Denoising using qiime2 got much slower

Hey everyone,

I’ve been running QIIME 2 on my MacBook Pro (M2 Pro, 10 cores), and the denoising step (DADA2) got much slower. It used to run quickly, and now it’s taking way longer, even though my input data and workflow haven’t changed.

I'm using qiime2 2023.5

I checked CPU usage, restarted everything, and made sure my Conda environment is up to date—still no luck. Attaching my system report for reference.

Has anyone else had this issue? Any ideas on how to fix it?

Thanks!

EtreCheckPro version: 6.8.8 (68072)
Report generated: 2025-02-21 12:24:41
Download EtreCheckPro from https://etrecheck.com
Runtime: 2:53
Performance: Excellent

Problem: Computer is too slow

Major Issues:
  Anything that appears on this list needs immediate attention. 
  Unsigned files - There are unsigned software files installed that could be malicious and should be reviewed.

Minor Issues:
  These issues do not need immediate attention but they may indicate future problems or opportunities for improvement. 
  Configuration profiles found - This computer may have configuration profiles installed.
  Heavy RAM usage - Apps are using a large amount of RAM.
  Clean up - There are orphan files that could be removed.
  System modifications - There are a large number of system modifications running in the background.
  Limited permissions - More information may be available with Full Disk Access.

Hardware Information:
  MacBook Pro (14-inch, 2023)
    Status: Supported
  MacBook Pro Model: Mac14,9
  Apple M2 Pro (m2 pro) CPU: 10-core
  16 GB RAM - Not upgradeable
  Battery: Health = Normal - Cycle count = 344

Video Information:
  Apple M2 Pro
    Color LCD 3024 x 1964

Drives:
  disk0 - APPLE SSD AP0512Z 500.28 GB (Solid State - TRIM: Yes) 
  Internal Apple Fabric NVM Express
  S.M.A.R.T. Details: 2% used, 57.60 TB written, 100% health, 8 unsafe shutdowns
    disk0s1 [APFS Container] 524 MB
      disk1 [APFS Virtual drive] 524 MB (Shared by 4 volumes)
        disk1s1 - iSCPreboot (APFS) [APFS Preboot] (6 MB used)
        disk1s2 - xART (APFS) (6 MB used)
        disk1s3 - Hardware (APFS) (3 MB used)
        disk1s4 - Recovery (APFS) [Recovery] (20 KB used)
    disk0s2 [APFS Container] 494.38 GB
      disk3 [APFS Virtual drive] 494.38 GB (Shared by 6 volumes)
        disk3s1 (APFS) [APFS Container] (11.16 GB used)
          disk3s1s1 - Macintosh HD (APFS) [APFS Snapshot] (11.16 GB used)
        disk3s2 - Preboot (APFS) [APFS Preboot] (6.85 GB used)
        disk3s3 - Recovery (APFS) [Recovery] (1.03 GB used)
        disk3s4 - Update (APFS) (3 MB used)
        disk3s5 - Data (APFS) [APFS Virtual drive] (335.66 GB used)
        disk3s6 - VM (APFS) [APFS VM] (5.37 GB used)
    disk0s3 [APFS Container] 5.37 GB
      disk2 [APFS Virtual drive] 5.37 GB (Shared by 2 volumes)
        disk2s1 - Recovery (APFS) [Recovery] (1.87 GB used)
        disk2s2 - Update (APFS) (2 MB used)

Mounted Volumes:
  disk1s1 - iSCPreboot [APFS Preboot]
    Filesystem: APFS
    Mount point: /System/Volumes/iSCPreboot
    Used: 6 MB
    Shared values
      Size: 524 MB
      Free: 505 MB

  disk1s2 - xART
    Filesystem: APFS
    Mount point: /System/Volumes/xarts
    Used: 6 MB
    Shared values
      Size: 524 MB
      Free: 505 MB

  disk1s3 - Hardware
    Filesystem: APFS
    Mount point: /System/Volumes/Hardware
    Used: 3 MB
    Shared values
      Size: 524 MB
      Free: 505 MB

  disk3s1s1 - Macintosh HD [APFS Snapshot]
    Filesystem: APFS
    Mount point: /
    Read-only: Yes
    Used: 11.16 GB
    Shared values
      Size: 494.38 GB
      Free: 134.15 GB
      Available: 138.33 GB

