nextlfow unable to communicate with conda

[amdf123]

Bug report

(Getting errors that Nextflow can't find Conda. I am trying to run this pipeline, https://github.com/PacificBiosciences/HiFi-16S-workflow. I have confirmed that conda is in fact installed, version 25.5.1, and I have been able to call it.

Our setup does limit the space we have in our home directory where conda is installed. However, I have changed the nextflow.config file execution profiles from the piepeline to reflect the working directory for the conda environments, which are in a different directory.)

Expected behavior and actual behavior

(nextflow should communicate with conda to create the environments and download the databases needed for the pipeline to run. However, multiple errors indicate that nextflow is not communicating or cannot find conda)

Steps to reproduce the problem

(git clone https://github.com/PacificBiosciences/HiFi-16S-workflow.git
cd HiFi-16S-workflow
nextflow run main.nf --download_db

I have run this both with and without singularity, so, nextflow run main.nf --download_db - profile singularity)

Program output

(Jul-02 15:25:33.073 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: ProxyConfig[protocol=http; host=atlas-prox.hpc.msstate.edu; port=3128]
Jul-02 15:25:33.116 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: ProxyConfig[protocol=https; host=atlas-prox.hpc.msstate.edu; port=3128]
Jul-02 15:25:33.117 [main] DEBUG nextflow.cli.Launcher - $> nextflow run main.nf --download_db -profile singularity
Jul-02 15:25:33.327 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.10.5
Jul-02 15:25:33.481 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/amanda.m.davilaflores/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Jul-02 15:25:33.536 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-02 15:25:33.537 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-02 15:25:33.541 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Jul-02 15:25:33.553 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jul-02 15:25:33.573 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /project/90daydata/pbarc/amanda.davilaflores/TEST16S/HiFi-16S-workflow/nextflow.config
Jul-02 15:25:33.576 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /project/90daydata/pbarc/amanda.davilaflores/TEST16S/HiFi-16S-workflow/nextflow.config
Jul-02 15:25:33.600 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/amanda.m.davilaflores/.nextflow/secrets/store.json
Jul-02 15:25:33.603 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@5d28bcd5] - activable => nextflow.secret.LocalSecretsProvider@5d28bcd5
Jul-02 15:25:33.615 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: singularity
Jul-02 15:25:34.433 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, conda, singularity, docker]
Jul-02 15:25:34.478 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jul-02 15:25:34.495 [main] DEBUG nextflow.cli.CmdRun - Launching main.nf [golden_edison] DSL2 - revision: c6a6ee205a
Jul-02 15:25:34.497 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jul-02 15:25:34.497 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jul-02 15:25:34.549 [main] DEBUG nextflow.Session - Session UUID: 93f7d9c3-0915-4674-bcf8-6175f7c05fc9
Jul-02 15:25:34.550 [main] DEBUG nextflow.Session - Run name: golden_edison
Jul-02 15:25:34.550 [main] DEBUG nextflow.Session - Executor pool size: 48
Jul-02 15:25:34.559 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jul-02 15:25:34.563 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=144; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Jul-02 15:25:35.035 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.10.5 build 5935
Created: 04-03-2025 17:55 UTC (11:55 CDT)
System: Linux 5.14.0-162.23.1.el9_1.x86_64
Runtime: Groovy 4.0.23 on OpenJDK 64-Bit Server VM 22.0.1-internal-adhoc.conda.src
Encoding: UTF-8 (UTF-8)
Process: 818846@atlas-0179 [172.19.15.179]
CPUs: 48 - Mem: 376.5 GB (258.8 GB) - Swap: 93.1 GB (90.8 GB)
Jul-02 15:25:35.085 [main] DEBUG nextflow.Session - Work-dir: /project/90daydata/pbarc/amanda.davilaflores/TEST16S/HiFi-16S-workflow/work [lustre]
Jul-02 15:25:35.086 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /project/90daydata/pbarc/amanda.davilaflores/TEST16S/HiFi-16S-workflow/bin
Jul-02 15:25:35.097 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jul-02 15:25:35.106 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jul-02 15:25:35.143 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jul-02 15:25:35.152 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 49; maxThreads: 1000
Jul-02 15:25:35.571 [main] DEBUG nextflow.Session - Session start
Jul-02 15:25:35.573 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /project/90daydata/pbarc/amanda.davilaflores/TEST16S/HiFi-16S-workflow/results/execution_trace.txt
Jul-02 15:25:36.133 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jul-02 15:25:37.485 [main] INFO nextflow.script.BaseScript - No input file given to --input!
Jul-02 15:25:37.551 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:cpu_def matches labels cpu_def for process with name pb16S:download_db
Jul-02 15:25:37.569 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: Local
Jul-02 15:25:37.570 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'Local'
Jul-02 15:25:37.575 [main] DEBUG nextflow.executor.Executor - [warm up] executor > Local
Jul-02 15:25:37.583 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'Local' > cpus=48; memory=376.5 GB; capacity=48; pollInterval=100ms; dumpInterval=5m
Jul-02 15:25:37.585 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: Local)
Jul-02 15:25:37.653 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: QC_fastq, dada2_assignTax, import_qiime2, filter_dada2, prepare_qiime2_manifest, export_biom, pb16S:download_db, demux_summarize, export_biom_skip_nb, class_tax, write_log, barplot, download_db, picrust2, dada2_denoise_with_error_model, html_rep, cutadapt, html_rep_skip_cutadapt, qiime2_phylogeny_diversity, QC_fastq_post_trim, dada2_denoise, collect_QC_skip_cutadapt, merge_manifest, collect_QC, mergeASV, krona_plot, prepare_qiime2_manifest_skip_cutadapt, barplot_nb, learn_error, dada2_rarefaction, dada2_qc
Jul-02 15:25:37.654 [main] DEBUG nextflow.Session - Igniting dataflow network (1)
Jul-02 15:25:37.654 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > pb16S:download_db
/90daydata/pbarc/amanda.davilaflores/TEST16S/HiFi-16S-workflow)

Environment

• Nextflow version: [24.10.5]
• Java version: [?]
• Operating system: [Windows 11]
• Bash version: (use the command $SHELL --version)

Additional context

(Add any other context about the problem here)