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Missing dependency - poppler #51

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BenjaminJPerry opened this issue Feb 13, 2025 · 2 comments
Open

Missing dependency - poppler #51

BenjaminJPerry opened this issue Feb 13, 2025 · 2 comments

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@BenjaminJPerry
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I've had an error message while testing the alpha which seems to point to a python library 'poppler' not being installed?

  File "/nix/store/rqmcwn00nrggids4mg8ghwdrhiawsqf4-python3.11-gbs-prism-api/lib/python3.11/site-packages/agr/gbs_prism/redun/stage2.py", line 420, in gusbase                                                                                        
    run_GUSbase(gusbase_rdata.path)                                                                                                                                                                                                                   
  File "/nix/store/rqmcwn00nrggids4mg8ghwdrhiawsqf4-python3.11-gbs-prism-api/lib/python3.11/site-packages/agr/gbs_prism/GUSbase.py", line 31, in run_GUSbase                                                                                          
    pages = pdf2image.convert_from_path(                                                                                                                                                                                                              
  File "/nix/store/3p9ap4d1ygfh08ywm7674jmdpid8m63r-python3.11-pdf2image-1.17.0/lib/python3.11/site-packages/pdf2image/pdf2image.py", line 127, in convert_from_path                                                                                  
    page_count = pdfinfo_from_path(                                                                                                                                                                                                                   
  File "/nix/store/3p9ap4d1ygfh08ywm7674jmdpid8m63r-python3.11-pdf2image-1.17.0/lib/python3.11/site-packages/pdf2image/pdf2image.py", line 607, in pdfinfo_from_path                                                                                  
    raise PDFInfoNotInstalledError(                                                                                                                                                                                                                   
PDFInfoNotInstalledError: Unable to get page count. Is poppler installed and in PATH?
@BenjaminJPerry BenjaminJPerry changed the title Error generating pdf Missing dependency - poppler Feb 13, 2025
@BenjaminJPerry
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Here is the full stdout:

