The bioBakery help forum

Pipeline and stdout stalls

BioBakery seems to have stalled with the last stdour being (May 09 09:20:44) [ 0/68 - 0.00%] **Started ** Task 5: kneaddata____HSC-10114-HC-01_S15_L001_R1_001, and only completing kneaddata on 1 out of 2 paired shotgun metagenomic samples. It also seems that only 1 job is submitted at a time to the slurm grid though I set grid-jobs 2. I got the following stdout and error when running my code below and it has not changed for several hours. top shows that wmgx.py is running but only at 0.3% CPU. It doesn’t seem that there is any job pending. I did run the pipeline code twice. After the first time I had to kill the program to start it again. I installed bioBakery via conda this week on my Linux machine (Red Hat) that has a Slurm grid.

biobakery_workflows wmgx  --input 
 Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/   --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test    --grid slurm --grid-jobs 2 --grid-partition NMLResearch --threads 8
(May 09 09:20:43) [ 0/68 -   0.00%] **Ready    ** Task  3: kneaddata____CHP-00030-PT-02_S14_L001_R2_001
(May 09 09:20:43) [ 0/68 -   0.00%] **Ready    ** Task  5: kneaddata____HSC-10114-HC-01_S15_L001_R1_001
(May 09 09:20:43) [ 0/68 -   0.00%] **Ready    ** Task  7: kneaddata____HSC-10114-HC-01_S15_L001_R2_001
(May 09 09:20:43) [ 0/68 -   0.00%] **Ready    ** Task  0: kneaddata____CHP-00030-PT-02_S14_L001_R1_001
(May 09 09:20:43) [ 0/68 -   0.00%] **Started  ** Task  3: kneaddata____CHP-00030-PT-02_S14_L001_R2_001
(May 09 09:20:43) [ 0/68 -   0.00%] **Started  ** Task  3: kneaddata____CHP-00030-PT-02_S14_L001_R2_001
(May 09 09:20:43) [ 0/68 -   0.00%] **Started  ** Task  5: kneaddata____HSC-10114-HC-01_S15_L001_R1_001
Exception in thread Thread-1:
Traceback (most recent call last):
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery/lib/python2.7/threading.py", line 801, in __bootstrap_inner
    self.run()
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery/lib/python2.7/site-packages/anadama2/grid/grid.py", line 465, in run
    self.reporter, self.lock)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery/lib/python2.7/site-packages/anadama2/runners.py", line 185, in worker_run_loop
    result = run_task(task, extra)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery/lib/python2.7/site-packages/anadama2/grid/grid.py", line 473, in run_task_by_type
    return cls.run_task_command(task, extra)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery/lib/python2.7/site-packages/anadama2/grid/grid.py", line 505, in run_task_command
    partition, tmpdir, commands, task, grid_queue, reporter, docker_image)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery/lib/python2.7/site-packages/anadama2/grid/grid.py", line 556, in submit_grid_job
    jobid = grid_queue.submit_job(grid_script)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery/lib/python2.7/site-packages/anadama2/grid/grid.py", line 403, in submit_job
    jobid=self.get_job_id_from_submit_output(stdout)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery/lib/python2.7/site-packages/anadama2/grid/grid.py", line 390, in get_job_id_from_submit_output
    return jobib
NameError: global name 'jobib' is not defined

(May 09 09:20:44) [ 0/68 -   0.00%] **Started  ** Task  5: kneaddata____HSC-10114-HC-01_S15_L001_R1_001

