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Code, unit tests, and tutorials for running PICRUSt2
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During pytest place_seqs.py fails and cannot run the full pipeline #347

Closed rassanjorjo closed 4 months ago

rassanjorjo commented 8 months ago

I have reinstalled picrust a dozen times already but the place_seqs.py always fails. I dont have qiime2 already in my system. what could be possibly wrong? Please help. thank you!

platform linux -- Python 3.8.19, pytest-8.1.1, pluggy-1.4.0 rootdir: /home/rey/picrust2-2.5.2 plugins: cov-5.0.0 collected 61 items

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

======================================================= FAILURES ======================================================= __ place_seqs_tests.test_run_place_seqs_pipeline_sepp __

self = 

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

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

tests/test_place_seqs.py:160:

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

cmd = ['run_sepp.py', '--tree', '/home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre', '--raxml', '/home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info', '--cpu', ...] print_command = True, print_stdout = True, print_stderr = True

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

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

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

    stdout_log = ""
    stderr_log = ""

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

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

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

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

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

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

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

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

            if stderr_log:
                print("\nStandard error of the above failed command:\n" +
                      stderr_log, file=sys.stderr)
          sys.exit(1)

E SystemExit: 1

picrust2/util.py:258: SystemExit ------------------------------------------------- Captured stdout call -------------------------------------------------

------------------------------------------------- Captured stderr call ------------------------------------------------- hmmalign --trim --dna --mapali /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --informat FASTA -o /tmp/tmprslmk87r/query_align.stockholm /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.hmm /home/rey/picrust2-2.5.2/tests/test_data/place_seqs/study_seqs_test.fasta

All raw input sequences were the same length (400)

run_sepp.py --tree /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmprslmk87r/sepp_out -seed 297834 --alignment /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmprslmk87r/study_seqs_filtered.fasta

Error running this command: run_sepp.py --tree /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre --raxml /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info --cpu 1 --molecule dna --outdir /tmp/tmprslmk87r/sepp_out -seed 297834 --alignment /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna --fragment /tmp/tmprslmk87r/study_seqs_filtered.fasta

