Fail to submit to slurm for annotating large file

[GreyGuoweiChen]

Dear Mr./Mrs,

I submit this bash script to slurm, but it fails. Could you please help to check which additional step is needed?

nextflow run EBI-Metagenomics/emg-viral-pipeline --fasta seq_test.fasta --databases nextflow-autodownload-databases --onlyannotate --length 200 -profile slurm,singularity -w high_test

Error:

Launching `https://github.com/EBI-Metagenomics/emg-viral-pipeline` [reverent_volhard] DSL2 - revision: 62d9d7bca1 [master]

ERROR ~ Cannot find latest version of nf-schema plugin

More detials:

Aug-22 17:28:59.162 [main] DEBUG nextflow.cli.Launcher - $> nextflow run EBI-Metagenomics/emg-viral-pipeline --fasta /home/gwchen3/vir_taxa/data/4_Split_3/low_genus_specific/seq_test.fasta --databases nextflow-autodownload-databases --onlyannotate --length 200 -profile local,singularity -w low_test
Aug-22 17:28:59.343 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W  ~  version 25.04.6
Aug-22 17:28:59.399 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/gwchen3/.nextflow/plugins; core-plugins: nf-amazon@2.15.0,nf-azure@1.16.0,nf-cloudcache@0.4.3,nf-codecommit@0.2.3,nf-console@1.2.1,nf-google@1.21.1,nf-k8s@1.0.0,nf-tower@1.11.4,nf-wave@1.12.1
Aug-22 17:28:59.442 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Aug-22 17:28:59.444 [main] INFO  o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Aug-22 17:28:59.448 [main] INFO  org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode
Aug-22 17:28:59.466 [main] INFO  org.pf4j.AbstractPluginManager - No plugins
Aug-22 17:28:59.483 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/gwchen3/.nextflow/scm
Aug-22 17:29:00.467 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/gwchen3/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/.git/config; branch: master; remote: origin; url: https://github.com/EBI-Metagenomics/emg-viral-pipeline.git
Aug-22 17:29:00.517 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Aug-22 17:29:00.532 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/gwchen3/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/.git/config; branch: master; remote: origin; url: https://github.com/EBI-Metagenomics/emg-viral-pipeline.git
Aug-22 17:29:00.855 [main] DEBUG nextflow.scm.AssetManager - WARN: Failed to check remote Git revision
org.eclipse.jgit.api.errors.TransportException: https://github.com/EBI-Metagenomics/emg-viral-pipeline.git: cannot open git-upload-pack
	at org.eclipse.jgit.api.LsRemoteCommand.execute(LsRemoteCommand.java:192)
	at org.eclipse.jgit.api.LsRemoteCommand.call(LsRemoteCommand.java:131)
	at nextflow.scm.AssetManager.getRemoteCommitId(AssetManager.groovy:1038)
	at nextflow.scm.AssetManager.checkRemoteStatus0(AssetManager.groovy:1049)
	at nextflow.scm.AssetManager.checkRemoteStatus(AssetManager.groovy:1067)
	at nextflow.cli.CmdRun.getScriptFile0(CmdRun.groovy:602)
	at nextflow.cli.CmdRun.getScriptFile(CmdRun.groovy:524)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:326)
	at nextflow.cli.Launcher.run(Launcher.groovy:513)
	at nextflow.cli.Launcher.main(Launcher.groovy:673)
Caused by: org.eclipse.jgit.errors.TransportException: https://github.com/EBI-Metagenomics/emg-viral-pipeline.git: cannot open git-upload-pack
	at org.eclipse.jgit.transport.TransportHttp.connect(TransportHttp.java:758)
	at org.eclipse.jgit.transport.TransportHttp.openFetch(TransportHttp.java:465)
	at org.eclipse.jgit.api.LsRemoteCommand.execute(LsRemoteCommand.java:170)
	... 9 common frames omitted
Caused by: java.net.UnknownHostException: github.com
	at java.base/sun.nio.ch.NioSocketImpl.connect(NioSocketImpl.java:567)
	at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:327)
	at java.base/java.net.Socket.connect(Socket.java:760)
	at java.base/sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:304)
	at java.base/sun.net.NetworkClient.doConnect(NetworkClient.java:178)
	at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:531)
	at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:636)
	at java.base/sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:264)
	at java.base/sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:377)
	at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:193)
	at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1288)
	at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1129)
	at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:179)
	at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1691)
	at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1615)
	at java.base/java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:531)
	at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:307)
	at org.eclipse.jgit.transport.http.JDKHttpConnection.getResponseCode(JDKHttpConnection.java:88)
	at org.eclipse.jgit.util.HttpSupport.response(HttpSupport.java:232)
	at org.eclipse.jgit.transport.TransportHttp.connect(TransportHttp.java:663)
	... 11 common frames omitted
Aug-22 17:29:00.871 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/gwchen3/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/nextflow.config
Aug-22 17:29:00.875 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/gwchen3/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/nextflow.config
Aug-22 17:29:00.887 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/gwchen3/.nextflow/secrets/store.json
Aug-22 17:29:00.891 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@2001e48c] - activable => nextflow.secret.LocalSecretsProvider@2001e48c
Aug-22 17:29:00.908 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `local,singularity`
Aug-22 17:29:01.798 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [slurm, standard, conda, singularity, local, lsf, docker]
Aug-22 17:29:01.875 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 by global default
Aug-22 17:29:01.877 [main] DEBUG nextflow.cli.CmdRun - Launching `https://github.com/EBI-Metagenomics/emg-viral-pipeline` [maniac_aryabhata] DSL2 - revision: 62d9d7bca1 [master]
Aug-22 17:29:01.880 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Aug-22 17:29:01.880 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Aug-22 17:29:01.940 [main] DEBUG nextflow.Session - Session UUID: 26311f7f-a326-4527-9568-e9ddc7267900
Aug-22 17:29:01.941 [main] DEBUG nextflow.Session - Run name: maniac_aryabhata
Aug-22 17:29:01.941 [main] DEBUG nextflow.Session - Executor pool size: 32