  disk3s2 - Preboot [APFS Preboot]
    Filesystem: APFS
    Mount point: /System/Volumes/Preboot
    Used: 6.85 GB
    Shared values
      Size: 494.38 GB
      Free: 134.15 GB
      Available: 138.33 GB

  disk3s3 - Recovery [Recovery]
    Filesystem: APFS
    Mount point: /Volumes/Recovery
    Used: 1.03 GB
    Shared values
      Size: 494.38 GB
      Free: 134.15 GB
      Available: 184.62 GB

  disk3s4 - Update
    Filesystem: APFS
    Mount point: /System/Volumes/Update
    Used: 3 MB
    Shared values
      Size: 494.38 GB
      Free: 134.15 GB
      Available: 138.33 GB

  disk3s5 - Data [APFS Virtual drive]
    Filesystem: APFS
    Mount point: /System/Volumes/Data
    Encrypted
    Used: 335.66 GB
    Shared values
      Size: 494.38 GB
      Free: 134.15 GB
      Available: 184.62 GB

  disk3s6 - VM [APFS VM]
    Filesystem: APFS
    Mount point: /System/Volumes/VM
    Used: 5.37 GB
    Shared values
      Size: 494.38 GB
      Free: 134.15 GB
      Available: 138.33 GB

USB:
  USB 3.1 bus
    <Empty>

  USB 3.1 bus
    <Empty>

  USB 3.1 bus
    <Empty>

Network:
  Interface en4: Ethernet Adapter (en4)
  Interface en5: Ethernet Adapter (en5)
  Interface en6: Ethernet Adapter (en6)
  Interface en8: USB 10/100/1000 LAN
  Interface bridge0: Thunderbolt Bridge
  Interface en0: Wi-Fi
    802.11 a/b/g/n/ac/ax
    Proxy Auto Discovery
  Interface en7: iPhone

  Firewall:
    Blocked apps:
      K832E2UXV7.com.riotgames.LeagueofLegends.GameClient

System Software:
  macOS Sequoia 15.3.1 (24D70) 
  Time since boot: About 5 hours

Configuration Profiles:
  com.apple.wifi.managed
    EAPClientConfiguration/EAPFastProvisionPACAnonymously
    EAPClientConfiguration/TLSAllowTrustExceptions
    EAPClientConfiguration/PayloadCertificateAnchorUUID[0]
    EAPClientConfiguration/UserPassword
    ProxyType
    EAPClientConfiguration/EAPFASTProvisionPAC
    SSID_STR
    HIDDEN_NETWORK
    EAPClientConfiguration/OneTimeUserPassword
    EAPClientConfiguration/UserName
    EAPClientConfiguration/TLSTrustedServerNames[0]
    EAPClientConfiguration/TTLSInnerAuthentication
    EAPClientConfiguration/AcceptEAPTypes[0]
    ProxyPACFallbackAllowed
    EncryptionType
    EAPClientConfiguration/EAPFASTUsePAC

Security:
  Gatekeeper: App Store and identified developers
  System Integrity Protection: Enabled
  Secure Boot: Full Security

  Antivirus software: Apple

Unsigned Files:
  Launchd: /Library/LaunchDaemons/com.microsoft.OneDriveUpdaterDaemon.plist
    Executable: /Applications/OneDrive.app/Contents/OneDriveUpdaterDaemon.xpc/Contents/MacOS/OneDriveUpdaterDaemon
    Details: Exact match found in the legitimate list - probably OK

  Launchd: /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Resources/com.oracle.java.Java-Updater.plist
    Command: /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Resources/Java Updater.app/Contents/MacOS/Java Updater -bgcheck
    Details: Exact match found in the legitimate list - probably OK

  Launchd: /Library/LaunchAgents/com.microsoft.SyncReporter.plist
    Executable: /Applications/OneDrive.app/Contents/SyncReporter.app/Contents/MacOS/SyncReporter

  Launchd: /Library/LaunchAgents/com.iboysoft.magicmenuguard.plist
    Command: /bin/bash -c 'while true do result=$(pluginkit -m -i com.iboysoft.swift-menu-website.SwiftMenu-Finder-Integration | grep +)   if [ -z "$result" ]  then  break  else  sleep 1  pluginkit -e ignore -i com.iboysoft.swift-menu-website.SwiftMenu-Finder-Integration  fi done  while true do result=$(pluginkit -m -i com.iboysoft.swift-menu-website.SwiftMenu-Finder-Integration | grep +)   if [ -z "$result" ]  then  sleep 1  pluginkit -e use -i com.iboysoft.swift-menu-website.SwiftMenu-Finder-Integration  else  break  fi done'
    Details: Gatekeeper bypass

