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jeetsukumaran / DendroPy

A Python library for phylogenetic scripting, simulation, data processing and manipulation.
https://pypi.org/project/DendroPy/.
BSD 3-Clause "New" or "Revised" License
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Error runnig picrust due to cannot import name '_convert_node_to_root_polytomy' #182

Closed Zathzk closed 4 months ago

Zathzk commented 7 months ago

i am trying to run the Chemrein tutorial mention in the picrust page but when i try to exectue this cmd: place_seqs.py -s seqs.fna -o out.tre -p 1 --intermediate place_working -t sepp --verbose

i got this error message:

hmmalign --trim --dna --mapali /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o place_working/query_align.stockholm /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm seqs.fna

All raw input sequences were the same length (400)

run_sepp.py --tree /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir place_working/sepp_out -seed 297834 --alignment /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment place_working/study_seqs_filtered.fasta

Error running this command: run_sepp.py --tree /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir place_working/sepp_out -seed 297834 --alignment /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment place_working/study_seqs_filtered.fasta

Standard error of the above failed command: Traceback (most recent call last): File "/home/kalai/miniconda3/envs/picrust2/bin/run_sepp.py", line 3, in from sepp.exhaustive import ExhaustiveAlgorithm File "/home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/exhaustive.py", line 6, in from sepp.algorithm import AbstractAlgorithm File "/home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/algorithm.py", line 11, in from sepp.tree import PhylogeneticTree File "/home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/tree.py", line 25, in from dendropy.datamodel.treemodel import _convert_node_to_root_polytomy as \ ImportError: cannot import name '_convert_node_to_root_polytomy' from 'dendropy.datamodel.treemodel' (/home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/dendropy/datamodel/treemodel/init.py)

so i searched for sultion and tried this refference downgrading from dendropy 4.6.1 to dendropy 4.5.2. however i ran into another problem, this time there is no error message available

place_seqs.py -s seqs.fna -o out.tre -p 1 --intermediate place_working -t sepp --verbose

hmmalign --trim --dna --mapali /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o place_working/query_align.stockholm /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm seqs.fna

All raw input sequences were the same length (400)

run_sepp.py --tree /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir place_working/sepp_out -seed 297834 --alignment /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment place_working/study_seqs_filtered.fasta

Error running this command: run_sepp.py --tree /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir place_working/sepp_out -seed 297834 --alignment /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment place_working/study_seqs_filtered.fasta

