Eggnog mapper question

[clydeugene]

Hi Robert,

I am trying to run the eggnog mapper workflow without much success.

Attempt 1

Initially, I ran the following:

bactopia --wf eggnog \
    --bactopia data/processed/ \
    --exclude bactopia-exclude.tsv \
    --eggnog_db ../eggnog/ \
    -profile singularity

I had downloaded the eggnog and diamond databases into ../eggnog/ and supplied the db path but this did not complete successfully at all, and it kept retrying the whole of yesterday, and it was exiting without specific error messages.

I ended up killing the whole run this morning and tried the step below. Unfortunately, when I tried the step below, my .nextflow.log was overwritten so I cannot post the error messages here.

Attempt 2

This is what I tried running earlier today:

bactopia --wf eggnog \
    --bactopia data/processed/ \
    --download_eggnog \
    --eggnog_save_as_tarball \
    --eggnog_db eggnog \
    --install_mmseq \
    --install_pfam \
    -profile singularity

The process is still running but I'm seeing the following in .nextflow.log

May-21 12:29:26.776 [main] DEBUG nextflow.cli.Launcher - $> nextflow run /home/clyde/miniforge3/envs/bactopia//share/bactopia-3.0.1/main.nf -w /mnt/e/cmakamure/nicole/work/ --wf eggnog --bactopia data/processed/ --download_eggnog --eggnog_save_as_tarball --eggnog_db eggnog --install_mmseq --install_pfam -profile singularity
May-21 12:29:26.875 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 23.10.1
May-21 12:29:26.891 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/clyde/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
May-21 12:29:26.916 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
May-21 12:29:26.918 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
May-21 12:29:26.922 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
May-21 12:29:26.947 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
May-21 12:29:26.964 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/nextflow.config
May-21 12:29:26.967 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/nextflow.config
May-21 12:29:26.992 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `singularity`
May-21 12:29:28.560 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, gcp, lugh, mccleary, unibe_ibu, vai, czbiohub_aws, jax, ccga_med, arcc_hawk, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, icr_davros, ceres, munin, arm, rosalind, hasta, cfc, uzh, ebi_codon_slurm, ebc, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, mana, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, imperial, maestro, software_license, utd_europa, standard, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, sge, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, einstein, ethz_euler, m3c, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, nygc, fgcz, crg, singularity, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, genouest, cbe, slurm, phoenix, seawulf, uod_hpc, fub_curta, uct_hpc, aws, aws_tower, binac]
May-21 12:29:28.593 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
May-21 12:29:28.604 [main] INFO  nextflow.cli.CmdRun - Launching `/home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/main.nf` [backstabbing_cori] DSL2 - revision: 0cd9f79ba7
May-21 12:29:28.605 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
May-21 12:29:28.605 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
May-21 12:29:28.609 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/clyde/.nextflow/secrets/store.json
May-21 12:29:28.613 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@179ee36b] - activable => nextflow.secret.LocalSecretsProvider@179ee36b
May-21 12:29:28.662 [main] DEBUG nextflow.Session - Session UUID: e38ce0ee-2af3-4680-9366-38994aab25d4
May-21 12:29:28.662 [main] DEBUG nextflow.Session - Run name: backstabbing_cori
May-21 12:29:28.663 [main] DEBUG nextflow.Session - Executor pool size: 8
May-21 12:29:28.669 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
May-21 12:29:28.690 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 23.10.1 build 5891
  Created: 12-01-2024 22:01 UTC (14:01 PDT)
  System: Linux 5.15.146.1-microsoft-standard-WSL2
  Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 21-internal-adhoc.conda.src
  Encoding: UTF-8 (UTF-8)
  Process: 1470074@LLUA4BB6D4CDEB6 [127.0.1.1]
  CPUs: 8 - Mem: 15.5 GB (13.2 GB) - Swap: 4 GB (4 GB) - Virtual threads ON
May-21 12:29:28.716 [main] DEBUG nextflow.Session - Work-dir: /mnt/e/cmakamure/nicole/work [v9fs]
May-21 12:29:28.731 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
May-21 12:29:28.742 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
May-21 12:29:28.791 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
May-21 12:29:28.799 [main] DEBUG nextflow.util.CustomPoolFactory - Creating virtual thread pool
May-21 12:29:29.112 [main] DEBUG nextflow.Session - Session start
May-21 12:29:29.121 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mnt/e/cmakamure/nicole/data/processed/bactopia-runs/eggnog-20240521-122928/nf-reports/eggnog-trace.txt
May-21 12:29:29.141 [main] DEBUG nextflow.Session - Using default localLib path: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/lib
May-21 12:29:29.143 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/lib
May-21 12:29:29.144 [main] DEBUG nextflow.Session - Adding to the classpath library: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/lib/nfcore_external_java_deps.jar
May-21 12:29:29.240 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
May-21 12:29:30.496 [main] WARN  nextflow.Nextflow - Maximum memory (32) was adjusted to fit your system (15)
May-21 12:29:30.627 [main] INFO  nextflow.Nextflow - 