Here is the log from anadama.log

2020-05-09 08:49:11,555 LoggerReporter  started INFO: Beginning AnADAMA run with 75 tasks.
2020-05-09 08:49:11,555 LoggerReporter  started INFO: Workflow configuration options
2020-05-09 08:49:11,555 LoggerReporter  started INFO: min_pred_qc_score = 2
2020-05-09 08:49:11,555 LoggerReporter  started INFO: bypass_taxonomic_profiling = False
2020-05-09 08:49:11,556 LoggerReporter  started INFO: strain_profiling_options =
2020-05-09 08:49:11,556 LoggerReporter  started INFO: run_assembly = False
2020-05-09 08:49:11,556 LoggerReporter  started INFO: barcode_file =
2020-05-09 08:49:11,556 LoggerReporter  started INFO: grid_benchmark = on
2020-05-09 08:49:11,556 LoggerReporter  started INFO: grid_partition = NMLResearch
2020-05-09 08:49:11,556 LoggerReporter  started INFO: pair_identifier = .R1
2020-05-09 08:49:11,556 LoggerReporter  started INFO: log_level = INFO
2020-05-09 08:49:11,556 LoggerReporter  started INFO: input_extension = fastq.gz
2020-05-09 08:49:11,556 LoggerReporter  started INFO: dry_run = False
2020-05-09 08:49:11,556 LoggerReporter  started INFO: exclude_target = None
2020-05-09 08:49:11,556 LoggerReporter  started INFO: until_task = None
2020-05-09 08:49:11,557 LoggerReporter  started INFO: remove_intermediate_output = False
2020-05-09 08:49:11,557 LoggerReporter  started INFO: grid_options = None
2020-05-09 08:49:11,557 LoggerReporter  started INFO: bypass_strain_profiling = False
2020-05-09 08:49:11,557 LoggerReporter  started INFO: dual_barcode_file =
2020-05-09 08:49:11,557 LoggerReporter  started INFO: input = /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/
2020-05-09 08:49:11,557 LoggerReporter  started INFO: bypass_quality_control = False
2020-05-09 08:49:11,557 LoggerReporter  started INFO: run_strain_gene_profiling = False
2020-05-09 08:49:11,557 LoggerReporter  started INFO: grid_jobs = 2
2020-05-09 08:49:11,557 LoggerReporter  started INFO: functional_profiling_options =
2020-05-09 08:49:11,557 LoggerReporter  started INFO: contaminate_databases = /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome
2020-05-09 08:49:11,557 LoggerReporter  started INFO: jobs = 1
2020-05-09 08:49:11,557 LoggerReporter  started INFO: index_identifier = _I1_001
2020-05-09 08:49:11,558 LoggerReporter  started INFO: max_strains = 20
2020-05-09 08:49:11,558 LoggerReporter  started INFO: grid = slurm
2020-05-09 08:49:11,558 LoggerReporter  started INFO: threads = 8
2020-05-09 08:49:11,558 LoggerReporter  started INFO: qc_options =
2020-05-09 08:49:11,558 LoggerReporter  started INFO: bypass_functional_profiling = False
2020-05-09 08:49:11,558 LoggerReporter  started INFO: interleaved = False
2020-05-09 08:49:11,558 LoggerReporter  started INFO: target = None
2020-05-09 08:49:11,558 LoggerReporter  started INFO: strain_list =
2020-05-09 08:49:11,558 LoggerReporter  started INFO: grid_environment = None
2020-05-09 08:49:11,558 LoggerReporter  started INFO: exclude_task = None
2020-05-09 08:49:11,558 LoggerReporter  started INFO: quit_early = False
2020-05-09 08:49:11,558 LoggerReporter  started INFO: assembly_options =
2020-05-09 08:49:11,559 LoggerReporter  started INFO: output = /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test
2020-05-09 08:49:11,559 LoggerReporter  started INFO: skip_nothing = False
2020-05-09 08:49:20,634 LoggerReporter  log_event       INFO: task 3, kneaddata____CHP-00030-PT-02_S14_L001_R2_001 : ready and waiting for resources
2020-05-09 08:49:20,641 LoggerReporter  log_event       INFO: task 3, kneaddata____CHP-00030-PT-02_S14_L001_R2_001 : starting to run
2020-05-09 08:49:20,643 LoggerReporter  log_event       INFO: task 5, kneaddata____HSC-10114-HC-01_S15_L001_R1_001 : ready and waiting for resources
2020-05-09 08:49:20,648 LoggerReporter  log_event       INFO: task 7, kneaddata____HSC-10114-HC-01_S15_L001_R2_001 : ready and waiting for resources
2020-05-09 08:49:20,650 LoggerReporter  log_event       INFO: task 0, kneaddata____CHP-00030-PT-02_S14_L001_R1_001 : ready and waiting for resources
2020-05-09 08:49:21,068 LoggerReporter  task_command    INFO: Tracked executable version:  kneaddata v0.7.2

