtxx09/root/P_3/pplacer.backbone.ix1qi2at.fasta -s /home/user_xi/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.zghtxx09/root/P_3/pplacer.tree.akrdfc_t.tre --groups 10 /tmp/sepp/output.zghtxx09/root/P_3/pplacer.extended.0.86xe71kn.fasta No error messages available

Hi there,

Could you perhaps try re-running with a lower chunk size (say 500 or 1000)? Sometimes memory errors don't give very useful error messages (and you don't have a lot of memory there) so I just want to rule that out before troubleshooting further.

Hi R-Wright-1，

Thanks for your help. I run it with 908 sequences with vbox Debian this time as your suggestion. It still make errors as follows. Then I tried 456 sequences I tried also failed.

picrust2_pipeline.py -s rep-seqs-no-mito_chloro.fasta -i feature-table.biom -o picrust2_output --placement_tool sepp --stratified --processes 4

Standard error of the above failed command:

Standard error of the above failed command: [10:14:20] config.py (line 349): INFO: Seed number: 297834 [10:14:20] algorithm.py (line 258): INFO: Reading input alignment: <_io.TextIOWrapper name='/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna' mode='r' encoding='UTF-8'> [10:14:20] algorithm.py (line 265): INFO: Reading input tree: <_io.TextIOWrapper name='/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre' mode='r' encoding='UTF-8'> [10:14:21] algorithm.py (line 238): INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000 [10:14:23] exhaustive.py (line 350): INFO: Breaking into 16 placement subsets. [10:14:24] exhaustive.py (line 397): INFO: Breaking into 16 alignment subsets. [10:14:24] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/output.v9sbhddj [10:14:24] exhaustive.py (line 412): INFO: Breaking each alignment subset into 1 fragment chunks. [10:14:25] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_0/A_0_0/hmmbuild.input.4e47lioi.fasta [10:14:25] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_1/A_1_0/hmmbuild.input.473eax65.fasta [10:14:25] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_3/A_3_0/hmmbuild.input.1gptutcg.fasta [10:14:25] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_2/A_2_0/hmmbuild.input.u82ihpzd.fasta [10:14:25] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_4/A_4_0/hmmbuild.input.wd53gw_7.fasta [10:14:25] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_7/A_7_0/hmmbuild.input.2ycngede.fasta [10:14:25] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_5/A_5_0/hmmbuild.input.xa979s81.fasta [10:14:25] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_6/A_6_0/hmmbuild.input.yz58kh23.fasta [10:14:26] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_8/A_8_0/hmmbuild.input.mnktp5sf.fasta [10:14:26] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_9/A_9_0/hmmbuild.input.gpea1ruc.fasta [10:14:26] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_10/A_10_0/hmmbuild.input.8gv7e74i.fasta [10:14:26] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_11/A_11_0/hmmbuild.input.pf5g33wy.fasta [10:14:26] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_12/A_12_0/hmmbuild.input.cmex6vyx.fasta [10:14:26] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_13/A_13_0/hmmbuild.input.t8p1wma9.fasta [10:14:26] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_14/A_14_0/hmmbuild.input.6400nmmc.fasta [10:14:26] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.v9sbhddj/root/P_15/A_15_0/hmmbuild.input.zl9l4qez.fasta [10:14:36] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_0/A_0_0/hmmbuild.model.okf29b8n, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.wf6uu5s5 [10:14:37] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_2/A_2_0/hmmbuild.model.abtfc2ug, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_2/A_2_0/FC_2_0_0/hmmsearch.results.jgwgcsyd [10:14:37] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_1/A_1_0/hmmbuild.model.lnfk8plv, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.gh6eg6qm [10:14:37] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_3/A_3_0/hmmbuild.model.jp4gyojk, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.yl_yvbm2 [10:14:47] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_7/A_7_0/hmmbuild.model.gg1jj5wv, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.hsh94hum [10:14:47] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_5/A_5_0/hmmbuild.model.w_1bsvz1, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.tehyxaiv [10:14:47] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_4/A_4_0/hmmbuild.model.7m1hn4j6, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.d506fl9n [10:14:47] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_6/A_6_0/hmmbuild.model.a0903dha, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.j47aegfu [10:14:57] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_8/A_8_0/hmmbuild.model.g_0qr4da, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.mqygj2rk [10:14:57] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_9/A_9_0/hmmbuild.model.otxsma2x, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.xvahxmsy [10:14:58] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_11/A_11_0/hmmbuild.model.b7oceciq, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.gbttj2gd [10:14:58] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_10/A_10_0/hmmbuild.model.7t4kuw4s, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.edw19466 [10:15:08] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_12/A_12_0/hmmbuild.model.ml0_uaan, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.73rx_g14 [10:15:08] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_13/A_13_0/hmmbuild.model.0pafu7re, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.tvyg1xpv [10:15:08] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_14/A_14_0/hmmbuild.model.p2df1dyu, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.231z5qp9 [10:15:08] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_15/A_15_0/hmmbuild.model.t2dnewvu, fragments:/tmp/sepp/output.v9sbhddj/fragment_chunks/fragment_chunk_0_psp92zs.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.v9sbhddj/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.iztqdfm5 [10:15:08] exhaustive.py (line 80): WARNING: Fragments [] are not scored against any subset [10:15:08] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_0. [10:15:09] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_3/A_3_0/hmmbuild.model.jp4gyojk, fragments:/tmp/sepp/output.v9sbhddj/root/P_3/A_3_0/FC_3_0_0/hmmalign.frag.8lqmq1_e.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_3/A_3_0/hmmbuild.input.1gptutcg.fasta [10:15:09] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_3. [10:15:09] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_1/A_1_0/hmmbuild.model.lnfk8plv, fragments:/tmp/sepp/output.v9sbhddj/root/P_1/A_1_0/FC_1_0_0/hmmalign.frag.ijq3449z.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_1/A_1_0/hmmbuild.input.473eax65.fasta [10:15:09] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_3/A_3_0/FC_3_0_0/hmmalign.results.3hb0vaz1) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_3/A_3_0/hmmbuild.input.1gptutcg.fasta). [10:15:09] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_1. [10:15:09] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_1/A_1_0/FC_1_0_0/hmmalign.results.he46rg1m) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_1/A_1_0/hmmbuild.input.473eax65.fasta). [10:15:09] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_4/A_4_0/hmmbuild.model.7m1hn4j6, fragments:/tmp/sepp/output.v9sbhddj/root/P_4/A_4_0/FC_4_0_0/hmmalign.frag._0wjsr4o.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_4/A_4_0/hmmbuild.input.wd53gw_7.fasta [10:15:09] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_4. [10:15:09] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_4/A_4_0/FC_4_0_0/hmmalign.results.98ivvl34) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_4/A_4_0/hmmbuild.input.wd53gw_7.fasta). [10:15:09] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_2/A_2_0/hmmbuild.model.abtfc2ug, fragments:/tmp/sepp/output.v9sbhddj/root/P_2/A_2_0/FC_2_0_0/hmmalign.frag.n61hy1ck.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_2/A_2_0/hmmbuild.input.u82ihpzd.fasta [10:15:09] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_2. [10:15:09] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_2/A_2_0/FC_2_0_0/hmmalign.results.axivv2ba) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_2/A_2_0/hmmbuild.input.u82ihpzd.fasta). [10:15:09] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_8. [10:15:09] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_9/A_9_0/hmmbuild.model.otxsma2x, fragments:/tmp/sepp/output.v9sbhddj/root/P_9/A_9_0/FC_9_0_0/hmmalign.frag.i77thstr.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_9/A_9_0/hmmbuild.input.gpea1ruc.fasta [10:15:10] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_9. [10:15:10] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_9/A_9_0/FC_9_0_0/hmmalign.results.1ilfy2ln) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_9/A_9_0/hmmbuild.input.gpea1ruc.fasta). [10:15:10] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_5/A_5_0/hmmbuild.model.w_1bsvz1, fragments:/tmp/sepp/output.v9sbhddj/root/P_5/A_5_0/FC_5_0_0/hmmalign.frag.rvpijl1x.