Error in qiime2 picrust2 plug-in
43 views
Skip to first unread message
Amal Arifi
Feb 25, 2025, 9:31:12 AMFeb 25
to picrust-users
Hi everyone. I have successfully installed q2-picrust in qiime2-amplicon-2024.5. However, I've got this following error for months running this command, even using tutorial data:
(qiime2-amplicon-2024.5) amal@amal:/mnt/c/q2-picrust2_tutorial$ qiime picrust2 full-pipeline \
--i-table mammal_biom.qza \
--i-seq mammal_seqs.qza \
--output-dir q2-picrust2_output \
--p-placement-tool sepp \
--p-threads 4 \
--p-hsp-method pic \
--p-max-nsti 2 \
--verbose
Error running this command:
place_seqs.py --study_fasta /tmp/tmp31wd1ol_/seqs.fna --ref_dir /home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree /tmp/tmp31wd1ol_/picrust2_out/out.tre --processes 4 --intermediate /tmp/tmp31wd1ol_/picrust2_out/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/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/amal/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 /tmp/tmp31wd1ol_/picrust2_out/intermediate/place_seqs/sepp_out -seed 297834 --alignment /home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmp31wd1ol_/picrust2_out/intermediate/place_seqs/study_seqs_filtered.fasta
Standard error of the above failed command:
[08:22:46] config.py (line 370): INFO: Seed number: 297834
[08:22:46] algorithm.py (line 267): INFO: Reading input alignment: <_io.TextIOWrapper name='/home/amal/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'>
[08:22:46] algorithm.py (line 274): INFO: Reading input tree: <_io.TextIOWrapper name='/home/amal/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'>
[08:22:48] algorithm.py (line 247): INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000
[08:22:51] exhaustive.py (line 351): INFO: Breaking into 16 placement subsets.
[08:22:54] exhaustive.py (line 398): INFO: Breaking into 16 alignment subsets.
[08:22:54] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/output.hqrfnpcq
[08:22:54] exhaustive.py (line 413): INFO: Breaking each alignment subset into 1 fragment chunks.
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_0/A_0_0/hmmbuild.input.cnvl7ild.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/hmmbuild.input.xom1sdqk.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/hmmbuild.input.eiamrmj4.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/hmmbuild.input.gh05obki.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/hmmbuild.input.mn56dkyx.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/hmmbuild.input.ovzqvgno.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/hmmbuild.input.8rsrg1sr.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/hmmbuild.input.159uy5tc.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_8/A_8_0/hmmbuild.input.oydpjn56.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_9/A_9_0/hmmbuild.input.kgxs_1q2.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/hmmbuild.input.ernfumof.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/hmmbuild.input.rwz_t0n9.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/hmmbuild.input.biz9oukj.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/hmmbuild.input.3d1hpqe6.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_14/A_14_0/hmmbuild.input.hbf4_rbi.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/hmmbuild.input.wt2ekvwo.fasta
[08:23:03] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/hmmbuild.model.829r529c, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.qfax0i_q
[08:23:03] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/hmmbuild.model.zzy7n95c, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.07b8xp0r
[08:23:03] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_0/A_0_0/hmmbuild.model.zdq4m8n9, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.k2rfdbyd
[08:23:04] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/hmmbuild.model._5k9wnlr, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/FC_2_0_0/hmmsearch.results.130xr5r7
[08:23:08] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/hmmbuild.model.atjrm4y0, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.io919s3q
[08:23:09] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/hmmbuild.model.lop52rrc, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.xbsiyv45
[08:23:09] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/hmmbuild.model.7s2g6lcd, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.qg7eol6y
[08:23:09] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/hmmbuild.model.wr9g5d2_, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.5stbrmo_
[08:23:14] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_8/A_8_0/hmmbuild.model.pg98q601, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.jpbn3zfi
[08:23:14] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_9/A_9_0/hmmbuild.model.whhaa4k1, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.tdsbjtd1
[08:23:14] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/hmmbuild.model.82tbuqs3, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.800vgkpu
[08:23:15] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/hmmbuild.model.0hrt27wq, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.hxg_v0lr
[08:23:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/hmmbuild.model.fs0os2n0, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.j7h0hcqj
[08:23:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/hmmbuild.model.cr6ocsta, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.va0s6z94
[08:23:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_14/A_14_0/hmmbuild.model.74ctaj8c, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.4wl5b_s4
[08:23:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/hmmbuild.model.sl2_mbak, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.0h_95uoe
[08:23:19] exhaustive.py (line 81): WARNING: Fragments [] are not scored against any subset
[08:23:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_0.