2020-05-09 08:49:21,068 LoggerReporter  task_command    INFO: Executing with shell:  kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/CHP-00030-PT-02_S14_L001_R2_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix CHP-00030-PT-02_S14_L001_R2_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.fastq
2020-05-09 08:49:21,068 LoggerReporter  log_event       INFO: task 3, kneaddata____CHP-00030-PT-02_S14_L001_R2_001 : starting to run
2020-05-09 08:49:21,069 root    run_task_command        INFO: Running commands for task id 3:
kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/CHP-00030-PT-02_S14_L001_R2_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix CHP-00030-PT-02_S14_L001_R2_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.fastq
2020-05-09 08:49:21,071 LoggerReporter  log_event       INFO: task 5, kneaddata____HSC-10114-HC-01_S15_L001_R1_001 : starting to run
2020-05-09 08:49:21,105 root    submit_grid_job INFO: Created grid files for task id 3: /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_FoBPzY.bash, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_K5vNCK.out, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_wMhyBH.err, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_phg2PD.rc
2020-05-09 08:49:21,449 LoggerReporter  task_command    INFO: Tracked executable version:  kneaddata v0.7.2

2020-05-09 08:49:21,449 LoggerReporter  task_command    INFO: Executing with shell:  kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/HSC-10114-HC-01_S15_L001_R1_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix HSC-10114-HC-01_S15_L001_R1_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.fastq
2020-05-09 08:49:21,450 LoggerReporter  log_event       INFO: task 5, kneaddata____HSC-10114-HC-01_S15_L001_R1_001 : starting to run
2020-05-09 08:49:21,450 root    run_task_command        INFO: Running commands for task id 5:
kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/HSC-10114-HC-01_S15_L001_R1_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix HSC-10114-HC-01_S15_L001_R1_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.fastq
2020-05-09 08:49:21,467 root    submit_grid_job INFO: Created grid files for task id 5: /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_1zFHxF.bash, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_29Pkue.out, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_HuaGP6.err, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_DnpfmV.rc
2020-05-09 09:20:36,558 LoggerReporter  started INFO: Beginning AnADAMA run with 75 tasks.
2020-05-09 09:20:36,558 LoggerReporter  started INFO: Workflow configuration options
2020-05-09 09:20:36,559 LoggerReporter  started INFO: min_pred_qc_score = 2
2020-05-09 09:20:36,559 LoggerReporter  started INFO: bypass_taxonomic_profiling = False
2020-05-09 09:20:36,559 LoggerReporter  started INFO: strain_profiling_options =
2020-05-09 09:20:36,559 LoggerReporter  started INFO: run_assembly = False
2020-05-09 09:20:36,559 LoggerReporter  started INFO: barcode_file =
2020-05-09 09:20:36,559 LoggerReporter  started INFO: grid_benchmark = on
2020-05-09 09:20:36,559 LoggerReporter  started INFO: grid_partition = NMLResearch
2020-05-09 09:20:36,559 LoggerReporter  started INFO: pair_identifier = .R1
2020-05-09 09:20:36,559 LoggerReporter  started INFO: log_level = INFO
2020-05-09 09:20:36,559 LoggerReporter  started INFO: input_extension = fastq.gz
2020-05-09 09:20:36,559 LoggerReporter  started INFO: dry_run = False
2020-05-09 09:20:36,559 LoggerReporter  started INFO: exclude_target = None
2020-05-09 09:20:36,560 LoggerReporter  started INFO: until_task = None
2020-05-09 09:20:36,560 LoggerReporter  started INFO: remove_intermediate_output = False
2020-05-09 09:20:36,560 LoggerReporter  started INFO: grid_options = None
2020-05-09 09:20:36,560 LoggerReporter  started INFO: bypass_strain_profiling = False
2020-05-09 09:20:36,560 LoggerReporter  started INFO: dual_barcode_file =