  Launchd: /Library/LaunchAgents/com.oracle.java.Java-Updater.plist
    Command: /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Resources/Java Updater.app/Contents/MacOS/Java Updater -bgcheck
    Details: Exact match found in the legitimate list - probably OK

  Launchd: /Library/LaunchDaemons/com.docker.socket.plist
    Command: /Library/PrivilegedHelperTools/com.docker.socket ~/.docker/run/docker.sock /var/run/docker.sock

  Launchd: /Library/LaunchDaemons/com.microsoft.OneDriveStandaloneUpdaterDaemon.plist
    Executable: /Applications/OneDrive.app/Contents/StandaloneUpdaterDaemon.xpc/Contents/MacOS/StandaloneUpdaterDaemon
    Details: Exact match found in the legitimate list - probably OK

  Launchd: /Library/LaunchAgents/com.macuncleheic.export.plist
    Executable: ~/HEICConverter/HEICConverterUninstall.sh
    Details: Gatekeeper bypass

  Apps: 5

System Launch Daemons:
  [Not Loaded]  41 Apple tasks
  [Loaded]  217 Apple tasks
  [Running]  150 Apple tasks
  [Other]  2 Apple tasks

System Launch Agents:
  [Not Loaded]  20 Apple tasks
  [Loaded]  233 Apple tasks
  [Running]  193 Apple tasks

Launch Daemons:
  [Running] com.apphousekitchen.aldente-pro.helper.plist (David Wernhart - installed 2024-11-15)
    Executable: /Library/PrivilegedHelperTools/com.apphousekitchen.aldente-pro.helper

  [Loaded] com.docker.socket.plist (Not signed - installed 2023-11-17)
    Command: /Library/PrivilegedHelperTools/com.docker.socket ~/.docker/run/docker.sock /var/run/docker.sock

  [Running] com.docker.vmnetd.plist (Docker Inc - installed 2023-11-17)
    Executable: /Library/PrivilegedHelperTools/com.docker.vmnetd

  [Other] com.expressvpn.expressvpnd.plist (Not signed - installed 2023-04-20)
    Executable: /Applications/ExpressVPN.app/Contents/MacOS/expressvpnd

  [Running] com.foxit.PDFReaderUpdateService.plist (Foxit Corporation - installed 2023-11-21)
    Executable: /Applications/Foxit PDF Reader.app/Contents/MacOS/FoxitPDFReaderUpdateService.app/Contents/MacOS/FoxitPDFReaderUpdateService

  [Other] com.iboysoft.magicmenud.plist (Not signed - installed 2022-11-05)
    Executable: /Applications/iBoysoft MagicMenu.app/Contents/MacOS/magicmenud.app/Contents/MacOS/magicmenud

  [Running] com.iboysoft.uninstall.plist (Chengdu Aibo Tech Co., Ltd. - installed 2023-05-25)
    Command: ~/Library/Group Containers/group.com.iboysoft.swift-menu/SupportingFiles/InstalledExtensions/AppUninstaller.magicmenux/Uninstall.app/Contents/Frameworks/uninstallDaemon loadBySystem

  [Running] com.logi.optionsplus.updater.plist (Logitech Inc. - installed 2025-02-04)
    Executable: /Library/Application Support/Logitech.localized/LogiOptionsPlus/logioptionsplus_agent.app/Contents/Frameworks/logioptionsplus_updater.app/Contents/MacOS/logioptionsplus_updater

  [Loaded] com.microsoft.OneDriveStandaloneUpdaterDaemon.plist (Not signed - installed 2023-02-22)
    Executable: /Applications/OneDrive.app/Contents/StandaloneUpdaterDaemon.xpc/Contents/MacOS/StandaloneUpdaterDaemon

  [Loaded] com.microsoft.OneDriveUpdaterDaemon.plist (Not signed - installed 2023-02-22)
    Executable: /Applications/OneDrive.app/Contents/OneDriveUpdaterDaemon.xpc/Contents/MacOS/OneDriveUpdaterDaemon