Standard error of the above failed command: [16:11:42] config.py (line 349): INFO: Seed number: 297834 [16:11:42] algorithm.py (line 258): INFO: Reading input alignment: <_io.TextIOWrapper name='/home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna' mode='r' encoding='UTF-8'> [16:11:42] algorithm.py (line 265): INFO: Reading input tree: <_io.TextIOWrapper name='/home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre' mode='r' encoding='UTF-8'> [16:11:43] algorithm.py (line 238): INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000 [16:11:44] exhaustive.py (line 350): INFO: Breaking into 16 placement subsets. [16:11:45] exhaustive.py (line 397): INFO: Breaking into 16 alignment subsets. [16:11:45] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/output.5zp54_ek [16:11:45] exhaustive.py (line 412): INFO: Breaking each alignment subset into 1 fragment chunks. [16:11:45] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_0/A_0_0/hmmbuild.input.qd_oab9r.fasta [16:11:46] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_1/A_1_0/hmmbuild.input.33m76xuy.fasta [16:11:46] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_2/A_2_0/hmmbuild.input.zlgaaphn.fasta [16:11:46] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_3/A_3_0/hmmbuild.input.pb_wxr37.fasta [16:11:46] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_4/A_4_0/hmmbuild.input.j0ce8n_m.fasta [16:11:46] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_5/A_5_0/hmmbuild.input.w5pa_r6c.fasta [16:11:47] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_6/A_6_0/hmmbuild.input.ccuwc_4l.fasta [16:11:47] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_7/A_7_0/hmmbuild.input.et31sokx.fasta [16:11:47] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_8/A_8_0/hmmbuild.input.8nskshma.fasta [16:11:47] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_9/A_9_0/hmmbuild.input.x_cq5crr.fasta [16:11:47] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_10/A_10_0/hmmbuild.input.du6sjb38.fasta [16:11:48] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_11/A_11_0/hmmbuild.input.ftjmdsuf.fasta [16:11:48] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_12/A_12_0/hmmbuild.input.oi52ui6s.fasta [16:11:48] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_13/A_13_0/hmmbuild.input.v8hrxy8h.fasta [16:11:48] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_14/A_14_0/hmmbuild.input._ea23t3y.fasta [16:11:48] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.5zp54_ek/root/P_15/A_15_0/hmmbuild.input.hk4b2_o0.fasta [16:11:49] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_0/A_0_0/hmmbuild.model.71f500qb, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_0/A_0_0/FC_0_00/hmmsearch.results.7waoyjh [16:11:49] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_1/A_1_0/hmmbuild.model.wzw4lmo2, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.01q6znzq [16:11:49] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_2/A_2_0/hmmbuild.model.ok1sl_y9, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_2/A_2_0/FC_2_0_0/hmmsearch.results.h0ghdk3h [16:11:49] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_3/A_3_0/hmmbuild.model.8w9tvipw, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.gv9x3lrj [16:11:50] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_4/A_4_0/hmmbuild.model.1ew_o6qs, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.wpcb9nm0 [16:11:50] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_5/A_5_0/hmmbuild.model.sosd_1kr, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.jb4kdr54 [16:11:50] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_6/A_6_0/hmmbuild.model.dnv2q60j, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.se00ps9s [16:11:50] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_7/A_7_0/hmmbuild.model.tq_yuqag, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.l4kc_05t [16:11:50] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_8/A_8_0/hmmbuild.model.zliai6va, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.siviiht5 [16:11:51] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_9/A_9_0/hmmbuild.model.01bh3z82, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.4e27dyl9 [16:11:51] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_10/A_10_0/hmmbuild.model.5n0l3t0m, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.ia8pdxxt [16:11:51] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_11/A_11_0/hmmbuild.model.as8c4e4t, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.yp_r0tit [16:11:51] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_12/A_12_0/hmmbuild.model.ypbtml4t, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.6ww00o0w [16:11:52] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_13/A_13_0/hmmbuild.model.n1pney03, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.wsbee_hc [16:11:52] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_14/A_14_0/hmmbuild.model.fz7lb1xy, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.zyas34vo [16:11:52] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_15/A_15_0/hmmbuild.model.al95m5tf, fragments:/tmp/sepp/output.5zp54_ek/fragment_chunks/fragment_chunk_0unem3r_q.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.5zp54_ek/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.dbivdrul [16:11:52] exhaustive.py (line 80): WARNING: Fragments [] are not scored against any subset [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_0. [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_1. [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_2. [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_3. [16:11:52] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_9/A_9_0/hmmbuild.model.01bh3z82, fragments:/tmp/sepp/output.5zp54_ek/root/P_9/A_9_0/FC_9_0_0/hmmalign.frag.waqxz2k4.fasta, trim:False, base_alignment:/tmp/sepp/output.5zp54_ek/root/P_9/A_9_0/hmmbuild.input.x_cq5crr.fasta [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_4. [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_5. [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_6. [16:11:52] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_11/A_11_0/hmmbuild.model.as8c4e4t, fragments:/tmp/sepp/output.5zp54_ek/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.t48txjup.fasta, trim:False, base_alignment:/tmp/sepp/output.5zp54_ek/root/P_11/A_11_0/hmmbuild.input.ftjmdsuf.fasta [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_7. [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_8. [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_9. [16:11:52] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.5zp54_ek/root/P_9/A_9_0/FC_9_0_0/hmmalign.results.fj5lyusc) into base alignment (/tmp/sepp/output.5zp54_ek/root/P_9/A_9_0/hmmbuild.input.x_cq5crr.fasta). [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_10. [16:11:52] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_11. [16:11:52] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.5zp54_ek/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.t87rlwqa) into base alignment (/tmp/sepp/output.5zp54_ek/root/P_11/A_11_0/hmmbuild.input.ftjmdsuf.fasta). [16:11:53] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_12/A_12_0/hmmbuild.model.ypbtml4t, fragments:/tmp/sepp/output.5zp54_ek/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.to9810fg.fasta, trim:False, base_alignment:/tmp/sepp/output.5zp54_ek/root/P_12/A_12_0/hmmbuild.input.oi52ui6s.fasta [16:11:53] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_12. [16:11:53] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.5zp54_ek/root/P_12/A_12_0/FC_12_0_0/hmmalign.results.yoopqhla) into base alignment (/tmp/sepp/output.5zp54_ek/root/P_12/A_12_0/hmmbuild.input.oi52ui6s.fasta). [16:11:53] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.5zp54_ek/root/P_13/A_13_0/hmmbuild.model.n1pney03, fragments:/tmp/sepp/output.5zp54_ek/root/P_13/A_13_0/FC_13_0_0/hmmalign.frag.8nh16bh5.fasta, trim:False, base_alignment:/tmp/sepp/output.5zp54_ek/root/P_13/A_13_0/hmmbuild.input.v8hrxy8h.fasta [16:11:53] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_13. [16:11:53] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.5zp54_ek/root/P_13/A_13_0/FC_13_0_0/hmmalign.results.dzt7ffpb) into base alignment (/tmp/sepp/output.5zp54_ek/root/P_13/A_13_0/hmmbuild.input.v8hrxy8h.fasta). [16:11:53] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_14. [16:11:53] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_15. multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/kalai/miniconda3/envs/picrust2/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/scheduler.py", line 74, in call return self.run() File "/home/kalai/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/kalai/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.5zp54_ek/root/P_9 -j 1 -r /tmp/sepp/output.5zp54_ek/root/P_9/pplacer.backbone.iudu1qy8.fasta -s /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.5zp54_ek/root/P_9/pplacer.tree.lo8ki89o.tre --groups 10 /tmp/sepp/output.5zp54_ek/root/P_9/pplacer.extended.0.sscnv87n.fasta No error messages available """