Standard error of the above failed command: [18:59:07] config.py (line 349): INFO: Seed number: 297834 [18:59:07] algorithm.py (line 258): INFO: Reading input alignment: <_io.TextIOWrapper name='/home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.fna' mode='r' encoding='UTF-8'> [18:59:07] algorithm.py (line 265): INFO: Reading input tree: <_io.TextIOWrapper name='/home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.tre' mode='r' encoding='UTF-8'> [18:59:08] algorithm.py (line 238): INFO: Decomposition Sizes are set to alignment: 2000 placement: 2000 [18:59:10] exhaustive.py (line 350): INFO: Breaking into 16 placement subsets. [18:59:12] exhaustive.py (line 397): INFO: Breaking into 16 alignment subsets. [18:59:12] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/output.ziutryl9 [18:59:12] exhaustive.py (line 412): INFO: Breaking each alignment subset into 1 fragment chunks. [18:59:12] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_0/A_0_0/hmmbuild.input.l0dv1zqq.fasta [18:59:13] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_1/A_1_0/hmmbuild.input.js7bzx9z.fasta [18:59:13] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_2/A_2_0/hmmbuild.input.injtgju8.fasta [18:59:13] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_3/A_3_0/hmmbuild.input.jp54cb6i.fasta [18:59:14] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_4/A_4_0/hmmbuild.input.vd_lvhg6.fasta [18:59:14] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_5/A_5_0/hmmbuild.input.c32y13u4.fasta [18:59:15] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_6/A_6_0/hmmbuild.input.hnmfk8ch.fasta [18:59:15] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_7/A_7_0/hmmbuild.input.p_jcl0c5.fasta [18:59:15] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_8/A_8_0/hmmbuild.input.qglp5vtk.fasta [18:59:16] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_9/A_9_0/hmmbuild.input.qk6u4w4j.fasta [18:59:16] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_10/A_10_0/hmmbuild.input.0kmir8wz.fasta [18:59:16] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_11/A_11_0/hmmbuild.input.2r4vfbmi.fasta [18:59:17] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_12/A_12_0/hmmbuild.input.of5d9sau.fasta [18:59:17] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_13/A_13_0/hmmbuild.input.v1feofeq.fasta [18:59:17] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_14/A_14_0/hmmbuild.input.vmiol6a5.fasta [18:59:18] jobs.py (line 131): INFO: Finished hmmbuild Job with input: /tmp/sepp/output.ziutryl9/root/P_15/A_15_0/hmmbuild.input.974lvlxz.fasta [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_0/A_0_0/hmmbuild.model.sxjfux_w, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_0/A_0_0/FC_0_0_0/hmmsearch.results.09y0blu1 [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_1/A_1_0/hmmbuild.model.iys7buk2, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_1/A_1_0/FC_1_0_0/hmmsearch.results.1w_s_2tk [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_2/A_2_0/hmmbuild.model.15l8k4od, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_2/A_2_0/FC_2_0_0/hmmsearch.results.yy90t3p4 [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_3/A_3_0/hmmbuild.model.sh39pw8g, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_3/A_3_0/FC_3_0_0/hmmsearch.results.dis4dy4w [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_4/A_4_0/hmmbuild.model.m9jzs8mk, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_4/A_4_0/FC_4_0_0/hmmsearch.results.dz1hmdz9 [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_5/A_5_0/hmmbuild.model.z7c6oilt, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_5/A_5_0/FC_5_0_0/hmmsearch.results.gep5wjkr [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_6/A_6_0/hmmbuild.model.hu245b99, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_6/A_6_0/FC_6_0_0/hmmsearch.results.9znx47ju [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_7/A_7_0/hmmbuild.model.1o07nh, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_7/A_7_0/FC_7_0_0/hmmsearch.results.urvm_nob [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_8/A_8_0/hmmbuild.model.egv_5eiv, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_8/A_8_0/FC_8_0_0/hmmsearch.results.h8n2qx_w [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_9/A_9_0/hmmbuild.model.gkq4uvvu, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_9/A_9_0/FC_9_0_0/hmmsearch.results.1uayjdtd [18:59:18] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_10/A_10_0/hmmbuild.model.qu3znbk5, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_10/A_10_0/FC_10_0_0/hmmsearch.results.y6_19w1g [18:59:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_11/A_11_0/hmmbuild.model.mvnj9xxc, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_11/A_11_0/FC_11_0_0/hmmsearch.results.a9dv_ma4 [18:59:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_12/A_12_0/hmmbuild.model.t05fw19c, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_12/A_12_0/FC_12_0_0/hmmsearch.results.wt0ddxve [18:59:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_13/A_13_0/hmmbuild.model.52vhlqai, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_13/A_13_0/FC_13_0_0/hmmsearch.results.9m48wig0 [18:59:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_14/A_14_0/hmmbuild.model.pxsw6cn5, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_14/A_14_0/FC_14_0_0/hmmsearch.results.zigt2owg [18:59:19] jobs.py (line 131): INFO: Finished hmmsearch Job with input: model:/tmp/sepp/output.ziutryl9/root/P_15/A_15_0/hmmbuild.model.ho7x3rjb, fragments:/tmp/sepp/output.ziutryl9/fragment_chunks/fragment_chunk_0hhu1zq7u.fasta, elim:99999999, filter:False, output:/tmp/sepp/output.ziutryl9/root/P_15/A_15_0/FC_15_0_0/hmmsearch.results.f0zmg87n [18:59:19] exhaustive.py (line 80): WARNING: Fragments [] are not scored against any subset [18:59:19] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_0. [18:59:19] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_1. [18:59:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.ziutryl9/root/P_11/A_11_0/hmmbuild.model.mvnj9xxc, fragments:/tmp/sepp/output.ziutryl9/root/P_11/A_11_0/FC_11_0_0/hmmalign.frag.q9pw3at8.fasta, trim:False, base_alignment:/tmp/sepp/output.ziutryl9/root/P_11/A_11_0/hmmbuild.input.2r4vfbmi.fasta [18:59:19] jobs.py (line 131): INFO: Finished hmmalign Job with input: model:/tmp/sepp/output.ziutryl9/root/P_12/A_12_0/hmmbuild.model.t05fw19c, fragments:/tmp/sepp/output.ziutryl9/root/P_12/A_12_0/FC_12_0_0/hmmalign.frag.n196udv8.fasta, trim:False, base_alignment:/tmp/sepp/output.ziutryl9/root/P_12/A_12_0/hmmbuild.input.of5d9sau.fasta [18:59:19] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_2. [18:59:19] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_3. [18:59:20] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_4. [18:59:20] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_5. [18:59:20] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_6. [18:59:20] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_7. [18:59:20] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_8. [18:59:20] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_9. [18:59:21] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_10. [18:59:21] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_11. [18:59:21] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.ziutryl9/root/P_11/A_11_0/FC_11_0_0/hmmalign.results.m_34mu_m) into base alignment (/tmp/sepp/output.ziutryl9/root/P_11/A_11_0/hmmbuild.input.2r4vfbmi.fasta). [18:59:21] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_12. [18:59:21] alignment.py (line 556): INFO: Merging extension sto file (/tmp/sepp/output.ziutryl9/root/P_12/A_12_0/FC_12_0_0/hmmalign.results.e28wyw11) into base alignment (/tmp/sepp/output.ziutryl9/root/P_12/A_12_0/hmmbuild.input.of5d9sau.fasta). [18:59:21] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_13. [18:59:21] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_14. [18:59:21] exhaustive.py (line 151): INFO: Merging sub-alignments for placement problem : P_15. multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/rey/miniconda3/envs/picrust2/lib/python3.8/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, **kwds)) File "/home/rey/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/scheduler.py", line 74, in call return self.run() File "/home/rey/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/rey/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.ziutryl9/root/P_11 -j 1 -r /tmp/sepp/output.ziutryl9/root/P_11/pplacer.backbone.3bmtzx2t.fasta -s /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.ziutryl9/root/P_11/pplacer.tree.8mh_4hm2.tre --groups 10 /tmp/sepp/output.ziutryl9/root/P_11/pplacer.extended.0.l63bj2as.fasta No error messages available """