2020-05-09 09:20:36,560 LoggerReporter  started INFO: input = /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/
2020-05-09 09:20:36,560 LoggerReporter  started INFO: bypass_quality_control = False
2020-05-09 09:20:36,560 LoggerReporter  started INFO: run_strain_gene_profiling = False
2020-05-09 09:20:36,560 LoggerReporter  started INFO: grid_jobs = 2
2020-05-09 09:20:36,560 LoggerReporter  started INFO: functional_profiling_options =
2020-05-09 09:20:36,560 LoggerReporter  started INFO: contaminate_databases = /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome
2020-05-09 09:20:36,560 LoggerReporter  started INFO: jobs = 1
2020-05-09 09:20:36,561 LoggerReporter  started INFO: index_identifier = _I1_001
2020-05-09 09:20:36,561 LoggerReporter  started INFO: max_strains = 20
2020-05-09 09:20:36,561 LoggerReporter  started INFO: grid = slurm
2020-05-09 09:20:36,561 LoggerReporter  started INFO: threads = 8
2020-05-09 09:20:36,561 LoggerReporter  started INFO: qc_options =
2020-05-09 09:20:36,561 LoggerReporter  started INFO: bypass_functional_profiling = False
2020-05-09 09:20:36,561 LoggerReporter  started INFO: interleaved = False
2020-05-09 09:20:36,561 LoggerReporter  started INFO: target = None
2020-05-09 09:20:36,561 LoggerReporter  started INFO: strain_list =
2020-05-09 09:20:36,561 LoggerReporter  started INFO: grid_environment = None
2020-05-09 09:20:36,561 LoggerReporter  started INFO: exclude_task = None
2020-05-09 09:20:36,562 LoggerReporter  started INFO: quit_early = False
2020-05-09 09:20:36,562 LoggerReporter  started INFO: assembly_options =
2020-05-09 09:20:36,562 LoggerReporter  started INFO: output = /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test
2020-05-09 09:20:36,562 LoggerReporter  started INFO: skip_nothing = False
2020-05-09 09:20:43,343 LoggerReporter  log_event       INFO: task 3, kneaddata____CHP-00030-PT-02_S14_L001_R2_001 : ready and waiting for resources
2020-05-09 09:20:43,349 LoggerReporter  log_event       INFO: task 5, kneaddata____HSC-10114-HC-01_S15_L001_R1_001 : ready and waiting for resources
2020-05-09 09:20:43,350 LoggerReporter  log_event       INFO: task 7, kneaddata____HSC-10114-HC-01_S15_L001_R2_001 : ready and waiting for resources
2020-05-09 09:20:43,351 LoggerReporter  log_event       INFO: task 0, kneaddata____CHP-00030-PT-02_S14_L001_R1_001 : ready and waiting for resources
2020-05-09 09:20:43,357 LoggerReporter  log_event       INFO: task 3, kneaddata____CHP-00030-PT-02_S14_L001_R2_001 : starting to run
2020-05-09 09:20:43,747 LoggerReporter  task_command    INFO: Tracked executable version:  kneaddata v0.7.2

2020-05-09 09:20:43,747 LoggerReporter  task_command    INFO: Executing with shell:  kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/CHP-00030-PT-02_S14_L001_R2_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix CHP-00030-PT-02_S14_L001_R2_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.fastq
2020-05-09 09:20:43,748 LoggerReporter  log_event       INFO: task 3, kneaddata____CHP-00030-PT-02_S14_L001_R2_001 : starting to run
2020-05-09 09:20:43,748 root    run_task_command        INFO: Running commands for task id 3:
kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/CHP-00030-PT-02_S14_L001_R2_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix CHP-00030-PT-02_S14_L001_R2_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.fastq
2020-05-09 09:20:43,748 LoggerReporter  log_event       INFO: task 5, kneaddata____HSC-10114-HC-01_S15_L001_R1_001 : starting to run
2020-05-09 09:20:43,778 root    submit_grid_job INFO: Created grid files for task id 3: /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_S5MXH8.bash, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_EbobK8.out, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_XwkQhf.err, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_YJ8S8W.rc
2020-05-09 09:20:44,130 LoggerReporter  task_command    INFO: Tracked executable version:  kneaddata v0.7.2