  [Not Loaded] com.microsoft.autoupdate.helper.plist (Microsoft Corporation - installed 2025-01-07)
    Executable: /Library/PrivilegedHelperTools/com.microsoft.autoupdate.helper
    Location: /Library/Application Support/Microsoft/MAU2.0/Microsoft AutoUpdate.app

  [Loaded] com.microsoft.autoupdate.helper.plist (Microsoft Corporation - installed 2025-01-07)
    Executable: /Library/PrivilegedHelperTools/com.microsoft.autoupdate.helper

  [Loaded] com.microsoft.office.licensingV2.helper.plist (Microsoft Corporation - installed 2023-10-20)
    Executable: /Library/PrivilegedHelperTools/com.microsoft.office.licensingV2.helper

  [Not Loaded] com.oracle.java.Helper-Tool.plist (Not signed - Not found!)
    

  [Not Loaded] com.piriform.ccleaner.engine.xpc.plist (Piriform Ltd - installed 2024-04-09)
    Executable: /Applications/CCleaner.app/Contents/Frameworks/CleaningEngine.framework/XPCServices/com.piriform.ccleaner.engine.xpc

  [Not Loaded] com.piriform.ccleaner.services.submit.plist (Piriform Ltd - installed 2024-04-09)
    Executable: /Applications/CCleaner.app/Contents/PlugIns/Services.framework/Versions/Current/com.piriform.ccleaner.services.crashReporter

  [Not Loaded] com.piriform.ccleaner.services.xpc.plist (Piriform Ltd - installed 2024-04-09)
    Executable: /Applications/CCleaner.app/Contents/PlugIns/Services.framework/XPCServices/com.piriform.ccleaner.services.xpc

  [Not Loaded] com.piriform.ccleaner.uninstall.plist (Piriform Ltd - installed 2024-04-09)
    Executable: /Applications/CCleaner.app/Contents/Uninstaller.app/Contents/XPCServices/com.piriform.ccleaner.uninstall.helper

  [Not Loaded] com.piriform.ccleaner.update.xpc.plist (Piriform Ltd - installed 2024-04-09)
    Executable: /Applications/CCleaner.app/Contents/Frameworks/com.piriform.ccleaner.update.bundle/Contents/XPCServices/com.piriform.ccleaner.update.xpc/Contents/MacOS/com.piriform.ccleaner.update.xpc

  [Other] org.filezilla-project.filezilla-server.service.plist (Not signed - installed 2023-08-09)
    Command: /Applications/FileZilla Server.app/Contents/MacOS/filezilla-server --config-dir=/Library/Preferences/org.filezilla-project.filezilla-server.service

  [Loaded] org.xquartz.privileged_startx.plist (Apple Inc. - XQuartz - installed 2023-01-26)
    Command: /opt/X11/libexec/privileged_startx -d /opt/X11/etc/X11/xinit/privileged_startx.d

  [Loaded] us.zoom.ZoomDaemon.plist (Zoom Video Communications, Inc. - installed 2024-11-18)
    Executable: /Library/PrivilegedHelperTools/us.zoom.ZoomDaemon

Launch Agents:
  [Running] com.iboysoft.magicmenuguard.plist (Not signed - installed 2025-02-04)
    Command: /bin/bash -c 'while true do result=$(pluginkit -m -i com.iboysoft.swift-menu-website.SwiftMenu-Finder-Integration | grep +)   if [ -z "$result" ]  then  break  else  sleep 1  pluginkit -e ignore -i com.iboysoft.swift-menu-website.SwiftMenu-Finder-Integration  fi done  while true do result=$(pluginkit -m -i com.iboysoft.swift-menu-website.SwiftMenu-Finder-Integration | grep +)   if [ -z "$result" ]  then  sleep 1  pluginkit -e use -i com.iboysoft.swift-menu-website.SwiftMenu-Finder-Integration  else  break  fi done'

  [Running] com.logi.optionsplus.plist (Logitech Inc. - installed 2025-02-04)
    Command: /Library/Application Support/Logitech.localized/LogiOptionsPlus/logioptionsplus_agent.app/Contents/MacOS/logioptionsplus_agent --launchd

  [Loaded] com.macuncleheic.export.plist (Not signed - installed 2024-06-05)
    Executable: ~/HEICConverter/HEICConverterUninstall.sh

  [Other] com.microsoft.OneDriveStandaloneUpdater.plist (Not signed - installed 2023-02-22)
    Executable: /Applications/OneDrive.app/Contents/StandaloneUpdater.app/Contents/MacOS/OneDriveStandaloneUpdater