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/hmmbuild.model.829r529c, fragments:/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/FC_1_0_0/hmmalign.frag.0b4jj9vi.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/hmmbuild.input.xom1sdqk.fasta
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/hmmbuild.model.atjrm4y0, fragments:/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/FC_4_0_0/hmmalign.frag.5rvtgi7s.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/hmmbuild.input.mn56dkyx.fasta
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/hmmbuild.model.zzy7n95c, fragments:/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/FC_3_0_0/hmmalign.frag.rxf7ln78.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/hmmbuild.input.eiamrmj4.fasta
[08:23:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_1.
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/hmmbuild.model._5k9wnlr, fragments:/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/FC_2_0_0/hmmalign.frag.c7xukkle.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/hmmbuild.input.gh05obki.fasta
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/hmmbuild.model.lop52rrc, fragments:/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/FC_5_0_0/hmmalign.frag.ta87ws0_.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/hmmbuild.input.ovzqvgno.fasta
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/hmmbuild.model.wr9g5d2_, fragments:/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/FC_6_0_0/hmmalign.frag.7kfp_l_k.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/hmmbuild.input.159uy5tc.fasta
[08:23:19] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/FC_1_0_0/hmmalign.results.biqc14cu) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/hmmbuild.input.xom1sdqk.fasta).
[08:23:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_4.
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/hmmbuild.model.7s2g6lcd, fragments:/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/FC_7_0_0/hmmalign.frag.x0x0tvrc.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/hmmbuild.input.8rsrg1sr.fasta
[08:23:19] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/FC_4_0_0/hmmalign.results.nmjz8m3c) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/hmmbuild.input.mn56dkyx.fasta).
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/hmmbuild.model.0hrt27wq, fragments:/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/FC_10_0_0/hmmalign.frag.scek5kjy.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/hmmbuild.input.rwz_t0n9.fasta
[08:23:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_3.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/FC_3_0_0/hmmalign.results.z66bd2d4) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/hmmbuild.input.eiamrmj4.fasta).
[08:23:20] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/hmmbuild.model.sl2_mbak, fragments:/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/FC_15_0_0/hmmalign.frag.yhy5e6is.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/hmmbuild.input.wt2ekvwo.fasta
[08:23:20] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/hmmbuild.model.cr6ocsta, fragments:/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/FC_13_0_0/hmmalign.frag.a1kfsvk0.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/hmmbuild.input.3d1hpqe6.fasta
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_2.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/FC_2_0_0/hmmalign.results.ah4f2jo7) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/hmmbuild.input.gh05obki.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_8.
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_9.
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_5.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/FC_5_0_0/hmmalign.results.aywcpqnd) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/hmmbuild.input.ovzqvgno.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_6.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/FC_6_0_0/hmmalign.results.kdhia1k3) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/hmmbuild.input.159uy5tc.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_7.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/FC_7_0_0/hmmalign.results.ug91137s) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/hmmbuild.input.8rsrg1sr.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_10.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/FC_10_0_0/hmmalign.results.2_t_esdo) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/hmmbuild.input.rwz_t0n9.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_14.
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_15.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/FC_15_0_0/hmmalign.results.kcbb5vwg) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/hmmbuild.input.wt2ekvwo.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_13.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/FC_13_0_0/hmmalign.results.7amvjqy6) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/hmmbuild.input.3d1hpqe6.fasta).
[08:23:21] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/hmmbuild.model.fs0os2n0, fragments:/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.f7hqt1z8.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/hmmbuild.input.biz9oukj.fasta
[08:23:21] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_12.
[08:23:21] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/FC_12_0_0/hmmalign.results.m385h4wt) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/hmmbuild.input.biz9oukj.fasta).