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

Traceback (most recent call last): File "/home/kalai/miniconda3/envs/picrust2/bin/run_sepp.py", line 26, in ExhaustiveAlgorithm().run() File "/home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/algorithm.py", line 174, in run if (not JobPool().wait_for_all_jobs()): File "/home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/scheduler.py", line 365, in wait_for_all_jobs result.get() File "/home/kalai/miniconda3/envs/picrust2/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value sepp.scheduler.JobError: The following execution failed: /home/kalai/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.5zp54_ek/root/P_9 -j 1 -r /tmp/sepp/output.5zp54_ek/root/P_9/pplacer.backbone.iudu1qy8.fasta -s /home/kalai/miniconda3/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.5zp54_ek/root/P_9/pplacer.tree.lo8ki89o.tre --groups 10 /tmp/sepp/output.5zp54_ek/root/P_9/pplacer.extended.0.sscnv87n.fasta No error messages available

mmore500 commented 7 months ago

Hi @Zathzk

Could you try running this a second time and see if you're able to reproduce the error? With multiprocessing, there are a broader range of factors that make it possible for errors to occur transiently.

Have you tried opening an issue on the sepp issue tracker? Given that you already repinned DendroPy for sepp compatibility and the error message does not have attribution it seems more likely to be an issue with sepp itself then DendroPy.

Let me know what you think.

mmore500 commented 4 months ago

Closing this as inactive. Happy to reopen if still an issue