I could not run strainphlan inside biobakery workflows.
2022-07-14 09:16:53,309 LoggerReporter finished ERROR: AnADAMA run finished with errors.
2022-07-15 12:28:07,641 LoggerReporter started INFO: Beginning AnADAMA run with 79 tasks.
2022-07-15 12:28:07,651 LoggerReporter started INFO: Workflow description = A workflow for whole metagenome shotgun sequences
2022-07-15 12:28:07,651 LoggerReporter started INFO: Workflow version = 0.1
2022-07-15 12:28:07,652 LoggerReporter started INFO: Workflow configuration options
2022-07-15 12:28:07,652 LoggerReporter started INFO: input_extension = fastq.gz
2022-07-15 12:28:07,652 LoggerReporter started INFO: barcode_file =
2022-07-15 12:28:07,652 LoggerReporter started INFO: dual_barcode_file =
2022-07-15 12:28:07,652 LoggerReporter started INFO: index_identifier = _I1_001
2022-07-15 12:28:07,652 LoggerReporter started INFO: min_pred_qc_score = 2
2022-07-15 12:28:07,652 LoggerReporter started INFO: threads = 2
2022-07-15 12:28:07,652 LoggerReporter started INFO: pair_identifier = .R1
2022-07-15 12:28:07,652 LoggerReporter started INFO: interleaved = False
2022-07-15 12:28:07,652 LoggerReporter started INFO: bypass_quality_control = True
2022-07-15 12:28:07,652 LoggerReporter started INFO: contaminate_databases = /home/microviable/biobakery_workflows_databases/kneaddata_db_human_genome
2022-07-15 12:28:07,652 LoggerReporter started INFO: qc_options =
2022-07-15 12:28:07,652 LoggerReporter started INFO: functional_profiling_options =
2022-07-15 12:28:07,652 LoggerReporter started INFO: remove_intermediate_output = False
2022-07-15 12:28:07,652 LoggerReporter started INFO: bypass_functional_profiling = True
2022-07-15 12:28:07,652 LoggerReporter started INFO: bypass_strain_profiling = False
2022-07-15 12:28:07,652 LoggerReporter started INFO: run_strain_gene_profiling = False
2022-07-15 12:28:07,652 LoggerReporter started INFO: bypass_taxonomic_profiling = False
2022-07-15 12:28:07,652 LoggerReporter started INFO: run_assembly = False
2022-07-15 12:28:07,652 LoggerReporter started INFO: strain_profiling_options =
2022-07-15 12:28:07,652 LoggerReporter started INFO: taxonomic_profiling_options =
2022-07-15 12:28:07,653 LoggerReporter started INFO: max_strains = 20
2022-07-15 12:28:07,653 LoggerReporter started INFO: strain_list =
2022-07-15 12:28:07,653 LoggerReporter started INFO: assembly_options =
2022-07-15 12:28:07,653 LoggerReporter started INFO: output = /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/
2022-07-15 12:28:07,653 LoggerReporter started INFO: input = /media/microviable/e/Liofilos_output/kneaddata/rarefied_paired
2022-07-15 12:28:07,653 LoggerReporter started INFO: config = None
2022-07-15 12:28:07,653 LoggerReporter started INFO: jobs = 1
2022-07-15 12:28:07,653 LoggerReporter started INFO: grid_jobs = 0
2022-07-15 12:28:07,653 LoggerReporter started INFO: grid = None
2022-07-15 12:28:07,667 LoggerReporter started INFO: grid_partition =
2022-07-15 12:28:07,667 LoggerReporter started INFO: grid_benchmark = off
2022-07-15 12:28:07,667 LoggerReporter started INFO: grid_options = None
2022-07-15 12:28:07,667 LoggerReporter started INFO: grid_environment = None
2022-07-15 12:28:07,667 LoggerReporter started INFO: grid_scratch = None
2022-07-15 12:28:07,667 LoggerReporter started INFO: dry_run = False
2022-07-15 12:28:07,667 LoggerReporter started INFO: skip_nothing = False
2022-07-15 12:28:07,667 LoggerReporter started INFO: quit_early = False
2022-07-15 12:28:07,668 LoggerReporter started INFO: until_task = None
2022-07-15 12:28:07,668 LoggerReporter started INFO: exclude_task = None
2022-07-15 12:28:07,668 LoggerReporter started INFO: target = None
2022-07-15 12:28:07,668 LoggerReporter started INFO: exclude_target = None
2022-07-15 12:28:07,668 LoggerReporter started INFO: log_level = INFO
2022-07-15 12:28:08,330 LoggerReporter log_event INFO: task 58, order_clade_list : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 57, strainphlan_print_clades : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 39, strainphlan_sample2markers____H15_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 38, metaphlan_count_species : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 37, metaphlan_join_taxonomic_profiles : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 0, metaphlan____H15_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 56, strainphlan_sample2markers____L25_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 35, metaphlan____L25_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 55, strainphlan_sample2markers____L24_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 33, metaphlan____L24_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 54, strainphlan_sample2markers____L23_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 31, metaphlan____L23_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 53, strainphlan_sample2markers____L22_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 29, metaphlan____L22_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 52, strainphlan_sample2markers____L19_rarefied : skipped