[08:23:21] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/hmmbuild.model.82tbuqs3, fragments:/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.kvy_fid9.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/hmmbuild.input.ernfumof.fasta
[08:23:21] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_11.
[08:23:21] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.t8vzlify) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/hmmbuild.input.ernfumof.fasta).
[08:23:22] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.backbone.hw_fyluz.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.tree.xa_cxvzo.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.extended.0.0r638zw7.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.extended.0.0r638zw7.jplace
[08:23:23] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.backbone.zc5mwnng.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.tree.zyomp9bs.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.extended.0._25v97n7.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.extended.0._25v97n7.jplace
[08:23:25] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.backbone.wst3nw0z.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.tree.spn6l7ou.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.extended.0.lvrzq6ku.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.extended.0.lvrzq6ku.jplace
[08:23:26] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.backbone.j5vyrf0r.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.tree.axwxsjeu.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.extended.0.9jd90t0a.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.extended.0.9jd90t0a.jplace
[08:23:28] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.backbone.__rpkjpq.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.tree.glbkoncb.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.extended.0.01kz24zw.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.extended.0.01kz24zw.jplace
[08:23:30] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.backbone.bj2nk_ce.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.tree.41rfwgeh.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.extended.0.omipwglj.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.extended.0.omipwglj.jplace
[08:23:33] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.backbone.v0yizlxt.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.tree.904r3g1l.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.extended.0.scex19hg.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.extended.0.scex19hg.jplace
[08:23:33] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.backbone.9lbza9lu.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.tree.rx9wlld6.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.extended.0.er109esb.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.extended.0.er109esb.jplace
[08:23:35] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.backbone.9vhto0b6.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.tree.8_xf49dw.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.extended.0.hn90ar4i.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.extended.0.hn90ar4i.jplace
[08:23:40] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.backbone.9fcvisxe.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.tree.vuvtirg9.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.extended.0.ucgaby53.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.extended.0.ucgaby53.jplace
[08:23:55] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.backbone.mhlhexgw.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.tree.b22bn6s7.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.extended.0.mfveb1uo.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.extended.0.mfveb1uo.jplace
[08:23:58] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.backbone.bwqgv_f7.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.tree.7ph4vszs.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.extended.0.fz8duc01.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.extended.0.fz8duc01.jplace
Traceback (most recent call last):
File "/home/amal/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:
java -jar /home/amal/miniconda3/envs/qiime2-amplicon-2024.5/bin/seppJsonMerger.jar - - /tmp/tmp31wd1ol_/picrust2_out/intermediate/place_seqs/sepp_out/output_placement.json
json locations: [/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.extended.0._25v97n7.jplace, /tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.extended.0.omipwglj.jplace, /tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.extended.0.lvrzq6ku.jplace, /tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.extended.0.0r638zw7.jplace, /tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.extended.0.9jd90t0a.jplace, /tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.extended.0.01kz24zw.jplace, /tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.extended.0.er109esb.jplace, /tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.extended.0.hn90ar4i.jplace, /tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.extended.0.fz8duc01.jplace, /tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.extended.0.mfveb1uo.jplace, /tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.extended.0.ucgaby53.jplace, /tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.extended.0.scex19hg.jplace]
Exception in thread "main" java.lang.NumberFormatException: Cannot parse null string
at java.base/java.lang.Integer.parseInt(Integer.java:550)
at java.base/java.lang.Integer.<init>(Integer.java:1065)
at phylolab.taxonamic.PPlacerJSONMerger.relabelJson(PPlacerJSONMerger.java:172)