2020-05-09 09:20:44,131 LoggerReporter  task_command    INFO: Executing with shell:  kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/HSC-10114-HC-01_S15_L001_R1_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix HSC-10114-HC-01_S15_L001_R1_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.fastq
2020-05-09 09:20:44,131 LoggerReporter  log_event       INFO: task 5, kneaddata____HSC-10114-HC-01_S15_L001_R1_001 : starting to run
2020-05-09 09:20:44,132 root    run_task_command        INFO: Running commands for task id 5:
kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/HSC-10114-HC-01_S15_L001_R1_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix HSC-10114-HC-01_S15_L001_R1_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.fastq
2020-05-09 09:20:44,148 root    submit_grid_job INFO: Created grid files for task id 5: /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_CrDhsN.bash, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_NzsuhB.out, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_afzaLW.err, /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_AindMP.rc

Here are all the contents of the slurm files. I noted where the file starts and ends:

for file in $(ls); do echo "############# Start of $file #############"; cat $file; echo "############# End of $file #############"; done                 
############# Start of task_3_EbobK8.out #############
Decompressing gzipped file ...

Reformatting file sequence identifiers ...

Initial number of reads ( /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/reformatted_identifiersUBWD3J_decompressed_zU86te_CHP-00030-PT-02_S14_L001_R2_001 ): 2345943
Running Trimmomatic ...
Total reads after trimming ( /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.trimmed.fastq ): 2048018
Decontaminating ...
Running bowtie2 ...
Total reads after removing those found in reference database ( /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001_Homo_sapiens_bowtie2_clean.fastq ): 2047354
Total reads after merging results from multiple databases ( /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.fastq ): 2047354
Running trf ...

Final output file created:
/Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.repeats.removed.fastq

############# End of task_3_EbobK8.out #############
############# Start of task_3_FoBPzY.bash #############
#!/bin/bash
#SBATCH -p NMLResearch
#SBATCH -N 1
#SBATCH -n 8
#SBATCH -t 12:00:00
#SBATCH --mem 24576
#SBATCH -o /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_K5vNCK.out
#SBATCH -e /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_wMhyBH.err

kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/CHP-00030-PT-02_S14_L001_R2_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix CHP-00030-PT-02_S14_L001_R2_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.fastq
export RC=$? ; echo $RC > /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_phg2PD.rc ; bash -c 'exit $RC'############# End of task_3_FoBPzY.bash #############
############# Start of task_3_K5vNCK.out #############
Decompressing gzipped file ...

Reformatting file sequence identifiers ...

Initial number of reads ( /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/reformatted_identifiers3WQ0J4_decompressed_QJDpc8_CHP-00030-PT-02_S14_L001_R2_001 ): 2345943
Running Trimmomatic ...
Total reads after trimming ( /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.trimmed.fastq ): 2048018
Decontaminating ...
Running bowtie2 ...
Total reads after removing those found in reference database ( /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001_Homo_sapiens_bowtie2_clean.fastq ): 2047354
Total reads after merging results from multiple databases ( /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.fastq ): 2047354
Running trf ...

Final output file created:
/Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.repeats.removed.fastq

############# End of task_3_K5vNCK.out #############
############# Start of task_3_phg2PD.rc #############
0
############# End of task_3_phg2PD.rc #############
############# Start of task_3_S5MXH8.bash #############
#!/bin/bash
#SBATCH -p NMLResearch
#SBATCH -N 1
#SBATCH -n 8
#SBATCH -t 12:00:00
#SBATCH --mem 24576
#SBATCH -o /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_EbobK8.out
#SBATCH -e /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_XwkQhf.err

kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/CHP-00030-PT-02_S14_L001_R2_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix CHP-00030-PT-02_S14_L001_R2_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/CHP-00030-PT-02_S14_L001_R2_001.fastq
export RC=$? ; echo $RC > /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_3_YJ8S8W.rc ; bash -c 'exit $RC'############# End of task_3_S5MXH8.bash #############
############# Start of task_3_wMhyBH.err #############
############# End of task_3_wMhyBH.err #############
############# Start of task_3_XwkQhf.err #############
############# End of task_3_XwkQhf.err #############
############# Start of task_3_YJ8S8W.rc #############
0
############# End of task_3_YJ8S8W.rc #############
############# Start of task_5_1zFHxF.bash #############
#!/bin/bash
#SBATCH -p NMLResearch
#SBATCH -N 1
#SBATCH -n 8
#SBATCH -t 12:00:00
#SBATCH --mem 24576
#SBATCH -o /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_29Pkue.out
#SBATCH -e /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_HuaGP6.err

kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/HSC-10114-HC-01_S15_L001_R1_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix HSC-10114-HC-01_S15_L001_R1_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.fastq
export RC=$? ; echo $RC > /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_DnpfmV.rc ; bash -c 'exit $RC'############# End of task_5_1zFHxF.bash #############
############# Start of task_5_29Pkue.out #############
############# End of task_5_29Pkue.out #############
############# Start of task_5_afzaLW.err #############
############# End of task_5_afzaLW.err #############
############# Start of task_5_AindMP.rc #############
############# End of task_5_AindMP.rc #############
############# Start of task_5_CrDhsN.bash #############
#!/bin/bash
#SBATCH -p NMLResearch
#SBATCH -N 1
#SBATCH -n 8
#SBATCH -t 12:00:00
#SBATCH --mem 24576
#SBATCH -o /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_NzsuhB.out
#SBATCH -e /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_afzaLW.err

kneaddata --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/HSC-10114-HC-01_S15_L001_R1_001.fastq.gz --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main --threads 8 --output-prefix HSC-10114-HC-01_S15_L001_R1_001   --reference-db /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome  --serial --run-trf  && mv /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.repeats.removed.fastq /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/kneaddata/main/HSC-10114-HC-01_S15_L001_R1_001.fastq
export RC=$? ; echo $RC > /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test/slurm_files/task_5_AindMP.rc ; bash -c 'exit $RC'############# End of task_5_CrDhsN.bash #############
############# Start of task_5_DnpfmV.rc #############
############# End of task_5_DnpfmV.rc #############
############# Start of task_5_HuaGP6.err #############
############# End of task_5_HuaGP6.err #############
############# Start of task_5_NzsuhB.out #############
############# End of task_5_NzsuhB.out #############

Hello, Thank you for the detailed error message. Sorry that you are having issues with the slurm feature. I think you have an older version of AnADAMA2 and if you upgrade it should resolve the error you are seeing. The version you have includes a AWS batch feature merge in which a slurm bug was introduced. This slum bug is fixed in future versions. Please upgrade and try running again.

Thank you,
Lauren

I see. Thank you. The AnADAMA2 version I had was the one that came with biobakery_workflows, which I installed last week. Would be great if the AnADAMA2 package was updated in the conda package biobakery_workflows.

So in installed a higher version of AnADAMA2 by installing biobakery_workflows via pip. However, I got an error after trying to install the database using biobakery_workflows_databases --install wmgx. Here are the steps I took to install biobakery_workflow and dependencies.

$ conda clean -a --yes
$ conda env remove --yes --name biobakery
$ conda create --yes --name biobakery -c bioBakery kneaddata humann2
$ source activate biobakery
$ export PATH=$PATH:/home/CSCScience.ca/amirza/.local/bin
$ pip install --user biobakery_workflows
$ biobakery_workflows_databases --install wmgx

Here is the stdout and error message

Download URL: http://huttenhower.sph.harvard.edu/humann2_data/full_mapping_1_1.tar.gz
Downloading file of size: 0.58 GB

0.58 GB 100.00 %  15.25 MB/sec  0 min -0 sec
Extracting: /home/CSCScience.ca/amirza/biobakery_workflows_databases/humann2/full_mapping_1_1.tar.gz

Database installed: /home/CSCScience.ca/amirza/biobakery_workflows_databases/humann2/utility_mapping