-�[2m------------------------------------------------------------------�[0m-
�[0;34m   _                _              _         _              _              �[0m
�[0;34m  | |__   __ _  ___| |_ ___  _ __ (_) __ _  | |_ ___   ___ | |___          �[0m
�[0;34m  | '_ \ / _` |/ __| __/ _ \| '_ \| |/ _` | | __/ _ \ / _ \| / __|    �[0m
�[0;34m  | |_) | (_| | (__| || (_) | |_) | | (_| | | || (_) | (_) | \__ \        �[0m
�[0;34m  |_.__/ \__,_|\___|\__\___/| .__/|_|\__,_|  \__\___/ \___/|_|___/ �[0m
�[0;34m                            |_|                                            �[0m
�[0;36m  bactopia tools eggnog v3.0.1�[0m
�[0;36m  Functional annotation of proteins using orthologous groups and phylogenies �[0m
-�[2m------------------------------------------------------------------�[0m-
�[1mCore Nextflow options�[0m
  �[0;34mrunName               : �[0;32mbackstabbing_cori�[0m
  �[0;34mcontainerEngine       : �[0;32msingularity�[0m
  �[0;34mcontainer             : �[0;32mquay.io/bactopia/bactopia:3.0.1�[0m
  �[0;34mlaunchDir             : �[0;32m/mnt/e/cmakamure/nicole�[0m
  �[0;34mworkDir               : �[0;32m/mnt/e/cmakamure/nicole/work�[0m
  �[0;34mprojectDir            : �[0;32m/home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1�[0m
  �[0;34muserName              : �[0;32mclyde�[0m
  �[0;34mprofile               : �[0;32msingularity�[0m
  �[0;34mconfigFiles           : �[0;32m/home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/nextflow.config�[0m

�[1mRequired Parameters�[0m
  �[0;34mbactopia              : �[0;32mdata/processed/�[0m

�[1meggNOG Downloader Parameters�[0m
  �[0;34meggnog_db             : �[0;32meggnog�[0m
  �[0;34mdownload_eggnog       : �[0;32mtrue�[0m
  �[0;34meggnog_save_as_tarball: �[0;32mtrue�[0m
  �[0;34minstall_mmseq         : �[0;32mtrue�[0m
  �[0;34minstall_pfam          : �[0;32mtrue�[0m

�[1mOptional Parameters�[0m
  �[0;34moutdir                : �[0;32mdata/processed/�[0m

�[1mNextflow Profile Parameters�[0m
  �[0;34mcondadir              : �[0;32m/home/clyde/.bactopia/conda�[0m
  �[0;34mdatasets_cache        : �[0;32m/home/clyde/.bactopia/datasets�[0m
  �[0;34msingularity_cache_dir : �[0;32m/home/clyde/.bactopia/singularity�[0m

�[1mHelpful Parameters�[0m
  �[0;34mwf                    : �[0;32meggnog�[0m

!! Only displaying parameters that differ from the pipeline defaults !!
-�[2m------------------------------------------------------------------�[0m-
If you use bactopia for your analysis please cite:

* Bactopia
  https://doi.org/10.1128/mSystems.00190-20

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://bactopia.github.io/acknowledgements/
-�[2m------------------------------------------------------------------�[0m-
May-21 12:29:30.882 [main] WARN  nextflow.Nextflow - Maximum memory (32) was adjusted to fit your system (15)
May-21 12:29:31.027 [main] WARN  nextflow.Nextflow - Maximum memory (32) was adjusted to fit your system (15)
May-21 12:29:31.138 [main] WARN  nextflow.Nextflow - Maximum memory (32) was adjusted to fit your system (15)
May-21 12:29:31.148 [main] INFO  nextflow.Nextflow - 
Each task will use 4 CPUs out of the available 8 CPUs. At most 
2 task(s) will be run at a time, this can affect the efficiency 
of Bactopia. You can use the '-qs' parameter to alter the number of 
tasks to run at a time (e.g. '-qs 2', means only 2 tasks or a maximum 
of 8 CPUs will be used at once)