at phylolab.taxonamic.PPlacerJSONMerger.main(PPlacerJSONMerger.java:288)
Traceback (most recent call last):
File "/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/bin/run_sepp.py", line 26, in <module>
ExhaustiveAlgorithm().run()
File "/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/algorithm.py", line 188, in run
self.merge_results()
File "/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/exhaustive.py", line 291, in merge_results
mergeJsonJob.run()
File "/home/amal/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:
java -jar /home/amal/miniconda3/envs/qiime2-amplicon-2024.5/bin/seppJsonMerger.jar - - /tmp/tmp31wd1ol_/picrust2_out/intermediate/place_seqs/sepp_out/output_placement.json
json locations: [/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.extended.0._25v97n7.jplace, /tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.extended.0.omipwglj.jplace, /tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.extended.0.lvrzq6ku.jplace, /tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.extended.0.0r638zw7.jplace, /tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.extended.0.9jd90t0a.jplace, /tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.extended.0.01kz24zw.jplace, /tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.extended.0.er109esb.jplace, /tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.extended.0.hn90ar4i.jplace, /tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.extended.0.fz8duc01.jplace, /tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.extended.0.mfveb1uo.jplace, /tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.extended.0.ucgaby53.jplace, /tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.extended.0.scex19hg.jplace]
Exception in thread "main" java.lang.NumberFormatException: Cannot parse null string
at java.base/java.lang.Integer.parseInt(Integer.java:550)
at java.base/java.lang.Integer.<init>(Integer.java:1065)
at phylolab.taxonamic.PPlacerJSONMerger.relabelJson(PPlacerJSONMerger.java:172)
at phylolab.taxonamic.PPlacerJSONMerger.main(PPlacerJSONMerger.java:288)
--i-table mammal_biom.qza \
--i-seq mammal_seqs.qza \
--output-dir q2-picrust2_output \
--p-placement-tool sepp \
--p-threads 4 \
--p-hsp-method pic \
--p-max-nsti 2 \
--verbose
Error running this command:
place_seqs.py --study_fasta /tmp/tmp31wd1ol_/seqs.fna --ref_dir /home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref --out_tree /tmp/tmp31wd1ol_/picrust2_out/out.tre --processes 4 --intermediate /tmp/tmp31wd1ol_/picrust2_out/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/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/amal/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 /tmp/tmp31wd1ol_/picrust2_out/intermediate/place_seqs/sepp_out -seed 297834 --alignment /home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmp31wd1ol_/picrust2_out/intermediate/place_seqs/study_seqs_filtered.fasta
Standard error of the above failed command:
[08:22:46] config.py (line 370): INFO: Seed number: 297834
[08:22:46] algorithm.py (line 267): INFO: Reading input alignment: <_io.TextIOWrapper name='/home/amal/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'>
[08:22:46] algorithm.py (line 274): INFO: Reading input tree: <_io.TextIOWrapper name='/home/amal/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'>
[08:22:48] algorithm.py (line 247): INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000
[08:22:51] exhaustive.py (line 351): INFO: Breaking into 16 placement subsets.
[08:22:54] exhaustive.py (line 398): INFO: Breaking into 16 alignment subsets.
[08:22:54] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/output.hqrfnpcq
[08:22:54] exhaustive.py (line 413): INFO: Breaking each alignment subset into 1 fragment chunks.
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_0/A_0_0/hmmbuild.input.cnvl7ild.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/hmmbuild.input.xom1sdqk.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/hmmbuild.input.eiamrmj4.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/hmmbuild.input.gh05obki.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/hmmbuild.input.mn56dkyx.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/hmmbuild.input.ovzqvgno.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/hmmbuild.input.8rsrg1sr.fasta
[08:22:57] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/hmmbuild.input.159uy5tc.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_8/A_8_0/hmmbuild.input.oydpjn56.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_9/A_9_0/hmmbuild.input.kgxs_1q2.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/hmmbuild.input.ernfumof.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/hmmbuild.input.rwz_t0n9.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/hmmbuild.input.biz9oukj.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/hmmbuild.input.3d1hpqe6.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_14/A_14_0/hmmbuild.input.hbf4_rbi.fasta
[08:22:58] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/hmmbuild.input.wt2ekvwo.fasta
[08:23:03] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/hmmbuild.model.829r529c, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.qfax0i_q
[08:23:03] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/hmmbuild.model.zzy7n95c, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.07b8xp0r
[08:23:03] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_0/A_0_0/hmmbuild.model.zdq4m8n9, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.k2rfdbyd
[08:23:04] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/hmmbuild.model._5k9wnlr, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/FC_2_0_0/hmmsearch.results.130xr5r7