2022-07-15 12:28:08,331 LoggerReporter log_event INFO: task 27, metaphlan____L19_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 51, strainphlan_sample2markers____L18_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 25, metaphlan____L18_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 50, strainphlan_sample2markers____L17_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 23, metaphlan____L17_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 49, strainphlan_sample2markers____L16_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 21, metaphlan____L16_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 48, strainphlan_sample2markers____L15_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 19, metaphlan____L15_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 47, strainphlan_sample2markers____H25_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 17, metaphlan____H25_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 46, strainphlan_sample2markers____H24_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 15, metaphlan____H24_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 45, strainphlan_sample2markers____H23_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 13, metaphlan____H23_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 44, strainphlan_sample2markers____H22_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 11, metaphlan____H22_rarefied : skipped
2022-07-15 12:28:08,332 LoggerReporter log_event INFO: task 43, strainphlan_sample2markers____H19_rarefied : skipped
2022-07-15 12:28:08,333 LoggerReporter log_event INFO: task 9, metaphlan____H19_rarefied : skipped
2022-07-15 12:28:08,333 LoggerReporter log_event INFO: task 42, strainphlan_sample2markers____H18_rarefied : skipped
2022-07-15 12:28:08,333 LoggerReporter log_event INFO: task 7, metaphlan____H18_rarefied : skipped
2022-07-15 12:28:08,333 LoggerReporter log_event INFO: task 41, strainphlan_sample2markers____H17_rarefied : skipped
2022-07-15 12:28:08,333 LoggerReporter log_event INFO: task 5, metaphlan____H17_rarefied : skipped
2022-07-15 12:28:08,333 LoggerReporter log_event INFO: task 40, strainphlan_sample2markers____H16_rarefied : skipped
2022-07-15 12:28:08,333 LoggerReporter log_event INFO: task 3, metaphlan____H16_rarefied : skipped
2022-07-15 12:28:08,333 LoggerReporter log_event INFO: task 59, strainphlan_clade_0 : ready and waiting for resources
2022-07-15 12:28:08,333 LoggerReporter log_event INFO: task 59, strainphlan_clade_0 : starting to run
2022-07-15 12:28:08,352 anadama2.helpers actually_sh INFO: Executing with shell: extract_markers.py --database /home/microviable/workflows/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.pkl --clade s__Ruminococcus_bromii --output_dir /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan
2022-07-15 12:29:03,288 anadama2.helpers actually_sh INFO: Execution complete. Stdout: b’Fri Jul 15 12:28:08 2022: Start extract markers execution\nFri Jul 15 12:28:08 2022: \tGenerating DB markers FASTA…\nFri Jul 15 12:28:49 2022: \tDone.\nFri Jul 15 12:28:49 2022: \tLoading MetaPhlan 3.0 database…\nFri Jul 15 12:28:56 2022: \tDone.\nFri Jul 15 12:28:56 2022: \tNumber of markers for the clade “s__Ruminococcus_bromii”: 138\nFri Jul 15 12:28:56 2022: \tExporting markers…\nFri Jul 15 12:29:03 2022: \tDone.\nFri Jul 15 12:29:03 2022: Finish extract markers execution (54.85 seconds): Results are stored at “/media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/”\n’
Stderr:
2022-07-15 12:29:03,298 anadama2.helpers actually_sh INFO: Executing with shell: strainphlan --samples /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan//.pkl --output_dir /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan --clade s__Ruminococcus_bromii --nprocs 2 --clade_markers /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/s__Ruminococcus_bromii.fna > /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/19_clade.log && touch /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/19_clade.tree && if [ -f /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/RAxML_bestTree.s__Ruminococcus_bromii.tree ]; then cp /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/RAxML_bestTree.s__Ruminococcus_bromii.tree /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/19_clade.tree; fi
2022-07-15 12:29:05,836 LoggerReporter task_failed ERROR: task 59, strainphlan_clade_0 : Failed! Error message : Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/tasks/shotgun.py”, line 762, in strainphlan
args=[os.path.abspath(os.path.join(os.path.dirname(task.depends[0].name),“…”)),os.path.dirname(task.targets[0].name),profile_clade,threads])
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/utilities.py”, line 1049, in run_task
return_code = sh(command)()
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/util/init.py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 1] Command `strainphlan --samples /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan//.pkl --output_dir /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan --clade s__Ruminococcus_bromii --nprocs 2 --clade_markers /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/s__Ruminococcus_bromii.fna > /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/19_clade.log && touch /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/19_clade.tree && if [ -f /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/RAxML_bestTree.s__Ruminococcus_bromii.tree ]; then cp /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/RAxML_bestTree.s__Ruminococcus_bromii.tree /media/microviable/e/Liofilos_output/metaphlan/rarefied_paired/strainphlan/19_clade.tree; fi’ failed.
Out: b’’
Err: b’[e] could not find “mafft” (“False”) executable in your PATH environment variable\n\n[e] An error was ocurred executing a external tool, exiting…\nFri Jul 15 12:29:05 2022: Stop StrainPhlAn 3.0 execution.\n’