  [Loaded] com.microsoft.SyncReporter.plist (Not signed - installed 2023-02-22)
    Executable: /Applications/OneDrive.app/Contents/SyncReporter.app/Contents/MacOS/SyncReporter

  [Not Loaded] com.microsoft.update.agent.plist (Microsoft Corporation - installed 2024-12-20)
    Command: /Library/Application Support/Microsoft/MAU2.0/Microsoft AutoUpdate.app/Contents/MacOS/Microsoft Update Assistant.app/Contents/MacOS/Microsoft Update Assistant --launchByAgent
    Location: /Library/Application Support/Microsoft/MAU2.0/Microsoft AutoUpdate.app

  [Loaded] com.microsoft.update.agent.plist (Microsoft Corporation - installed 2025-01-07)
    Command: /Library/Application Support/Microsoft/MAU2.0/Microsoft AutoUpdate.app/Contents/MacOS/Microsoft Update Assistant.app/Contents/MacOS/Microsoft Update Assistant --launchByAgent

  [Not Loaded] com.oracle.java.Java-Updater.plist (Not signed - installed 2024-12-04)
    Command: /Library/Internet Plug-Ins/JavaAppletPlugin.plugin/Contents/Resources/Java Updater.app/Contents/MacOS/Java Updater -bgcheck

  [Not Loaded] com.piriform.ccleaner.plist (Piriform Ltd - installed 2024-04-09)
    Command: /Applications/CCleaner.app/Contents/MacOS/CCleaner -standaloneInstanceAllowed YES

  [Not Loaded] com.piriform.ccleaner.update.plist (Piriform Ltd - installed 2024-04-09)
    Executable: /Applications/CCleaner.app/Contents/Frameworks/com.piriform.ccleaner.update.bundle/Contents/MacOS/com.piriform.ccleaner.update

  [Loaded] org.xquartz.startx.plist (Apple Inc. - XQuartz - installed 2023-01-26)
    Command: /opt/X11/libexec/launchd_startx /opt/X11/bin/startx -- /opt/X11/bin/Xquartz

User Launch Agents:
  [Loaded] com.google.GoogleUpdater.wake.plist (Google LLC - installed 2025-02-18)
    Command: ~/Library/Application Support/Google/GoogleUpdater/Current/GoogleUpdater.app/Contents/MacOS/GoogleUpdater --wake-all --enable-logging --vmodule=*/components/update_client/*=2,*/chrome/enterprise_companion/*=2,*/chrome/updater/*=2

  [Not Loaded] com.google.keystone.agent.plist (Not signed - installed 2023-12-07)
    <Empty>

  [Not Loaded] com.google.keystone.xpcservice.plist (Not signed - installed 2023-12-07)
    <Empty>

  [Loaded] com.macpaw.CleanMyMac4.Updater.plist (MacPaw Inc. - installed 2023-08-19)
    Executable: ~/Library/Application Support/CleanMyMac X/CleanMyMac X Updater.app/Contents/MacOS/CleanMyMac X Updater

  [Running] com.microsoft.msbwapp.plist (Microsoft Corporation - installed 2024-12-19)
    Executable: /Applications/Bing Wallpaper.app/Contents/MacOS/Bing Wallpaper

  [Not Loaded] com.microsoft.msbwupdater.plist (Not signed - installed 2024-12-19)
    Executable: ~/Library/Application\ Support/Microsoft/Bing\ Wallpaper/BingWallpaperAppUpdater.app

User Login Items:
  [Not Loaded] LaunchAtLoginHelper (David Wernhart - installed 2024-09-19)
    Modern Login Item
    /Applications/AlDente.app/Contents/Library/LoginItems/LaunchAtLoginHelper.app

  [Not Loaded] LaunchAtLoginHelperApp (App Store - installed 2025-01-27)
    Modern Login Item
    /Applications/Be Focused.app/Contents/Library/LoginItems/LaunchAtLoginHelperApp.app

  [Loaded] MonitorControlHelper (Joni Van Roost - installed 2023-09-10)
    Modern Login Item
    /Applications/MonitorControl.app/Contents/Library/LoginItems/MonitorControlHelper.app

  [Not Loaded] PasswordsMenuBarExtra (Apple - installed 2025-02-04)
    Modern Login Item
    /System/Applications/Passwords.app/Contents/Library/LoginItems/PasswordsMenuBarExtra.app