[08:23:08] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/hmmbuild.model.atjrm4y0, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.io919s3q
[08:23:09] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/hmmbuild.model.lop52rrc, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.xbsiyv45
[08:23:09] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/hmmbuild.model.7s2g6lcd, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.qg7eol6y
[08:23:09] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/hmmbuild.model.wr9g5d2_, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.5stbrmo_
[08:23:14] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_8/A_8_0/hmmbuild.model.pg98q601, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.jpbn3zfi
[08:23:14] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_9/A_9_0/hmmbuild.model.whhaa4k1, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.tdsbjtd1
[08:23:14] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/hmmbuild.model.82tbuqs3, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.800vgkpu
[08:23:15] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/hmmbuild.model.0hrt27wq, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.hxg_v0lr
[08:23:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/hmmbuild.model.fs0os2n0, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.j7h0hcqj
[08:23:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/hmmbuild.model.cr6ocsta, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.va0s6z94
[08:23:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_14/A_14_0/hmmbuild.model.74ctaj8c, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.4wl5b_s4
[08:23:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/hmmbuild.model.sl2_mbak, fragments:/tmp/sepp/output.hqrfnpcq/fragment_chunks/fragment_chunk_0iv3eombu.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.0h_95uoe
[08:23:19] exhaustive.py (line 81): WARNING: Fragments [] are not scored against any subset
[08:23:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_0.
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/hmmbuild.model.829r529c, fragments:/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/FC_1_0_0/hmmalign.frag.0b4jj9vi.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/hmmbuild.input.xom1sdqk.fasta
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/hmmbuild.model.atjrm4y0, fragments:/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/FC_4_0_0/hmmalign.frag.5rvtgi7s.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/hmmbuild.input.mn56dkyx.fasta
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/hmmbuild.model.zzy7n95c, fragments:/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/FC_3_0_0/hmmalign.frag.rxf7ln78.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/hmmbuild.input.eiamrmj4.fasta
[08:23:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_1.
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/hmmbuild.model._5k9wnlr, fragments:/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/FC_2_0_0/hmmalign.frag.c7xukkle.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/hmmbuild.input.gh05obki.fasta
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/hmmbuild.model.lop52rrc, fragments:/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/FC_5_0_0/hmmalign.frag.ta87ws0_.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/hmmbuild.input.ovzqvgno.fasta
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/hmmbuild.model.wr9g5d2_, fragments:/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/FC_6_0_0/hmmalign.frag.7kfp_l_k.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/hmmbuild.input.159uy5tc.fasta
[08:23:19] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/FC_1_0_0/hmmalign.results.biqc14cu) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_1/A_1_0/hmmbuild.input.xom1sdqk.fasta).
[08:23:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_4.
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/hmmbuild.model.7s2g6lcd, fragments:/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/FC_7_0_0/hmmalign.frag.x0x0tvrc.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/hmmbuild.input.8rsrg1sr.fasta
[08:23:19] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/FC_4_0_0/hmmalign.results.nmjz8m3c) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_4/A_4_0/hmmbuild.input.mn56dkyx.fasta).
[08:23:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/hmmbuild.model.0hrt27wq, fragments:/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/FC_10_0_0/hmmalign.frag.scek5kjy.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/hmmbuild.input.rwz_t0n9.fasta
[08:23:19] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_3.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/FC_3_0_0/hmmalign.results.z66bd2d4) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_3/A_3_0/hmmbuild.input.eiamrmj4.fasta).
[08:23:20] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/hmmbuild.model.sl2_mbak, fragments:/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/FC_15_0_0/hmmalign.frag.yhy5e6is.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/hmmbuild.input.wt2ekvwo.fasta
[08:23:20] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/hmmbuild.model.cr6ocsta, fragments:/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/FC_13_0_0/hmmalign.frag.a1kfsvk0.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/hmmbuild.input.3d1hpqe6.fasta
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_2.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/FC_2_0_0/hmmalign.results.ah4f2jo7) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_2/A_2_0/hmmbuild.input.gh05obki.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_8.
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_9.
