Heyy, can someone help me with this, I think I am losing my mind trying figure it out :(( I am trying to run "nextflow run nf-core/differentialabundance -r 1.5.0 -resume -params-file nf-params.json -profile rnaseq,docker" but it just doesnt run. No error gets shown in the terminal. It just ends. When I checked the nextflow log - this is what it says - I am guessing the problem is here "Sep-04 211729.360 [main] DEBUG nextflow.Session - Work-dir: /mnt/d/Shivani/bulkrna_activerun/deseq2_pipeline/work [v9fs] Sep-04 211729.361 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/fl/.nextflow/assets/nf-core/differentialabundance/bin Sep-04 211729.367 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Sep-04 211729.372 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Sep-04 211729.420 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Sep-04 211729.429 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 25; maxThreads: 1000" I checked the "/home/fl/.nextflow/assets/nf-core/differentialabundance" folder and yes it does not have any bin in it. But I dont know what to do now? When I run the same thing with the test profile, it works. Entire nextflow.log: "Sep-04 211727.278 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/differentialabundance -r 1.5.0 -resume -params-file nf-params.json -profile rnaseq,docker Sep-04 211727.321 [main] DEBUG nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.4 Sep-04 211727.334 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/home/fl/.nextflow/plugins; core-plugins: nf-amazon@2.5.3,nf-azure@1.6.1,nf-cloudcache@0.4.1,nf-codecommit@0.2.1,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2-patch1,nf-tower@1.9.1,nf-wave@1.4.2-patch1 Sep-04 211727.342 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: [] Sep-04 211727.344 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: [] Sep-04 211727.347 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.12.0 in 'deployment' mode Sep-04 211727.360 [main] INFO org.pf4j.AbstractPluginManager - No plugins Sep-04 211727.367 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /home/fl/.nextflow/scm Sep-04 211727.933 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/fl/.nextflow/assets/nf-core/differentialabundance/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/differentialabundance.git Sep-04 211727.949 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory] Sep-04 211727.954 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/fl/.nextflow/assets/nf-core/differentialabundance/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/differentialabundance.git Sep-04 211728.541 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/fl/.nextflow/assets/nf-core/differentialabundance/nextflow.config Sep-04 211728.542 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/fl/.nextflow/assets/nf-core/differentialabundance/nextflow.config Sep-04 211728.546 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /home/fl/.nextflow/secrets/store.json Sep-04 211728.548 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@93501be] - activable => nextflow.secret.LocalSecretsProvider@93501be Sep-04 211728.563 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile:

rnaseq,docker

Sep-04 211729.226 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [bih, cfc_dev, uzl_omics, ifb_core, embl_hd, denbi_qbic, alice, mjolnir_globe, uppmax, maxquant, incliva, ilifu, uge, rosalind_uge, lugh, mccleary, unibe_ibu, vai, soft, test_soft, czbiohub_aws, jax, roslin, ccga_med, scw, unc_longleaf, tigem, tubingen_apg, google, apollo, ipop_up, vsc_calcua, pdc_kth, googlels, daisybio, eddie, medair, biowulf, test_maxquant, apptainer, bi, bigpurple, adcra, cedars, pawsey_setonix, vsc_kul_uhasselt, pawsey_nimbus, ucl_myriad, utd_ganymede, charliecloud, icr_davros, ceres, munin, arm, rosalind, rnaseq, hasta, cfc, uzh, ebi_codon_slurm, ebc, ccga_dx, crick, ku_sund_danhead, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, arcc, imperial, maestro, software_license, genotoul, nci_gadi, abims, janelia, nu_genomics, googlebatch, oist, sahmri, affy, mpcdf, leicester, vsc_ugent, create, sage, cambridge, jex, podman, ebi_codon, cheaha, xanadu, nyu_hpc, test, marjorie, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, einstein, ethz_euler, m3c, test_full, imb, ucl_cscluster, tuos_stanage, azurebatch, hki, crukmi, csiro_petrichor, qmul_apocrita, docker, engaging, gis, hypatia, psmn, eva, nygc, test_nogtf, fgcz, conda, crg, singularity, mpcdf_viper, self_hosted_runner, tufts, uw_hyak_pedslabs, debug, test_affy, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac] Sep-04 211729.230 [main] WARN nextflow.config.ConfigBuilder - It appears you have never run this project before -- Option

-resume

is ignored Sep-04 211729.248 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration Sep-04 211729.249 [main] DEBUG nextflow.cli.CmdRun - Launching