  [Not Loaded] WeatherMenu (Apple - installed 2025-02-04)
    Modern Login Item
    /System/Applications/Weather.app/Contents/Library/LoginItems/WeatherMenu.app

Applications:
  718 Apple apps
  90 3rd party apps
  22 x86-only apps
  5 unsigned apps

App Extensions:
  Widgets:
    [Loaded] Be Focused Widget - /Applications/Be Focused.app
    [Loaded] PowerPointWidgetKit - /Applications/Microsoft PowerPoint.app
    [Loaded] WordWidgetKit - /Applications/Microsoft Word.app
    [Loaded] ExcelWidgetKit - /Applications/Microsoft Excel.app

  Share services:
    [Loaded] Telegram - /Applications/Telegram.app

  Safari extensions:
    [Loaded] MKPlayer Extension - /Applications/MKPlayer.app
    [Loaded] Zotero Connector - /Applications/Zotero.app

  QuickLook Previews:
    [Loaded] EtreCheckQuickLook - ~/Downloads/EtreCheckPro.app
      com.etresoft.etrecheck4 *.etrecheck

Internet Plug-ins:
  JavaAppletPlugin: Java 8 Update 441 build 07 (? - installed 2025-02-05)

Audio Plug-ins:
  MSTeamsAudioDevice: 2023.31.01.2 (Microsoft Corporation - installed 2023-08-07)

3rd Party Preference panels:
  Java (? - installed 2024-12-04)
  Toolkit (Seagate Technologies LLC - installed 2023-08-09)

Backup:
  Time Machine information is limited without Full Disk Access
  Destinations: 
    T*********e [Local] (Last used)
    L***e [Local]
  3 local snapshots
  Oldest local snapshot: 2024-12-09 09:25:11
  Last local snapshot: 2025-02-17 12:44:03

Performance:
  System Load: 1.78 (1 min ago) 2.30 (5 min ago) 2.60 (15 min ago)
  Nominal I/O usage: 0.60 MB/s
  File system: 8.86 seconds
  Write speed: 2610 MB/s
  Read speed: 2870 MB/s

CPU Usage Snapshot:
  Type Overall
  System: 5 %
  User: 8 %
  Idle: 87 %

Top Processes Snapshot by CPU:
  Process (count) CPU (Source - Location)
  WindowServer 16.98 % (Apple)
  EtreCheckPro 16.38 % (Etresoft, Inc.)
  kernel_task 8.57 % (Apple)
  Google Chrome Helper (GPU) 7.64 % (Google LLC)
  Google Chrome Helper (Renderer) (127) 7.56 % (Google LLC)

Top Processes Snapshot by Memory:
  Process (count) RAM usage (Source - Location)
  Google Chrome Helper (Renderer) (127) 10.42 GB (Google LLC)
  EtreCheckPro 838 MB (Etresoft, Inc.)
  Google Chrome 455 MB (Google LLC)
  mdworker_shared (24) 384 MB (Apple)
  Notion Helper (Renderer) (6) 355 MB (Notion Labs, Incorporated)

Top Processes Snapshot by Network Use:
  Process (count) Input / Output (Source - Location)
  mDNSResponder 327 KB / 288 KB (Apple)
  ChatGPT 229 KB / 17 KB (OpenAI, L.L.C.)
  apsd 64 KB / 154 KB (Apple)
  zotero 18 KB / 15 KB (Corporation for Digital Scholarship)
  idleassetsd 8 KB / 2 KB (Apple)

Top Processes Snapshot by Energy Use:
  Process (count) Energy (0-100) (Source - Location)
  WindowServer 5 (Apple)
  Google Chrome Helper (Renderer) (127) 4 (Google LLC)
  Google Chrome Helper (GPU) 3 (Google LLC)
  Google Chrome 3 (Google LLC)
  Microsoft PowerPoint 1 (Microsoft Corporation)