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_5.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/FC_5_0_0/hmmalign.results.aywcpqnd) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_5/A_5_0/hmmbuild.input.ovzqvgno.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_6.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/FC_6_0_0/hmmalign.results.kdhia1k3) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_6/A_6_0/hmmbuild.input.159uy5tc.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_7.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/FC_7_0_0/hmmalign.results.ug91137s) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_7/A_7_0/hmmbuild.input.8rsrg1sr.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_10.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/FC_10_0_0/hmmalign.results.2_t_esdo) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_10/A_10_0/hmmbuild.input.rwz_t0n9.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_14.
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_15.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/FC_15_0_0/hmmalign.results.kcbb5vwg) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_15/A_15_0/hmmbuild.input.wt2ekvwo.fasta).
[08:23:20] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_13.
[08:23:20] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/FC_13_0_0/hmmalign.results.7amvjqy6) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_13/A_13_0/hmmbuild.input.3d1hpqe6.fasta).
[08:23:21] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/hmmbuild.model.fs0os2n0, fragments:/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.f7hqt1z8.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/hmmbuild.input.biz9oukj.fasta
[08:23:21] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_12.
[08:23:21] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/FC_12_0_0/hmmalign.results.m385h4wt) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_12/A_12_0/hmmbuild.input.biz9oukj.fasta).
[08:23:21] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/hmmbuild.model.82tbuqs3, fragments:/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.kvy_fid9.fasta, trim:False, base_alignment:/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/hmmbuild.input.ernfumof.fasta
[08:23:21] exhaustive.py (line 152): INFO: Merging sub-alignments for placement problem : P_11.
[08:23:21] alignment.py (line 566): INFO: Merging extension sto file (/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.t8vzlify) into base alignment (/tmp/sepp/output.hqrfnpcq/root/P_11/A_11_0/hmmbuild.input.ernfumof.fasta).
[08:23:22] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.backbone.hw_fyluz.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.tree.xa_cxvzo.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.extended.0.0r638zw7.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.extended.0.0r638zw7.jplace
[08:23:23] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.backbone.zc5mwnng.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.tree.zyomp9bs.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.extended.0._25v97n7.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.extended.0._25v97n7.jplace
[08:23:25] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.backbone.wst3nw0z.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.tree.spn6l7ou.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.extended.0.lvrzq6ku.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.extended.0.lvrzq6ku.jplace
[08:23:26] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.backbone.j5vyrf0r.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.tree.axwxsjeu.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.extended.0.9jd90t0a.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.extended.0.9jd90t0a.jplace
[08:23:28] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.backbone.__rpkjpq.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.tree.glbkoncb.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.extended.0.01kz24zw.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.extended.0.01kz24zw.jplace
[08:23:30] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.backbone.bj2nk_ce.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.tree.41rfwgeh.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.extended.0.omipwglj.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.extended.0.omipwglj.jplace
[08:23:33] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.backbone.v0yizlxt.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.tree.904r3g1l.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.extended.0.scex19hg.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.extended.0.scex19hg.jplace
[08:23:33] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.backbone.9lbza9lu.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.tree.rx9wlld6.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.extended.0.er109esb.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.extended.0.er109esb.jplace