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_5/A_5_0/hmmbuild.input.xa979s81.fasta [10:15:10] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_5. [10:15:10] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_5/A_5_0/FC_5_0_0/hmmalign.results.cq_wh4sd) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_5/A_5_0/hmmbuild.input.xa979s81.fasta). [10:15:10] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_10/A_10_0/hmmbuild.model.7t4kuw4s, fragments:/tmp/sepp/output.v9sbhddj/root/P_10/A_10_0/FC_10_0_0/hmmalign.frag.k8w44fgt.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_10/A_10_0/hmmbuild.input.8gv7e74i.fasta [10:15:10] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_10. [10:15:10] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_10/A_10_0/FC_10_0_0/hmmalign.results.cyh5nl33) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_10/A_10_0/hmmbuild.input.8gv7e74i.fasta). [10:15:13] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_11/A_11_0/hmmbuild.model.b7oceciq, fragments:/tmp/sepp/output.v9sbhddj/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.ucykrva7.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_11/A_11_0/hmmbuild.input.pf5g33wy.fasta [10:15:13] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_11. [10:15:13] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.82g8gslv) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_11/A_11_0/hmmbuild.input.pf5g33wy.fasta). [10:15:14] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_7/A_7_0/hmmbuild.model.gg1jj5wv, fragments:/tmp/sepp/output.v9sbhddj/root/P_7/A_7_0/FC_7_0_0/hmmalign.frag.uauwrqqg.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_7/A_7_0/hmmbuild.input.2ycngede.fasta [10:15:14] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_7. [10:15:14] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_7/A_7_0/FC_7_0_0/hmmalign.results.h0fziccw) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_7/A_7_0/hmmbuild.input.2ycngede.fasta). [10:15:16] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_12/A_12_0/hmmbuild.model.ml0_uaan, fragments:/tmp/sepp/output.v9sbhddj/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.fi6cz_qg.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_12/A_12_0/hmmbuild.input.cmex6vyx.fasta [10:15:16] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_12. [10:15:16] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_12/A_12_0/FC_12_00/hmmalign.results.a36evwr) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_12/A_12_0/hmmbuild.input.cmex6vyx.fasta). [10:15:16] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_15. [10:15:17] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_6/A_6_0/hmmbuild.model.a0903dha, fragments:/tmp/sepp/output.v9sbhddj/root/P_6/A_6_0/FC_6_0_0/hmmalign.frag.igstcwgg.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_6/A_6_0/hmmbuild.input.yz58kh23.fasta [10:15:17] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_6. [10:15:17] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_6/A_6_0/FC_6_0_0/hmmalign.results.s5_wk9tk) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_6/A_6_0/hmmbuild.input.yz58kh23.fasta). [10:15:20] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_14/A_14_0/hmmbuild.model.p2df1dyu, fragments:/tmp/sepp/output.v9sbhddj/root/P_14/A_14_0/FC_14_0_0/hmmalign.frag.ih0w650y.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_14/A_14_0/hmmbuild.input.6400nmmc.fasta [10:15:20] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_14. [10:15:20] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_14/A_14_0/FC_14_0_0/hmmalign.results.aj1k4ma1) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_14/A_14_0/hmmbuild.input.6400nmmc.fasta). [10:15:22] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.v9sbhddj/root/P_13/A_13_0/hmmbuild.model.0pafu7re, fragments:/tmp/sepp/output.v9sbhddj/root/P_13/A_13_0/FC_13_0_0/hmmalign.frag.dxsy0u2b.fasta, trim:False, base_alignment:/tmp/sepp/output.v9sbhddj/root/P_13/A_13_0/hmmbuild.input.t8p1wma9.fasta [10:15:22] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_13. [10:15:22] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.v9sbhddj/root/P_13/A_13_0/FC_13_0_0/hmmalign.results.xn2td_ql) into base alignment (/tmp/sepp/output.v9sbhddj/root/P_13/A_13_0/hmmbuild.input.t8p1wma9.fasta). multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/scheduler.py", line 74, in call return self.run() File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.v9sbhddj/root/P_3 -j 1 -r /tmp/sepp/output.v9sbhddj/root/P_3/pplacer.backbone.uqi7aji2.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.v9sbhddj/root/P_3/pplacer.tree.iu1wsyp4.tre --groups 10 /tmp/sepp/output.v9sbhddj/root/P_3/pplacer.extended.0.3o4s6_22.fasta No error messages available """