Virtual Memory Information:
  Physical RAM: 16 GB

  Free RAM: 72 MB
  Used RAM: 13.38 GB
  Cached files: 2.55 GB

  Available RAM: 2.62 GB
  Swap Used: 3.34 GB

Software Installs (past 60 days):
  Install Date Name (Version)
  2025-01-07 Microsoft AutoUpdate (4.77.24121924)
  2025-01-27 Be Focused (2.4.2)
  2025-02-04 Logi Plugin Service (1.0)
  2025-02-05 Java 8 Update 441 (1.8.441.07)
  2025-02-06 XProtectPlistConfigData (5287)
  2025-02-13 Microsoft PowerPoint (16.94.25020927)
  2025-02-16 Goodnotes (6.6.10)
  2025-02-19 Telegram (11.7)
  2025-02-20 FBReader (2.1.3)
  2025-02-20 Microsoft Excel (16.94.25020927)
  2025-02-20 Microsoft Word (16.94.25020927)
  2025-02-21 Command Line Tools for Xcode (16.2)
  2025-02-21 macOS 15.3.1 (15.3.1)
  2025-02-21 RosettaUpdateAuto (1.0.0.0.1.1738696874)

Clean up:
  /Library/LaunchDaemons/com.iboysoft.magicmenud.plist
    /Applications/iBoysoft MagicMenu.app/Contents/MacOS/magicmenud.app/Contents/MacOS/magicmenud
    Executable not found
  /Library/LaunchDaemons/com.expressvpn.expressvpnd.plist
    /Applications/ExpressVPN.app/Contents/MacOS/expressvpnd
    Executable not found
  /Library/LaunchDaemons/org.filezilla-project.filezilla-server.service.plist
    /Applications/FileZilla Server.app/Contents/MacOS/filezilla-server
    Executable not found
  ~/Library/LaunchAgents/com.microsoft.msbwupdater.plist
    ~/Library/Application\ Support/Microsoft/Bing\ Wallpaper/BingWallpaperAppUpdater.app
    Executable not found
  /Library/LaunchAgents/com.microsoft.OneDriveStandaloneUpdater.plist
    /Applications/OneDrive.app/Contents/StandaloneUpdater.app/Contents/MacOS/OneDriveStandaloneUpdater
    Executable not found

Diagnostics Information (past 60 days):
  2025-02-21 11:44:36 spotlightknowledged High CPU Use (2 times)
    First occurrence: 2025-02-21 11:25:46
    Executable: /System/Library/Frameworks/CoreSpotlight.framework/spotlightknowledged

  2025-02-21 11:17:59 apfsd High CPU Use
    Executable: /usr/libexec/apfsd

  2025-02-21 11:17:31 CGPDFService High CPU Use (2 times)
    First occurrence: 2025-02-21 11:05:46
    Executable: /System/Library/Frameworks/CoreGraphics.framework/Versions/A/XPCServices/CGPDFService.xpc/Contents/MacOS/CGPDFService


End of report

Hi @scilexenko,
In my experience, RAM usage is most frequently to blame, and I see this in your report:

I would monitor that as you're running your jobs. If you're maxing out RAM, your computer as a whole will effectively grind to a halt.

It's possible that different sequencing runs will require different amounts of RAM.

Hope this helps you track it down!

1 Like

Hello Greg,

Thank you for your quick response. My bad—I was running diagnostics while the denoising process was running, which could explain the high RAM load.

I also want to point out that not only resource-heavy tasks have slowed down, but even basic commands like qiime tools view now take about 3 seconds to launch. The same goes for conda activate qiime2-2023.5, which now takes 5–10 seconds, whereas it used to take only 1–2 seconds.

I tried clearing my computer’s cache, but it didn’t seem to help. Do you think there might be an issue with my Conda environment? Would a reinstallation help, or should I reinstall Conda entirely?

Thank you for your help!

Ivan

Hi Ivan,

I would start here:

Top Processes Snapshot by Memory:
Process (count) RAM usage (Source - Location)
Google Chrome Helper (Renderer) (127) 10.42 GB (Google LLC)

If DADA2 needs > 6GB to run, you will overflow into swap and that makes everything slow!

Try closing Google Chrome when running DADA2!

You can check this with Activity Monitor. On my mac, Chrome is also using lots of ram


even basic commands like qiime tools view now take about 3 seconds to launch

That's probably not ram! :thinking:

You may have checked this already, but do you have low power mode turned on?
Spotlight > settings > battery

@scilexenko, happy to help you try to sort this out.

We did push a fix into the recent development environments that addresses slow responses from commands (like qiime --help, for example), and this will be part of the upcoming 2025.4 (April) release. If you want to try that out to see if it addresses your issue, you can find instructions for installing the most recent development version of QIIME 2 here. Want to try that and see if it addresses the issues you're experiencing?

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