<https://github.com/nf-core/differentialabundance>

[clever_picasso] DSL2 - revision: 3dd360fed0 [1.5.0] Sep-04 211729.250 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation@1.1.3] Sep-04 211729.250 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[] Sep-04 211729.250 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation@1.1.3] Sep-04 211729.250 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: 1.1.3 Sep-04 211729.300 [main] INFO org.pf4j.AbstractPluginManager - Plugin 'nf-validation@1.1.3' resolved Sep-04 211729.301 [main] INFO org.pf4j.AbstractPluginManager - Start plugin 'nf-validation@1.1.3' Sep-04 211729.304 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started nf-validation@1.1.3 Sep-04 211729.331 [main] DEBUG nextflow.Session - Session UUID: 1a1a6594-de3a-4579-8b02-391ab41dee23 Sep-04 211729.331 [main] DEBUG nextflow.Session - Run name: clever_picasso Sep-04 211729.331 [main] DEBUG nextflow.Session - Executor pool size: 24 Sep-04 211729.335 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null Sep-04 211729.338 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=72; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false Sep-04 211729.347 [main] DEBUG nextflow.cli.CmdRun - Version: 24.04.4 build 5917 Created: 01-08-2024 07:05 UTC (01:05 MDT) System: Linux 5.15.153.1-microsoft-standard-WSL2 Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 11.0.24+8-post-Ubuntu-1ubuntu322.04 Encoding: UTF-8 (UTF-8) Process: 26129@Lacy-Lab [127.0.1.1] CPUs: 24 - Mem: 31.2 GB (29.3 GB) - Swap: 8 GB (8 GB) Sep-04 211729.360 [main] DEBUG nextflow.Session - Work-dir: /mnt/d/Shivani/bulkrna_activerun/deseq2_pipeline/work [v9fs] Sep-04 211729.361 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /home/fl/.nextflow/assets/nf-core/differentialabundance/bin Sep-04 211729.367 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[] Sep-04 211729.372 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory Sep-04 211729.420 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory Sep-04 211729.429 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 25; maxThreads: 1000 Sep-04 211729.495 [main] DEBUG nextflow.Session - Session start Sep-04 211729.497 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /mnt/d/Shivani/bulkrna_activerun/deseq2_pipeline/pipeline_info/execution_trace_2024-09-04_21-17-29.txt Sep-04 211729.555 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution Sep-04 211731.039 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsHelp:paramsHelp]; plugin Id: nf-validation Sep-04 211731.046 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog]; plugin Id: nf-validation Sep-04 211731.047 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters]; plugin Id: nf-validation Sep-04 211731.049 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation Sep-04 211731.049 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [fromSamplesheet:fromSamplesheet]; plugin Id: nf-validation Sep-04 211731.137 [main] INFO nextflow.Nextflow - nf-core/differentialabundance v1.5.0-g3dd360f"

Hey there, the lack of bin message should not be an issue. Can you share the nf-params.json file?

{ "input": "/mnt/d/Shivani/bulkrna_activerun/deseq2_pipeline/samplesheetdeseq.csv", "contrasts": "/mnt/d/Shivani/bulkrna_activerun/deseq2_pipeline/contrasts.csv", "outdir": "/mnt/d/Shivani/bulkrna_activerun/deseq2_pipeline", "study_abundance_type": "count", "matrix": "/mnt/d/Shivani/bulkrna_activerun/deseq2_pipeline/gene_count.tsv", "features_gtf_feature_type": "gene", "features_gtf_table_first_field": "gene_name", "affy_file_name_col": "null", "filtering_min_samples": 4, "deseq2_min_replicates_for_replace": 5, "deseq2_alpha": 0.05, "deseq2_cores": 10, "deseq2_vst_nsub": 5000, "gsea_run": true, "gsea_permute": "gene_set", "gene_sets_files": "/mnt/d/Shivani/bulkrna_activerun/deseq2_pipeline/HALLMARK_INFLAMMATORY_RESPONSE.v2024.1.Mm.gmt", "gprofiler2_organism": "musmusculus", "gprofiler2_correction_method": "gSCS", "report_title": "hypothalamus_rnaanalysis", "report_round_digits": 3, "gtf": "/mnt/d/Shivani/bulkrna_activerun/deseq2_pipeline/mouse.gtf.gz", "igenomes_ignore": true, "max_cpus": 10, "max_memory": "25.GB", "version": true, }

Hmm, not really. The only thing I can spot is that

gprofiler2_organism

should be set to

mmusculus

, but that should not cause the entire pipeline to halt. I’m wondering if this is a general nextflow issue. Is your nextflow up-to-date?

Yep I updated it. I updated docker too to see if that was the problem. But it didn't work. I'll try again today. Since the test profile works, maybe I'll run the test but with my input files and see what happens?

Well, I imagine that if you run the test with your input files, it will effectively not run the test (because your input files override the test parameters). But feel free to give it a try!

It didnt work as you said. I really dont know what to do

Hmm, so what you could do is run it again with the test profile repeatedly, each time only supplying one of your own files; that way maybe it becomes visible if any of the files is the issue. So e.g. the first run you do

nextflow run nf-core/differentialabundance -profile docker,test --input samplesheetdeseq.csv

, the next time you replace input with your contrast, then matrix, then gtf. The first three runs will probably still not work as your files will clash with the test files, but maybe the pipeline will at least “properly” fail, i.e. throw an error, instead of just doing nothing.