Aug-22 17:29:01.950 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Aug-22 17:29:01.956 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=96; workQueue=LinkedBlockingQueue[-1]; allowCoreThreadTimeout=false
Aug-22 17:29:01.977 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 25.04.6 build 5954
  Created: 01-07-2025 11:27 UTC (19:27 HKST)
  System: Linux 5.14.0-427.28.1.el9_4.x86_64
  Runtime: Groovy 4.0.26 on OpenJDK 64-Bit Server VM 23.0.2-internal-adhoc.conda.src
  Encoding: UTF-8 (UTF-8)
  Process: 3726851@cpu1 [10.10.1.61]
  CPUs: 32 - Mem: 251.8 GB (30.6 GB) - Swap: 1.8 TB (1.8 TB)
Aug-22 17:29:02.006 [main] DEBUG nextflow.Session - Work-dir: /home/gwchen3/software/low_test [nfs]
Aug-22 17:29:02.057 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Aug-22 17:29:02.068 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Aug-22 17:29:02.099 [main] DEBUG nextflow.Session - Observer factory (v2): LinObserverFactory
Aug-22 17:29:02.143 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Aug-22 17:29:02.154 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 33; maxThreads: 1000
Aug-22 17:29:02.279 [main] DEBUG nextflow.Session - Session start
Aug-22 17:29:02.286 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /home/gwchen3/software/results/pipeline_info/execution_trace_2025-08-22_17-29-01.txt
Aug-22 17:29:02.496 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Aug-22 17:29:02.611 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-schema version: latest
Aug-22 17:29:02.613 [main] ERROR o.p.update.DefaultUpdateRepository - raw.githubusercontent.com
java.net.UnknownHostException: raw.githubusercontent.com
	at java.base/sun.nio.ch.NioSocketImpl.connect(NioSocketImpl.java:567)
	at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:327)
	at java.base/java.net.Socket.connect(Socket.java:760)
	at java.base/sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:304)
	at java.base/sun.security.ssl.BaseSSLSocketImpl.connect(BaseSSLSocketImpl.java:181)
	at java.base/sun.net.NetworkClient.doConnect(NetworkClient.java:183)
	at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:531)
	at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:636)
	at java.base/sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:264)
	at java.base/sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:377)
	at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:193)
	at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1243)
	at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1129)
	at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:179)
	at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1691)
	at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1615)
	at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:223)
	at java.base/java.net.URL.openStream(URL.java:1325)
	at org.pf4j.update.DefaultUpdateRepository.initPlugins(DefaultUpdateRepository.java:96)
	at org.pf4j.update.DefaultUpdateRepository.getPlugins(DefaultUpdateRepository.java:80)
	at org.pf4j.update.UpdateManager.getPluginsMap(UpdateManager.java:149)
	at org.pf4j.update.UpdateManager.getLastPluginRelease(UpdateManager.java:392)
	at nextflow.plugin.PluginUpdater.load0(PluginUpdater.groovy:359)
	at nextflow.plugin.PluginUpdater.installPlugin(PluginUpdater.groovy:224)
	at nextflow.plugin.PluginUpdater.prepareAndStart(PluginUpdater.groovy:171)
	at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:399)
	at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:374)
	at nextflow.plugin.PluginsFacade.startIfMissing(PluginsFacade.groovy:515)
	at nextflow.plugin.Plugins.startIfMissing(Plugins.groovy:90)
	at nextflow.script.IncludeDef.loadPlugin0(IncludeDef.groovy:231)
	at nextflow.script.IncludeDef.load0(IncludeDef.groovy:105)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at Script_b18a67dc892ccc43.runScript(Script_b18a67dc892ccc43:8)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.script.BaseScript.run0(BaseScript.groovy:159)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.script.BaseScript.run(BaseScript.groovy:193)
	at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy:246)
	at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy)
	at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:246)
	at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:139)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:379)
	at nextflow.cli.Launcher.run(Launcher.groovy:513)
	at nextflow.cli.Launcher.main(Launcher.groovy:673)
Aug-22 17:29:02.614 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
  Script_5be97259b96d1d39: /home/gwchen3/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/modules/local/warnings.nf
  Script_b18a67dc892ccc43: /home/gwchen3/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/main.nf
  Script_d220be531a56f940: /home/gwchen3/.nextflow/assets/EBI-Metagenomics/emg-viral-pipeline/modules/local/help.nf
Aug-22 17:29:02.615 [main] DEBUG nextflow.Session - Session aborted -- Cause: Cannot find latest version of nf-schema plugin
Aug-22 17:29:02.629 [main] ERROR nextflow.cli.Launcher - @unknown
java.lang.IllegalStateException: Cannot find latest version of nf-schema plugin
	at nextflow.plugin.PluginUpdater.load0(PluginUpdater.groovy:371)
	at nextflow.plugin.PluginUpdater.installPlugin(PluginUpdater.groovy:224)
	at nextflow.plugin.PluginUpdater.prepareAndStart(PluginUpdater.groovy:171)
	at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:399)
	at nextflow.plugin.PluginsFacade.start(PluginsFacade.groovy:374)
	at nextflow.plugin.PluginsFacade.startIfMissing(PluginsFacade.groovy:515)
	at nextflow.plugin.Plugins.startIfMissing(Plugins.groovy:90)
	at nextflow.script.IncludeDef.loadPlugin0(IncludeDef.groovy:231)
	at nextflow.script.IncludeDef.load0(IncludeDef.groovy:105)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at Script_b18a67dc892ccc43.runScript(Script_b18a67dc892ccc43:8)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.script.BaseScript.run0(BaseScript.groovy:159)
	at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
	at nextflow.script.BaseScript.run(BaseScript.groovy:193)
	at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy:246)
	at nextflow.script.parser.v1.ScriptLoaderV1.runScript(ScriptLoaderV1.groovy)
	at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:246)
	at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:139)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:379)
	at nextflow.cli.Launcher.run(Launcher.groovy:513)
	at nextflow.cli.Launcher.main(Launcher.groovy:673)