May-21 12:29:31.149 [main] INFO  nextflow.Nextflow - 
May-21 12:29:31.256 [main] INFO  nextflow.Nextflow - Found 15 samples to process
May-21 12:29:31.257 [main] INFO  nextflow.Nextflow - 
If this looks wrong, now's your chance to back out (CTRL+C 3 times).
May-21 12:29:31.257 [main] INFO  nextflow.Nextflow - Sleeping for 5 seconds...
May-21 12:29:31.257 [main] INFO  nextflow.Nextflow - --------------------------------------------------------------------
May-21 12:29:36.330 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low,process_long` for process with name BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD
May-21 12:29:36.331 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_long` matches labels `process_low,process_long` for process with name BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD
May-21 12:29:36.334 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-21 12:29:36.335 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-21 12:29:36.340 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
May-21 12:29:36.346 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=15.5 GB; capacity=8; pollInterval=100ms; dumpInterval=5m
May-21 12:29:36.348 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
May-21 12:29:36.413 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name BACTOPIATOOLS:EGGNOG:EGGNOG_MAPPER
May-21 12:29:36.418 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-21 12:29:36.418 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-21 12:29:36.486 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_low` matches labels `process_low` for process with name BACTOPIATOOLS:CUSTOM_DUMPSOFTWAREVERSIONS
May-21 12:29:36.487 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
May-21 12:29:36.488 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
May-21 12:29:36.490 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: EGGNOG_DOWNLOAD, CUSTOM_DUMPSOFTWAREVERSIONS, EGGNOG_MAPPER, BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD, BACTOPIATOOLS:EGGNOG:EGGNOG_MAPPER, BACTOPIATOOLS:CUSTOM_DUMPSOFTWAREVERSIONS
May-21 12:29:36.493 [main] DEBUG nextflow.Session - Igniting dataflow network (9)
May-21 12:29:36.495 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD
May-21 12:29:36.496 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BACTOPIATOOLS:EGGNOG:EGGNOG_MAPPER
May-21 12:29:36.497 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > BACTOPIATOOLS:CUSTOM_DUMPSOFTWAREVERSIONS
May-21 12:29:36.497 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_f447eb07a737d27b: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/./workflows/../subworkflows/local/eggnog/../../../lib/nf/functions.nf
  Script_5a9dd689e212d883: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/./workflows/../lib/nf/bactopia_tools.nf
  Script_b0a616080cd7c108: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/./workflows/../subworkflows/local/eggnog/main.nf
  Script_7ce2a1340c5b703e: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/./workflows/../modules/nf-core/custom/dumpsoftwareversions/main.nf
  Script_782b6716bd4a0f26: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/./workflows/../subworkflows/local/eggnog/../../../modules/nf-core/eggnog/download/main.nf
  Script_ab5b97328c0641fa: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/./workflows/bactopia-tools.nf
  Script_d9ab0911f8c1151f: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/./workflows/../subworkflows/local/eggnog/../../../modules/nf-core/eggnog/mapper/main.nf
  Script_28b956a88b5bebd6: /home/clyde/miniforge3/envs/bactopia/share/bactopia-3.0.1/main.nf
May-21 12:29:36.498 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination 
May-21 12:29:36.498 [main] DEBUG nextflow.Session - Session await
May-21 12:29:36.545 [Actor Thread 28] DEBUG nextflow.container.SingularityCache - Singularity found local store for image=https://depot.galaxyproject.org/singularity/eggnog-mapper:2.1.12--pyhdfd78af_0; path=/home/clyde/.bactopia/singularity/depot.galaxyproject.org-singularity-eggnog-mapper-2.1.12--pyhdfd78af_0.img
May-21 12:29:36.637 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
May-21 12:29:36.639 [Task submitter] INFO  nextflow.Session - [58/0f7165] Submitted process > BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD
May-21 12:34:36.511 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 12:39:36.553 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 12:44:36.647 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 12:49:36.654 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 12:54:36.658 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 12:59:36.698 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:04:36.753 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:09:36.831 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:14:36.913 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:19:36.997 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:24:37.085 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:29:37.162 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:34:37.254 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:39:37.279 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:44:37.352 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:49:37.357 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]
May-21 13:54:37.438 [Task monitor] DEBUG n.processor.TaskPollingMonitor - !! executor local > tasks to be completed: 1 -- submitted tasks are shown below
~> TaskHandler[id: 1; name: BACTOPIATOOLS:EGGNOG:EGGNOG_DOWNLOAD; status: RUNNING; exit: -; error: -; workDir: /mnt/e/cmakamure/nicole/work/58/0f71657c01cf273fa731923f350b22]

So I just thought to reach out and ask if I am running this correctly or if I am missing something important?