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

Traceback (most recent call last): File "/home/rey/miniconda3/envs/picrust2/bin/run_sepp.py", line 26, in ExhaustiveAlgorithm().run() File "/home/rey/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/algorithm.py", line 174, in run if (not JobPool().wait_for_all_jobs()): File "/home/rey/miniconda3/envs/picrust2/lib/python3.8/site-packages/sepp/scheduler.py", line 365, in wait_for_all_jobs result.get() File "/home/rey/miniconda3/envs/picrust2/lib/python3.8/multiprocessing/pool.py", line 771, in get raise self._value sepp.scheduler.JobError: The following execution failed: /home/rey/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.ziutryl9/root/P_11 -j 1 -r /tmp/sepp/output.ziutryl9/root/P_11/pplacer.backbone.3bmtzx2t.fasta -s /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.ziutryl9/root/P_11/pplacer.tree.8mh_4hm2.tre --groups 10 /tmp/sepp/output.ziutryl9/root/P_11/pplacer.extended.0.l63bj2as.fasta No error messages available Traceback (most recent call last): File "/home/rey/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/rey/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.ziutryl9/root/P_11 -j 1 -r /tmp/sepp/output.ziutryl9/root/P_11/pplacer.backbone.3bmtzx2t.fasta -s /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.ziutryl9/root/P_11/pplacer.tree.8mh_4hm2.tre --groups 10 /tmp/sepp/output.ziutryl9/root/P_11/pplacer.extended.0.l63bj2as.fasta No error messages available Traceback (most recent call last): File "/home/rey/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/rey/miniconda3/envs/picrust2/bin/pplacer --out-dir /tmp/sepp/output.ziutryl9/root/P_12 -j 1 -r /tmp/sepp/output.ziutryl9/root/P_12/pplacer.backbone.4upgh484.fasta -s /home/rey/picrust2-2.5.2/picrust2/default_files/prokaryotic/pro_ref/pro_ref.raxml_info -t /tmp/sepp/output.ziutryl9/root/P_12/pplacer.tree.4lc_bd7f.tre --groups 10 /tmp/sepp/output.ziutryl9/root/P_12/pplacer.extended.0.wfr64ivs.fasta No error messages available

=============================================== short test summary info ================================================ FAILED tests/test_place_seqs.py::place_seqs_tests::test_run_place_seqs_pipeline_sepp - SystemExit: 1 ======================================= 1 failed, 60 passed in 106.70s (0:01:46) =======================================

R-Wright-1 commented 8 months ago

Hi there, could you see if the fix in issue #314 works?

rassanjorjo commented 8 months ago

Good day!

I tried to run as outlined in issue #314 but another error popped out after pip install --editable .

(picrust2-src) rey@H110M-DESK:~/picrust2-2.5.2$ pip install --editable . /home/rey/miniconda3/envs/picrust2-src/bin/pip: line 3: import: command not found /home/rey/miniconda3/envs/picrust2-src/bin/pip: line 4: import: command not found from: can't read /var/mail/pip._internal.cli.main /home/rey/miniconda3/envs/picrust2-src/bin/pip: line 9: syntax error near unexpected token (' /home/rey/miniconda3/envs/picrust2-src/bin/pip: line 9: sys.argv[0] = re.sub(r'(-script.pyw?|.exe)?$', '', sys.argv[0])'

and i cannot run pytest successfully.

Thank you so much

R-Wright-1 commented 8 months ago

Can you give some details about what system you're using, etc?

rassanjorjo commented 8 months ago

Im using ubuntu on windows, RAM is at 12GB but an i3-6100 processor using a 64bit operating system

R-Wright-1 commented 8 months ago

Hmm, I think that the RAM might be the issue. You can see in the installation instructions that at least 16GB is needed - I think that trying the version within QIIME2 is your best bet.

R-Wright-1 commented 4 months ago

I'm just closing this as there has been no further response.