Nextflow not continuing past MUFFIN launch

[dzolier]

Nextflow launches MUFFIN but then doesn't continue. I'm running this under a conda environment, which may have something to do with it. Although maybe I installed nextflow or MUFFIN wrong, or the command is messed up; I'm pasting the command and all the feedback before nextflow stopped below:

(medaka) ubuntu:~$ sudo nextflow -log /var/log/nextflow.log run RVanDamme/MUFFIN --output /home/ubuntu/hopes_and_dreams -with-report /home/ubuntu/hopes_and_dreams/MUFFIN_RUN_1.txt -with-timeline -with-trace -with-dag /home/ubuntu/hopes_and_dreams/flowchart.png --cpus 8 --memory 32g --assembler metaflye -profile local,conda,test
N E X T F L O W  ~  version 21.10.5
Launching `RVanDamme/MUFFIN` [sharp_borg] - revision: 3695f30cc3 [master]

The folder hopes_and_dreams is empty afterwards, and the only things it gets to in that command are the log file (which will be pasted below) and the trace file (which will be before it).

(medaka) ubuntu:~$ cat trace.txt
task_id hash    native_id       name    status  exit    submit  duration       realtime %cpu    peak_rss        peak_vmem       rchar   wchar

(medaka) ubuntu:~$ cat /var/log/nextflow.log
Dec-14 21:02:30.556 [main] DEBUG nextflow.cli.Launcher - $> nextflow -log /var/log/nextflow.log run RVanDamme/MUFFIN --output /home/ubuntu/hopes_and_dreams -with-report /home/ubuntu/hopes_and_dreams/MUFFIN_RUN_1.txt -with-timeline -with-trace -with-dag /home/ubuntu/hopes_and_dreams/flowchart.png --cpus 8 --memory 32g --assembler metaflye -profile local,conda,test
Dec-14 21:02:30.607 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 21.10.5
Dec-14 21:02:31.200 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/RVanDamme/MUFFIN/.git/config; branch: master; remote: origin; url: https://github.com/RVanDamme/MUFFIN.git
Dec-14 21:02:31.214 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/RVanDamme/MUFFIN/.git/config; branch: master; remote: origin; url: https://github.com/RVanDamme/MUFFIN.git
Dec-14 21:02:31.276 [main] INFO  nextflow.cli.CmdRun - Launching `RVanDamme/MUFFIN` [sharp_borg] - revision: 3695f30cc3 [master]
Dec-14 21:02:31.525 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /root/.nextflow/assets/RVanDamme/MUFFIN/nextflow.config
Dec-14 21:02:31.526 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /root/.nextflow/assets/RVanDamme/MUFFIN/nextflow.config
Dec-14 21:02:31.532 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `local,conda,test`
Dec-14 21:02:31.704 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, slurm, local_engine, test, gcloud, conda, singularity, local, docker]
Dec-14 21:02:31.737 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; plugins-dir=/root/.nextflow/plugins
Dec-14 21:02:31.739 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Dec-14 21:02:31.745 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Dec-14 21:02:31.746 [main] INFO  org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Dec-14 21:02:31.749 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Dec-14 21:02:31.762 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Dec-14 21:02:31.795 [main] DEBUG nextflow.Session - Session uuid: bf7e5a42-dc21-437b-8ce2-b3a3b1a5588e
Dec-14 21:02:31.795 [main] DEBUG nextflow.Session - Run name: sharp_borg
Dec-14 21:02:31.795 [main] DEBUG nextflow.Session - Executor pool size: 16
Dec-14 21:02:31.815 [main] DEBUG nextflow.cli.CmdRun -
  Version: 21.10.5 build 5658
  Created: 08-12-2021 14:39 UTC
  System: Linux 5.11.0-1022-aws
  Runtime: Groovy 3.0.9 on OpenJDK 64-Bit Server VM 11.0.11+9-Ubuntu-0ubuntu2.20.04
  Encoding: UTF-8 (UTF-8)
  Process: 1826@ip-172-31-13-118 [172.31.13.118]
  CPUs: 16 - Mem: 61.8 GB (60.6 GB) - Swap: 0 (0)
Dec-14 21:02:31.824 [main] DEBUG nextflow.Session - Work-dir: /home/ubuntu/work [ext2/ext3]
Dec-14 21:02:31.833 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Dec-14 21:02:31.840 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Dec-14 21:02:31.889 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000
Dec-14 21:02:31.938 [main] DEBUG nextflow.Session - Session start invoked
Dec-14 21:02:31.941 [main] DEBUG nextflow.trace.TraceFileObserver - Flow starting -- trace file: /home/ubuntu/trace.txt
Dec-14 21:02:32.654 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Dec-14 21:02:32.699 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 17; maxThreads: 1000

I'm grateful for any help you can provide.

[replikation]

• what is the file input? i dont see anything?

[dzolier]

I'm afraid I don't know what you mean. I just copied the command for the test run in the documentation (with some extra bits to help track how the program worked); did I miss something?

[dzolier]

It turns out, nextflow defaults to a version MUFFIN doesn't support. Solution: Use NXF_VER=20.10.0 before my initial command, sets the nextflow version to 20.10.0 which seems like it works fine.

[replikation]

• @dzolier so a higher version is currently not working? thanks for clarifying this