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

Traceback (most recent call last): File "/home/jxi/miniconda3/envs/picrust2/bin/run_sepp.py", line 26, in ExhaustiveAlgorithm().run() File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/algorithm.py", line 174, in run if (not JobPool().wait_for_all_jobs()): File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/scheduler.py", line 382, in wait_for_all_jobs result.get() File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value sepp.scheduler.JobError: The following execution failed: /home/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.v9sbhddj/root/P_3 -j 1 -r /tmp/sepp/output.v9sbhddj/root/P_3/pplacer.backbone.uqi7aji2.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.v9sbhddj/root/P_3/pplacer.tree.iu1wsyp4.tre --groups 10 /tmp/sepp/output.v9sbhddj/root/P_3/pplacer.extended.0.3o4s6_22.fasta No error messages available Traceback (most recent call last): File "/home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/jobs.py", line 150, in run raise JobError("\n".join([ sepp.scheduler.JobError: The following execution failed: /home/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.v9sbhddj/root/P_14 -j 1 -r /tmp/sepp/output.v9sbhddj/root/P_14/pplacer.backbone.4pb7v_fl.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.v9sbhddj/root/P_14/pplacer.tree.39bs0yh6.tre --groups 10 /tmp/sepp/output.v9sbhddj/root/P_14/pplacer.extended.0.hhgjico6.fasta No error messages available

I meant changing this parameter --chunk_size 5000 to 1000 (or 500 or 100). If this doesn't work, are you able to try running outside of the virtual box? I am afraid that I have no experience using them and therefore can't rule out issues there.

Robyn

where can set the parameter --chunk_size? I used command as follows but it said "no picrust2_pipeline.py: error: unrecognized arguments: --chunk_size 1000". Picrust2 2.5.2 or 2.5.3 are the same. Thanks.

picrust2_pipeline.py \ -s rep-seqs-no-mito_chloro.fasta \ -i feature-table.biom \ -o picrust2_output \ --placement_tool sepp \ --stratified \ --processes 4 \ --chunk_size 1000

Oh sorry, I was looking at the place_seqs command in your error output. Perhaps you can try this (modified from the above):

place_seqs.py --study_fasta rep-seqs-no-mito_chloro.fasta --ref_dir /home/jxi/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree picrust2_output/out.tre --processes 4 --intermediate picrust2_output/intermediate/place_seqs --min_align 0.8 --chunk_size 100 --placement_tool sepp

Thanks for your response. Here is the running results. It seems the same problem happened. Thanks for your help.

place_seqs.py --study_fasta rep-seqs-no-mito_chloro.fasta --ref_dir /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree picrust2_output/out.tre --processes 4 --intermediate picrust2_output/intermediate/place_seqs --min_align 0.8 --chunk_size 100 --placement_tool sepp

Error running this command: run_sepp.py --tree /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 4 --molecule dna --outdir picrust2_output/intermediate/place_seqs/sepp_out -seed 297834 --alignment /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment picrust2_output/intermediate/place_seqs/study_seqs_filtered.fasta