HUMAnN2 configuration file updated: database_folders : utility_mapping = /home/CSCScience.ca/amirza/biobakery_workflows_databases/humann2/utility_mapping
Traceback (most recent call last):
  File "/home/CSCScience.ca/amirza/.local/bin/biobakery_workflows_databases", line 8, in <module>
    sys.exit(main())
  File "/home/CSCScience.ca/amirza/.local/lib/python3.7/site-packages/biobakery_workflows/biobakery_workflows_databases.py", line 168, in main
    create_strainphlan_db(args.location)
  File "/home/CSCScience.ca/amirza/.local/lib/python3.7/site-packages/biobakery_workflows/biobakery_workflows_databases.py", line 90, in create_strainphlan_db
    strainphlan_db=os.path.join(os.path.dirname(subprocess.check_output(["which","strainphlan.py"])),"metaphlan_databases","mpa_v20_m200")
  File "/home/CSCScience.ca/amirza/miniconda3/lib/python3.7/posixpath.py", line 94, in join
    genericpath._check_arg_types('join', a, *p)
  File "/home/CSCScience.ca/amirza/miniconda3/lib/python3.7/genericpath.py", line 151, in _check_arg_types
    raise TypeError("Can't mix strings and bytes in path components") from None
TypeError: Can't mix strings and bytes in path components

OK. I tried re-installing using conda only and no pip installs. Oddly, when installing biobakery_workflows via condo it does not install the latest version of AnADAMA2 available in conda. So I updated AnADAMA2 via conda. biobakery_workflows was downgraded when upgrading AnADAMA2. Still get errors. I think Im going to give up using biobakery_workflows :disappointed:

Here is exactly how I installed, parameters I had to use, and the errors:

$ conda create --yes --name biobakery-conda -c biobakery biobakery_workflows

Must install the database before updating AnADAMA2, else cant install the database.

$ biobakery_workflows_databases --install wmgx 
$ conda install anadama2=0.6.7

The following packages will be DOWNGRADED:

  biobakery_workflo~                          0.13.2-py27_0 --> 0.13.1-py27_0

$ biobakery_workflows wmgx --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/ --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test2 --grid slurm --grid-jobs 4 --grid-partition NMLResearch --grid-scratch test2/slurm-scratch --threads 8

Error:

ERROR: Unable to find bowtie2 index files in directory: /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_ribosomal_rna

Can get rid of this error by specifying location of database. I think this older version of biobakery_workflows has a bug, it expects to have two databases according to the help page, when there is only one directory.

$ biobakery_workflows wmgx --input /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/data/sample_data/ --output /Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test2 --grid slurm --grid-jobs 4 --grid-partition NMLResearch --grid-scratch test2/slurm-scratch --threads 8 --contaminate-databases /home/CSCScience.ca/amirza/biobakery_workflows_databases/kneaddata_db_human_genome

2020-05-12 19:51:39,386 root    log_grid_output INFO: Grid 10 from task id standard error:

Downloading MetaPhlAn2 database
Please note due to the size this might take a few minutes

Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/mpa_v20_m200.tar
Traceback (most recent call last):
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/metaphlan2.py", line 1564, in <module>
    metaphlan2()
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/metaphlan2.py", line 1357, in metaphlan2
    check_and_install_database(pars['index'], pars['bowtie2db'], pars['bowtie2_build'], pars['nproc'])
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/metaphlan2.py", line 826, in check_and_install_database
    download_unpack_tar(DATABASE_DOWNLOAD, index, bowtie2_db, bowtie2_build, nproc)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/metaphlan2.py", line 736, in download_unpack_tar
    download(url_tar_file, tar_file)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/metaphlan2.py", line 710, in download
    reporthook=ReportHook().report)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 98, in urlretrieve
    return opener.retrieve(url, filename, reporthook, data)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 245, in retrieve
    fp = self.open(url, data)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 213, in open
    return getattr(self, name)(url)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 457, in open_https
    return self.http_error(url, fp, errcode, errmsg, headers)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 377, in http_error
    result = method(url, fp, errcode, errmsg, headers)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 704, in http_error_401
    return getattr(self,name)(url, realm)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 781, in retry_https_basic_auth
    user, passwd = self.get_user_passwd(host, realm, i)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 797, in get_user_passwd
    user, passwd = self.prompt_user_passwd(host, realm)
  File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/lib/python2.7/urllib.py", line 806, in prompt_user_passwd
    host))
EOFError: EOF when reading a line