Best,
Guowei

[KateSakharova]

Hi @GreyGuoweiChen ,
have you tried installing plugin?
nextflow plugin install nf-schema@2.4.2
Best,
Kate

[GreyGuoweiChen]

Hi @KateSakharova ,

Thanks for your timely reply.
I have tied your command, I suppose I have install that package, because no message is replied from teminal.
And then, it doesn't work after this command.

Best,
Guowei

[GreyGuoweiChen]

And you know what...
I can run the command locally.

nextflow run EBI-Metagenomics/emg-viral-pipeline --fasta seq_test.fasta --databases nextflow-autodownload-databases --onlyannotate --length 200 -profile local,singularity -w high_test

Best,
Guowei

[KateSakharova]

I feel it is issue with your execution engine/cluster but not with pipeline... Have you tried installing nextflow into venv or conda env?

[GreyGuoweiChen]

I did install nextflow in conda. And I run both command under the same environment.

When I said "I can run the command locally.", it means in the login node in the server. But this doesn't work in the computation node. Kind of strange...

Guowei

[mberacochea]

Hi @GreyGuoweiChen

It looks like Nextflow is having issues pulling the pipeline code:

Aug-22 17:29:00.855 [main] DEBUG nextflow.scm.AssetManager - WARN: Failed to check remote Git revision
org.eclipse.jgit.api.errors.TransportException: https://github.com/EBI-Metagenomics/emg-viral-pipeline.git: cannot open git-upload-pack
	at org.eclipse.jgit.api.LsRemoteCommand.execute(LsRemoteCommand.java:192)

Have you tried removing your .nextflow folder in your home folder? (~/.nextflow/assets/ebi-metagenomics/emg-viral-pipeline/).

Also, it is recommended to use the -r flag to pull releases of the pipeline instead of running from the master branch.

Something like:

nextflow run EBI-Metagenomics/emg-viral-pipeline \
-r v3.0.1 \
--fasta seq_test.fasta \
--databases nextflow-autodownload-databases \
--onlyannotate \
--length 200 \
-profile slurm,singularity \
-w high_test