Standard error of the above failed command: [11:44:01] config.py (line 370): INFO: Seed number: 297834 [11:44:01] algorithm.py (line 267): INFO: Reading input alignment: <_io.TextIOWrapper name='/home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna' mode='r' encoding='UTF-8'> [11:44:01] algorithm.py (line 274): INFO: Reading input tree: <_io.TextIOWrapper name='/home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre' mode='r' encoding='UTF-8'> [11:44:03] algorithm.py (line 247): INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000 [11:44:05] exhaustive.py (line 351): INFO: Breaking into 16 placement subsets. [11:44:06] exhaustive.py (line 398): INFO: Breaking into 16 alignment subsets. [11:44:06] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/output.i2mdajhb [11:44:06] exhaustive.py (line 413): INFO: Breaking each alignment subset into 1 fragment chunks. [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_1/A_1_0/hmmbuild.input.wpcodcve.fasta [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_2/A_2_0/hmmbuild.input.hyhbiu4d.fasta [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_3/A_3_0/hmmbuild.input.l__frza9.fasta [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_0/A_0_0/hmmbuild.input.002_fq8n.fasta [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_4/A_4_0/hmmbuild.input.nzmj46y4.fasta [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_5/A_5_0/hmmbuild.input.x5qvaxmj.fasta [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_6/A_6_0/hmmbuild.input.n1ggecls.fasta [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_7/A_7_0/hmmbuild.input.2o2id3_r.fasta [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_8/A_8_0/hmmbuild.input._meqjet0.fasta [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_9/A_9_0/hmmbuild.input.vcc4v8bk.fasta [11:44:09] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_10/A_10_0/hmmbuild.input.0glyoesr.fasta [11:44:10] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_11/A_11_0/hmmbuild.input._4s8gw30.fasta [11:44:10] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_12/A_12_0/hmmbuild.input.3c61gi5u.fasta [11:44:10] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_13/A_13_0/hmmbuild.input.xfas8ssc.fasta [11:44:10] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_14/A_14_0/hmmbuild.input.j03l6ib0.fasta [11:44:10] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.i2mdajhb/root/P_15/A_15_0/hmmbuild.input.w1j9c9gf.fasta [11:44:14] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_1/A_1_0/hmmbuild.model.av8a7e2z, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.i3p5abaa [11:44:15] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_3/A_3_0/hmmbuild.model._5zouzgo, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.b0teu5t1 [11:44:15] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_2/A_2_0/hmmbuild.model.dzu94dz9, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_2/A_2_0/FC_2_00/hmmsearch.results.72dd42e [11:44:15] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_0/A_0_0/hmmbuild.model.8mrbua30, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.fa18yr_9 [11:44:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_4/A_4_0/hmmbuild.model.w4wp2k9f, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.0hjywdzc [11:44:20] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_5/A_5_0/hmmbuild.model.3n7pl2hj, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.tyhrx_u2 [11:44:20] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_7/A_7_0/hmmbuild.model.v88pufqo, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.wdu6tnou [11:44:20] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_6/A_60/hmmbuild.model.ynmpbh4, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.i_c7kz4u [11:44:24] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_8/A_8_0/hmmbuild.model.4ifadj33, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.1v92nlt4 [11:44:25] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_9/A_9_0/hmmbuild.model.u99wl0ic, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.q5nxiz7r [11:44:25] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_10/A_10_0/hmmbuild.model.hq5pxof1, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.1_6zonhd [11:44:25] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_11/A_11_0/hmmbuild.model.1x7cin91, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.55fai_mn [11:44:30] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_12/A_12_0/hmmbuild.model.nycvlk2b, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.psg0uctg [11:44:30] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_13/A_13_0/hmmbuild.model.9w1wan0g, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.0gbyoaey [11:44:30] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_14/A_14_0/hmmbuild.model.odgliqb6, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.tuzf0rs8 [11:44:30] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_15/A_15_0/hmmbuild.model.xf15kxqz, fragments:/tmp/sepp/output.i2mdajhb/fragment_chunks/fragment_chunk_0af10375c.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.i2mdajhb/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.da0z0w7w [11:44:30] exhaustive.py (line 81): WARNING: Fragments [] are not scored against any subset [11:44:30] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_0. [11:44:31] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_1. [11:44:31] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_3/A_3_0/hmmbuild.model._5zouzgo, fragments:/tmp/sepp/output.i2mdajhb/root/P_3/A_3_0/FC_3_0_0/hmmalign.frag.crh1h6cu.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_3/A_3_0/hmmbuild.input.lfrza9.fasta [11:44:31] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_3. [11:44:31] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_3/A_3_0/FC_3_0_0/hmmalign.results.6bxgdqdh) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_3/A_3_0/hmmbuild.input.lfrza9.fasta). [11:44:31] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_4/A_4_0/hmmbuild.model.w4wp2k9f, fragments:/tmp/sepp/output.i2mdajhb/root/P_4/A_4_0/FC_4_0_0/hmmalign.frag.8d5reg0j.