Task 13 failed
  Name: metaphlan2____HSC-10114-HC-01_S15_L001_R1_001
  Original error:
  Failed to produce target `/Drives/W/Projects/Project_Tremlett_lab/MetagenomicMSPeds/biobakery_pipeline/test2/metaphlan2/main/HSC-10114-HC-01_S15_L001_R1_001_ta
xonomic_profile.tsv'.

biobakery_workflows installed an older version of metaphlan (2.7.7) which still points to the URLs pre-migration. Update to version 2.8.

$ conda install -c bioconda metaphlan2=2.8

It downgraded samtools

samtools 1.10-h9402c20_2 --> 0.1.19-h94a8ba4_6

error

T    ask 13 failed
      Name: metaphlan2____HSC-10114-HC-01_S15_L001_R1_001
      Original error:
    Traceback (most recent call last):
      File "/home/CSCScience.ca/amirza/miniconda3/envs/biobakery-conda/bin/wmgx.py", line 174, in <module>
        workflow.go()
      File "/home/CSCScience.ca/amirza/.local/lib/python2.7/site-packages/anadama2/workflow.py", line 800, in go
        self._handle_finished()
      File "/home/CSCScience.ca/amirza/.local/lib/python2.7/site-packages/anadama2/workflow.py", line 830, in _handle_finished
        self._reporter.finished()
      File "/home/CSCScience.ca/amirza/.local/lib/python2.7/site-packages/anadama2/reporters.py", line 218, in finished
        r.finished()
      File "/home/CSCScience.ca/amirza/.local/lib/python2.7/site-packages/anadama2/reporters.py", line 463, in finished
        sys.stdout.write(six.u("  "+print_line+"\n"))
      File "/home/CSCScience.ca/amirza/.local/lib/python2.7/site-packages/six.py", line 658, in u
        return unicode(s.replace(r'\\', r'\\\\'), "unicode_escape")
    TypeError: decoding Unicode is not supported

I thought maybe I should update python

$ conda update python

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
humann2-2.8.1              |           py27_0        61.0 MB  bioconda
------------------------------------------------------------
                                       Total:        61.0 MB

The following NEW packages will be INSTALLED:

  bmfilter           bioconda/linux-64::bmfilter-3.101-hfc679d8_2
  bmtagger           bioconda/linux-64::bmtagger-3.101-h470a237_4
  bmtool             bioconda/linux-64::bmtool-3.101-hfc679d8_2
  extract_fullseq    bioconda/linux-64::extract_fullseq-3.101-3
  srprism            bioconda/linux-64::srprism-2.4.24-h96824bc_3
  trimmomatic        bioconda/noarch::trimmomatic-0.39-1

The following packages will be REMOVED:

  glpk-4.65-he80fd80_1002
  gmp-6.2.0-he1b5a44_2
  htslib-1.10.2-h78d89cc_0
  java-jdk-8.0.92-1

The following packages will be UPDATED:

  kneaddata          biobakery/linux-64::kneaddata-0.7.2-p~ --> bioconda/noarch::kneaddata-0.7.4-py_0
  libdeflate                                 1.3-h516909a_0 --> 1.5-h516909a_0
  pysam                               0.15.3-py27hbcae180_3 --> 0.15.4-py27hbcae180_0

updating python fixed the error but two new errors popped up:

ERROR: Unable to find trimmomatic. Please provide the full path to trimmomatic with --trimmomatic.

Error! numpy python library not detected!!

Hello, Sorry to hear you are having issues installing the workflows with conda. The last two errors you posted can hopefully be resolved with installing trf and numpy in your conda environment. Please post if you are still seeing errors with the conda install.

Thank you,
Lauren