[08:23:35] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.backbone.9vhto0b6.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.tree.8_xf49dw.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.extended.0.hn90ar4i.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.extended.0.hn90ar4i.jplace
[08:23:40] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.backbone.9fcvisxe.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.tree.vuvtirg9.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.extended.0.ucgaby53.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.extended.0.ucgaby53.jplace
[08:23:55] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.backbone.mhlhexgw.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.tree.b22bn6s7.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.extended.0.mfveb1uo.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.extended.0.mfveb1uo.jplace
[08:23:58] jobs.py (line 131): INFO: Finished pplacer Job with input: backbone_alignment_file:/tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.backbone.bwqgv_f7.fasta, tree_file:/tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.tree.7ph4vszs.tre, info_file:/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info, extended alignment:/tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.extended.0.fz8duc01.fasta, output:/tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.extended.0.fz8duc01.jplace
Traceback (most recent call last):
File "/home/amal/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:
java -jar /home/amal/miniconda3/envs/qiime2-amplicon-2024.5/bin/seppJsonMerger.jar - - /tmp/tmp31wd1ol_/picrust2_out/intermediate/place_seqs/sepp_out/output_placement.json
json locations: [/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.extended.0._25v97n7.jplace, /tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.extended.0.omipwglj.jplace, /tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.extended.0.lvrzq6ku.jplace, /tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.extended.0.0r638zw7.jplace, /tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.extended.0.9jd90t0a.jplace, /tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.extended.0.01kz24zw.jplace, /tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.extended.0.er109esb.jplace, /tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.extended.0.hn90ar4i.jplace, /tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.extended.0.fz8duc01.jplace, /tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.extended.0.mfveb1uo.jplace, /tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.extended.0.ucgaby53.jplace, /tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.extended.0.scex19hg.jplace]
Exception in thread "main" java.lang.NumberFormatException: Cannot parse null string
at java.base/java.lang.Integer.parseInt(Integer.java:550)
at java.base/java.lang.Integer.<init>(Integer.java:1065)
at phylolab.taxonamic.PPlacerJSONMerger.relabelJson(PPlacerJSONMerger.java:172)
at phylolab.taxonamic.PPlacerJSONMerger.main(PPlacerJSONMerger.java:288)
Traceback (most recent call last):
File "/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/bin/run_sepp.py", line 26, in <module>
ExhaustiveAlgorithm().run()
File "/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/algorithm.py", line 188, in run
self.merge_results()
File "/home/amal/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/sepp/exhaustive.py", line 291, in merge_results
mergeJsonJob.run()
File "/home/amal/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:
java -jar /home/amal/miniconda3/envs/qiime2-amplicon-2024.5/bin/seppJsonMerger.jar - - /tmp/tmp31wd1ol_/picrust2_out/intermediate/place_seqs/sepp_out/output_placement.json
json locations: [/tmp/sepp/output.hqrfnpcq/root/P_1/pplacer.extended.0._25v97n7.jplace, /tmp/sepp/output.hqrfnpcq/root/P_2/pplacer.extended.0.omipwglj.jplace, /tmp/sepp/output.hqrfnpcq/root/P_3/pplacer.extended.0.lvrzq6ku.jplace, /tmp/sepp/output.hqrfnpcq/root/P_4/pplacer.extended.0.0r638zw7.jplace, /tmp/sepp/output.hqrfnpcq/root/P_5/pplacer.extended.0.9jd90t0a.jplace, /tmp/sepp/output.hqrfnpcq/root/P_6/pplacer.extended.0.01kz24zw.jplace, /tmp/sepp/output.hqrfnpcq/root/P_7/pplacer.extended.0.er109esb.jplace, /tmp/sepp/output.hqrfnpcq/root/P_10/pplacer.extended.0.hn90ar4i.jplace, /tmp/sepp/output.hqrfnpcq/root/P_11/pplacer.extended.0.fz8duc01.jplace, /tmp/sepp/output.hqrfnpcq/root/P_12/pplacer.extended.0.mfveb1uo.jplace, /tmp/sepp/output.hqrfnpcq/root/P_13/pplacer.extended.0.ucgaby53.jplace, /tmp/sepp/output.hqrfnpcq/root/P_15/pplacer.extended.0.scex19hg.jplace]
Exception in thread "main" java.lang.NumberFormatException: Cannot parse null string
at java.base/java.lang.Integer.parseInt(Integer.java:550)
at java.base/java.lang.Integer.<init>(Integer.java:1065)
at phylolab.taxonamic.PPlacerJSONMerger.relabelJson(PPlacerJSONMerger.java:172)
at phylolab.taxonamic.PPlacerJSONMerger.main(PPlacerJSONMerger.java:288)
Thank you for all your help!
Kind regards,
Amal
Robyn Wright
Feb 25, 2025, 9:37:02 AMFeb 25
to picrust-users
Hi there,
Could you give some more information on where you're running this - how much memory do you have? Also, can you try using epa-ng (i.e. --p-placement-tool epa-ng) and see if this works?
Thanks,
Robyn
Reply all
Reply to author
Forward
0 new messages