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_4/A_4_0/hmmbuild.input.nzmj46y4.fasta [11:44:31] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_4. [11:44:31] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_4/A_4_0/FC_4_0_0/hmmalign.results.7cwc3ird) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_4/A_4_0/hmmbuild.input.nzmj46y4.fasta). [11:44:31] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_2/A_2_0/hmmbuild.model.dzu94dz9, fragments:/tmp/sepp/output.i2mdajhb/root/P_2/A_2_0/FC_2_0_0/hmmalign.frag.jedjt_ks.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_2/A_2_0/hmmbuild.input.hyhbiu4d.fasta [11:44:31] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_2. [11:44:31] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_2/A_2_0/FC_2_0_0/hmmalign.results.63_4w6cy) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_2/A_2_0/hmmbuild.input.hyhbiu4d.fasta). [11:44:31] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_9/A_9_0/hmmbuild.model.u99wl0ic, fragments:/tmp/sepp/output.i2mdajhb/root/P_9/A_9_0/FC_9_0_0/hmmalign.frag.7xhey2pf.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_9/A_9_0/hmmbuild.input.vcc4v8bk.fasta [11:44:31] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_8. [11:44:31] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_9. [11:44:31] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_9/A_9_0/FC_9_0_0/hmmalign.results.tylnn4u9) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_9/A_9_0/hmmbuild.input.vcc4v8bk.fasta). [11:44:31] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_5/A_5_0/hmmbuild.model.3n7pl2hj, fragments:/tmp/sepp/output.i2mdajhb/root/P_5/A_5_0/FC_5_0_0/hmmalign.frag.631amqbf.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_5/A_5_0/hmmbuild.input.x5qvaxmj.fasta [11:44:31] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_5. [11:44:31] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_5/A_5_0/FC_5_0_0/hmmalign.results.8a8u6gb3) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_5/A_5_0/hmmbuild.input.x5qvaxmj.fasta). [11:44:32] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_10/A_10_0/hmmbuild.model.hq5pxof1, fragments:/tmp/sepp/output.i2mdajhb/root/P_10/A_10_0/FC_10_0_0/hmmalign.frag.qm4ucf4f.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_10/A_10_0/hmmbuild.input.0glyoesr.fasta [11:44:32] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_10. [11:44:32] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_10/A_10_0/FC_10_0_0/hmmalign.results.m3f1p3v4) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_10/A_10_0/hmmbuild.input.0glyoesr.fasta). [11:44:33] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_11/A_11_0/hmmbuild.model.1x7cin91, fragments:/tmp/sepp/output.i2mdajhb/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.tbu1f5jh.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_11/A_11_0/hmmbuild.input._4s8gw30.fasta [11:44:33] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_11. [11:44:33] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.w5lssfml) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_11/A_11_0/hmmbuild.input._4s8gw30.fasta). [11:44:33] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_7/A_7_0/hmmbuild.model.v88pufqo, fragments:/tmp/sepp/output.i2mdajhb/root/P_7/A_7_0/FC_7_0_0/hmmalign.frag.u3mcelin.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_7/A_7_0/hmmbuild.input.2o2id3_r.fasta [11:44:33] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_7. [11:44:33] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_7/A_7_0/FC_7_0_0/hmmalign.results.r38dvoz0) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_7/A_7_0/hmmbuild.input.2o2id3_r.fasta). [11:44:35] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_12/A_12_0/hmmbuild.model.nycvlk2b, fragments:/tmp/sepp/output.i2mdajhb/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.i3h1em6i.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_12/A_12_0/hmmbuild.input.3c61gi5u.fasta [11:44:35] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_12. [11:44:35] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_12/A_12_0/FC_12_0_0/hmmalign.results.g1nwyhnd) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_12/A_12_0/hmmbuild.input.3c61gi5u.fasta). [11:44:35] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_15. Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_3 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_3/pplacer.backbone.iia6oqh7.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_3/pplacer.tree.btys47ib.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_3/pplacer.extended.0.z33zh46t.fasta No error messages available Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_4 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_4/pplacer.backbone.5lwhg7ew.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_4/pplacer.tree.fyeun_lj.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_4/pplacer.extended.0.f5blkaqe.fasta No error messages available Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_2 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_2/pplacer.backbone.m008xpzh.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_2/pplacer.tree.r8yvkayk.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_2/pplacer.extended.0.6dfpftmd.fasta No error messages available Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_9 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_9/pplacer.backbone.43s7in58.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_9/pplacer.tree.h7wlads9.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_9/pplacer.extended.0.lskuusf1.fasta No error messages available Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_5 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_5/pplacer.backbone.c0_fz5mr.