[redun] | TASK                                    PENDING RUNNING  FAILED  CACHED    DONE   TOTAL
[redun] | 
[redun] | ALL                                          67      14       5      73     302     461
[redun] | agr.gbs_prism.bam_stats_all                   0       0       0       0       8       8
[redun] | agr.gbs_prism.bam_stats_one                   0       0       0       0      32      32
[redun] | agr.gbs_prism.bclconvert                      0       0       0       1       0       1
[redun] | agr.gbs_prism.bwa_all_reference_genomes       0       0       0       0       8       8
[redun] | agr.gbs_prism.bwa_aln_all                     0       0       0       0      16      16
[redun] | agr.gbs_prism.bwa_aln_one                     0       0       0       0      32      32
[redun] | agr.gbs_prism.bwa_samse_all                   0       0       0       0      16      16
[redun] | agr.gbs_prism.bwa_samse_one                   0       0       0       0      32      32
[redun] | agr.gbs_prism.cook_sample_sheet               0       0       0       1       0       1
[redun] | agr.gbs_prism.create_cohort_fastq_links       0       0       0       0       8       8
[redun] | agr.gbs_prism.create_peacock                  1       0       0       0       0       1
[redun] | agr.gbs_prism.cutadapt_all                    0       0       0       0       8       8
[redun] | agr.gbs_prism.cutadapt_one                    0       0       0       0      16      16
[redun] | agr.gbs_prism.dedupe_all                      0       0       0       1       0       1
[redun] | agr.gbs_prism.dedupe_one                      0       0       0      12       0      12
[redun] | agr.gbs_prism.fastqc_all                      0       0       0       1       0       1
[redun] | agr.gbs_prism.fastqc_one                      0       0       0      12       0      12
[redun] | agr.gbs_prism.get_fastq_to_tag_count          0       6       0       0       2       8
[redun] | agr.gbs_prism.get_gbs_keyfiles                0       0       0       1       0       1
[redun] | agr.gbs_prism.get_gbs_targets                 0       0       0       1       0       1
[redun] | agr.gbs_prism.get_keyfile_for_gbsx            0       0       0       0       8       8
[redun] | agr.gbs_prism.get_keyfile_for_tassel          0       0       0       0       8       8
[redun] | agr.gbs_prism.get_tag_count                   6       0       0       0       2       8
[redun] | agr.gbs_prism.get_tags_reads_cv               6       0       0       0       2       8
[redun] | agr.gbs_prism.get_tags_reads_summary          6       0       0       0       2       8
[redun] | agr.gbs_prism.gusbase                         7       0       1       0       0       8
[redun] | agr.gbs_prism.kgd                             7       0       0       0       1       8
[redun] | agr.gbs_prism.kmer_analysis_all               0       0       0       1       0       1
[redun] | agr.gbs_prism.kmer_analysis_one               0       0       0      12       0      12
[redun] | agr.gbs_prism.kmer_sample_all                 0       0       0       1       0       1
[redun] | agr.gbs_prism.kmer_sample_one                 0       0       0      12       0      12
[redun] | agr.gbs_prism.main                            0       0       1       0       0       1
[redun] | agr.gbs_prism.map_info_to_hap_map             7       0       0       0       1       8
[redun] | agr.gbs_prism.merge_taxa_tag_count            6       1       0       0       1       8
[redun] | agr.gbs_prism.run_cohort                      0       7       1       0       0       8
[redun] | agr.gbs_prism.run_stage1                      0       0       0       1       0       1
[redun] | agr.gbs_prism.run_stage2                      0       0       1       0       0       1
[redun] | agr.gbs_prism.sample_all_for_bwa              0       0       0       0       8       8
[redun] | agr.gbs_prism.sample_one_for_bwa              0       0       0       0      16      16
[redun] | agr.gbs_prism.tag_count_to_tag_pair           7       0       0       0       1       8
[redun] | agr.gbs_prism.tag_pair_to_tbt                 7       0       0       0       1       8
[redun] | agr.gbs_prism.tbt_to_map_info                 7       0       0       0       1       8
[redun] | agr.util.all_forall                           0       0       0       1       0       1
[redun] | agr.util.concat                               0       0       0      12      16      28
[redun] | agr.util.one_forall                           0       0       0       3      56      59
[redun] | redun.root_task                               0       0       1       0       0       1
[redun] 
[redun] 
[redun] Execution duration: 984.43 seconds
[redun] *** Execution failed. Traceback (most recent task last):
[redun]   Job a42dbee1: File "/nix/store/kn6w417zbjk9zqvksjgv7img9b8160nw-python3.11-redun-0.25.0/lib/python3.11/site-packages/redun/scheduler.py", line 824, in root_task
[redun]     def root_task(expr: QuotedExpression[Result]) -> Result:
[redun]     expr = QuotedExpression(agr.gbs_prism.main(run='241105_A01439_0310_BHLLMWDRX3'))
[redun]   Job 8be50fa1: File "/nix/store/7d47246c8d01csxiwabvdx3kc5v3v620-pipeline.py/pipeline/pipeline.py", line 28, in main
[redun]     def main(
[redun]     path_context = {'seq_root': '/agr/persist/projects/2024_illumina_sequencing_e/active', 'postprocessing_root': '/agr/scratch/projects/2024_legacy_pipeline_migration/gbs_prism.test/postprocessing', 'gbs_backup_dir'...
[redun]     run          = '241105_A01439_0310_BHLLMWDRX3'
[redun]   Job 77eadc77: File "/nix/store/rqmcwn00nrggids4mg8ghwdrhiawsqf4-python3.11-gbs-prism-api/lib/python3.11/site-packages/agr/gbs_prism/redun/stage2.py", line 499, in run_stage2
[redun]     def run_stage2(run: str, spec: GbsTargetSpec, gbs_paths: GbsPaths) -> Stage2Output:
[redun]     gbs_paths = <agr.gbs_prism.paths.GbsPaths object at 0x7fd0333c3f10>
[redun]     run       = '241105_A01439_0310_BHLLMWDRX3'
[redun]     spec      = GbsTargetSpec(libraries={'SQ5002': LibraryTargetSpec(cohorts={'SQ5002.all.deer.PstI': CohortTargetSpec(fastq_links={'SQ5002_S1_L001_R1_001.fastq.gz': '/agr/scratch/projects/2024_legacy_pipeline_mig...
[redun]   Job b7f0acf4: File "/nix/store/rqmcwn00nrggids4mg8ghwdrhiawsqf4-python3.11-gbs-prism-api/lib/python3.11/site-packages/agr/gbs_prism/redun/stage2.py", line 448, in run_cohort
[redun]     def run_cohort(spec: CohortSpec) -> CohortOutput:
[redun]     spec = CohortSpec(run='241105_A01439_0310_BHLLMWDRX3', cohort=Cohort(libname='SQ5004', qc_cohort='all', gbs_cohort='deer', enzyme='PstI'), target=CohortTargetSpec(fastq_links={'SQ5004_S3_L002_R1_001.fastq...
[redun]   Job 28c3fe5f: File "/nix/store/rqmcwn00nrggids4mg8ghwdrhiawsqf4-python3.11-gbs-prism-api/lib/python3.11/site-packages/agr/gbs_prism/redun/stage2.py", line 417, in gusbase
[redun]     def gusbase(spec: CohortSpec, gusbase_rdata: File) -> File:
[redun]     gusbase_rdata = File(path=/agr/scratch/projects/2024_legacy_pipeline_migration/gbs_prism.test/postprocessing/gbs/241105_A01439_0310_BHLLMWDRX3/SQ5004.all.deer.PstI/blind/KGD/GUSbase.RData, hash=736032fa)
[redun]     spec          = CohortSpec(run='241105_A01439_0310_BHLLMWDRX3', cohort=Cohort(libname='SQ5004', qc_cohort='all', gbs_cohort='deer', enzyme='PstI'), target=CohortTargetSpec(fastq_links={'SQ5004_S3_L002_R1_001.fastq...
[redun]   File "/nix/store/rqmcwn00nrggids4mg8ghwdrhiawsqf4-python3.11-gbs-prism-api/lib/python3.11/site-packages/agr/gbs_prism/redun/stage2.py", line 420, in gusbase
[redun]     run_GUSbase(gusbase_rdata.path)
[redun]   File "/nix/store/rqmcwn00nrggids4mg8ghwdrhiawsqf4-python3.11-gbs-prism-api/lib/python3.11/site-packages/agr/gbs_prism/GUSbase.py", line 31, in run_GUSbase
[redun]     pages = pdf2image.convert_from_path(
[redun]   File "/nix/store/3p9ap4d1ygfh08ywm7674jmdpid8m63r-python3.11-pdf2image-1.17.0/lib/python3.11/site-packages/pdf2image/pdf2image.py", line 127, in convert_from_path
[redun]     page_count = pdfinfo_from_path(
[redun]   File "/nix/store/3p9ap4d1ygfh08ywm7674jmdpid8m63r-python3.11-pdf2image-1.17.0/lib/python3.11/site-packages/pdf2image/pdf2image.py", line 607, in pdfinfo_from_path
[redun]     raise PDFInfoNotInstalledError(
[redun] PDFInfoNotInstalledError: Unable to get page count. Is poppler installed and in PATH?
Traceback (most recent call last):
  File "/nix/store/3p9ap4d1ygfh08ywm7674jmdpid8m63r-python3.11-pdf2image-1.17.0/lib/python3.11/site-packages/pdf2image/pdf2image.py", line 581, in pdfinfo_from_path
    proc = Popen(command, env=env, stdout=PIPE, stderr=PIPE)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/s0p1kr5mvs0j42dq5r08kgqbi0k028f2-python3-3.11.10/lib/python3.11/subprocess.py", line 1026, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/nix/store/s0p1kr5mvs0j42dq5r08kgqbi0k028f2-python3-3.11.10/lib/python3.11/subprocess.py", line 1955, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'pdfinfo'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/nix/store/kn6w417zbjk9zqvksjgv7img9b8160nw-python3.11-redun-0.25.0/bin/.redun-wrapped", line 11, in <module>
    client.execute()
  File "/nix/store/kn6w417zbjk9zqvksjgv7img9b8160nw-python3.11-redun-0.25.0/lib/python3.11/site-packages/redun/cli.py", line 921, in execute
    return args.func(args, extra_args, argv)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/kn6w417zbjk9zqvksjgv7img9b8160nw-python3.11-redun-0.25.0/lib/python3.11/site-packages/redun/cli.py", line 1620, in run_command
    result = scheduler.run(
             ^^^^^^^^^^^^^^
  File "/nix/store/kn6w417zbjk9zqvksjgv7img9b8160nw-python3.11-redun-0.25.0/lib/python3.11/site-packages/redun/scheduler.py", line 1149, in run
    raise result.error
  File "/nix/store/kn6w417zbjk9zqvksjgv7img9b8160nw-python3.11-redun-0.25.0/lib/python3.11/site-packages/redun/executors/local.py", line 149, in on_done
    self._scheduler.done_job(job, future.result())
                                  ^^^^^^^^^^^^^^^
  File "/nix/store/s0p1kr5mvs0j42dq5r08kgqbi0k028f2-python3-3.11.10/lib/python3.11/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/nix/store/s0p1kr5mvs0j42dq5r08kgqbi0k028f2-python3-3.11.10/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/nix/store/s0p1kr5mvs0j42dq5r08kgqbi0k028f2-python3-3.11.10/lib/python3.11/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/kn6w417zbjk9zqvksjgv7img9b8160nw-python3.11-redun-0.25.0/lib/python3.11/site-packages/redun/executors/local.py", line 27, in exec_task
    return task.func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/rqmcwn00nrggids4mg8ghwdrhiawsqf4-python3.11-gbs-prism-api/lib/python3.11/site-packages/agr/gbs_prism/redun/stage2.py", line 420, in gusbase
    run_GUSbase(gusbase_rdata.path)
  File "/nix/store/rqmcwn00nrggids4mg8ghwdrhiawsqf4-python3.11-gbs-prism-api/lib/python3.11/site-packages/agr/gbs_prism/GUSbase.py", line 31, in run_GUSbase
    pages = pdf2image.convert_from_path(
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/nix/store/3p9ap4d1ygfh08ywm7674jmdpid8m63r-python3.11-pdf2image-1.17.0/lib/python3.11/site-packages/pdf2image/pdf2image.py", line 127, in convert_from_path
    page_count = pdfinfo_from_path(
                 ^^^^^^^^^^^^^^^^^^
  File "/nix/store/3p9ap4d1ygfh08ywm7674jmdpid8m63r-python3.11-pdf2image-1.17.0/lib/python3.11/site-packages/pdf2image/pdf2image.py", line 607, in pdfinfo_from_path
    raise PDFInfoNotInstalledError(
pdf2image.exceptions.PDFInfoNotInstalledError: Unable to get page count. Is poppler installed and in PATH?

@tesujimath
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The fix to this will be in flake.nix, which I can't really do until I get back.

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@tesujimath @BenjaminJPerry