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_5/pplacer.tree.h2ir5zge.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_5/pplacer.extended.0.th4qvg2e.fasta No error messages available Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_10 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_10/pplacer.backbone.a3g6p5e6.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_10/pplacer.tree.cei1b9cd.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_10/pplacer.extended.0.b_qmyfhe.fasta No error messages available Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_11 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_11/pplacer.backbone.7ddkc5od.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_11/pplacer.tree.lhndbj0d.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_11/pplacer.extended.0.aw9qgvcj.fasta No error messages available Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_7 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_7/pplacer.backbone._ygxt2xr.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_7/pplacer.tree.o1365jbp.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_7/pplacer.extended.0.wc2jypd2.fasta No error messages available Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_12 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_12/pplacer.backbone.7h5yr_02.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_12/pplacer.tree.sx8zlfda.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_12/pplacer.extended.0.d8_znrhb.fasta No error messages available [11:44:35] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_6/A_60/hmmbuild.model.ynmpbh4, fragments:/tmp/sepp/output.i2mdajhb/root/P_6/A_6_0/FC_6_0_0/hmmalign.frag.8qhdsibh.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_6/A_6_0/hmmbuild.input.n1ggecls.fasta [11:44:35] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_6. [11:44:35] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_6/A_6_0/FC_6_0_0/hmmalign.results.ee6b_t0x) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_6/A_6_0/hmmbuild.input.n1ggecls.fasta). Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_6 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_6/pplacer.backbone.2h_vj2v2.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_6/pplacer.tree.m6ht5ntx.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_6/pplacer.extended.0.dhkiw_jq.fasta No error messages available [11:44:36] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_14/A_14_0/hmmbuild.model.odgliqb6, fragments:/tmp/sepp/output.i2mdajhb/root/P_14/A_14_0/FC_14_0_0/hmmalign.frag._ruzonu8.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_14/A_14_0/hmmbuild.input.j03l6ib0.fasta [11:44:36] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_14. [11:44:36] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_14/A_14_0/FC_14_0_0/hmmalign.results.6qn6kpn4) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_14/A_14_0/hmmbuild.input.j03l6ib0.fasta). Traceback (most recent call last): File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_14 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_14/pplacer.backbone.45f6l_cm.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_14/pplacer.tree.j6ma8_7u.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_14/pplacer.extended.0.jb5s8jtf.fasta No error messages available [11:44:36] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.i2mdajhb/root/P_13/A_13_0/hmmbuild.model.9w1wan0g, fragments:/tmp/sepp/output.i2mdajhb/root/P_13/A_13_0/FC_13_0_0/hmmalign.frag.jmse64sr.fasta, trim:False, base_alignment:/tmp/sepp/output.i2mdajhb/root/P_13/A_13_0/hmmbuild.input.xfas8ssc.fasta [11:44:36] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_13. [11:44:36] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.i2mdajhb/root/P_13/A_13_0/FC_13_0_0/hmmalign.results.fpgerzq8) into base alignment (/tmp/sepp/output.i2mdajhb/root/P_13/A_13_0/hmmbuild.input.xfas8ssc.fasta). multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/jxi/miniconda3/envs/picrust2/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/sepp/scheduler.py", line 74, in call return self.run() File "/home/jxi/miniconda3/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/jxi/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.i2mdajhb/root/P_3 -j 1 -r /tmp/sepp/output.i2mdajhb/root/P_3/pplacer.backbone.iia6oqh7.fasta -s /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.i2mdajhb/root/P_3/pplacer.tree.btys47ib.tre --groups 10 /tmp/sepp/output.i2mdajhb/root/P_3/pplacer.extended.0.z33zh46t.fasta No error messages available """

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

Is there a reason that you're trying to run with sepp? Could you try with epa-ng?

place_seqs.py --study_fasta rep-seqs-no-mito_chloro.fasta --ref_dir /home/jxi/miniconda3/envs/picrust2/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree picrust2_output/out.tre --processes 4 --intermediate picrust2_output/intermediate/place_seqs --min_align 0.8 --chunk_size 100 --placement_tool epa-ng

No special reason for using sepp. Someone told me sepp is more acurrate than epa-ng, so I use it. And the code you gave with epa-ng could work successfully. Very much thanks!

OK great, no problem - glad it works now! I think your issue may be related to that mentioned in #198, but I'm not really sure.

Yes, I've read #198 when I did it on WSL2 ubantu. So I moved to use vbox running debian and unfortunately it did not solved as #198 stated. Thank you for the great help.

picrust / picrust2

sepp.scheduler.JobError #360

where can set the parameter --chunk_size? I used command as follows but it said "no picrust2_pipeline.py: error: unrecognized arguments: --chunk_size 1000". Picrust2 2.5.2 or 2.5.3 are the same. Thanks.