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Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode) terminated with an error exit status (125) #252

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dgoswamia opened this issue Mar 15, 2024 · 4 comments
Closed

Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode) terminated with an error exit status (125) #252

dgoswamia opened this issue Mar 15, 2024 · 4 comments
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@dgoswamia
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dgoswamia commented Mar 15, 2024 •
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Description of the bug

[issue in downloading](docker: failed to register layer: rename /docker/image/overlay2/layerdb/tmp/write-set-2818107168 /docker/image/overlay2/layerdb/sha256/968f331861f0ab0535ba337d320dac4aaca7ee4b11048be407a4dbd4915004f5: file exists.)

even tried Conda and Singularity same issue for biocontainers/atlas-gene-annotation-manipulation

Command used and terminal output

nextflow run nf-core/differentialabundance \
     --input user1/running_nextflow/differentialabundance/input_data/samplesheet_copy/samplesheet_RNASeq_v2.csv \
     --contrasts user1/running_nextflow/differentialabundance/input_data/contrasts_observations/contrasts_file.csv \
     --matrix user1/running_nextflow/differentialabundance/input_data/countmatrix/salmon.merged.gene_counts.tsv \
     --gtf user1/running_nextflow/differentialabundance/input_data/gtf_annotation/gencode.v21.ATP.chr_patch_hapl_scaff.annotation.gtf \
     --outdir user1/running_nextflow/differentialabundance/output_03_14_2024 \
     -profile rnaseq,docker \
     -r 1.4.0

Relevant files

.nextflow.log

Mar-15 15:44:18.892 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/differentialabundance --input user1/running_nextflow/differentialabundance/input_data/samplesheet_copy/samplesheet_RNASeq_v2.csv --contrasts user1/running_nextflow/differentialabundance/input_data/contrasts_observations/contrasts_file.csv --matrix user1/running_nextflow/differentialabundance/input_data/countmatrix/salmon.merged.gene_counts.tsv --gtf user1/running_nextflow/differentialabundance/input_data/gtf_annotation/gencode.v21.ATP.chr_patch_hapl_scaff.annotation.gtf --outdir user1/running_nextflow/differentialabundance/output_03_14_2024 -profile rnaseq,docker -r 1.4.0
Mar-15 15:44:19.065 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.10.1
Mar-15 15:44:19.084 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=user1/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Mar-15 15:44:19.101 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Mar-15 15:44:19.104 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Mar-15 15:44:19.107 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Mar-15 15:44:19.119 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Mar-15 15:44:19.132 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: user1/.nextflow/scm
Mar-15 15:44:19.157 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Mar-15 15:44:19.165 [main] INFO nextflow.cli.CmdRun - Pulling nf-core/differentialabundance ...
Mar-15 15:44:19.166 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/differentialabundance/contents/nextflow.config?ref=1.4.0
Mar-15 15:44:20.373 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/differentialabundance/contents/main.nf?ref=1.4.0
Mar-15 15:44:20.428 [main] DEBUG nextflow.scm.RepositoryProvider - Request [credentials -:-] -> https://api.github.com/repos/nf-core/differentialabundance
Mar-15 15:44:20.493 [main] DEBUG nextflow.scm.AssetManager - Pulling nf-core/differentialabundance -- Using remote clone url: https://github.com/nf-core/differentialabundance.git
Mar-15 15:44:27.386 [main] INFO nextflow.cli.CmdRun - downloaded from https://github.com/nf-core/differentialabundance.git
Mar-15 15:44:27.429 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: user1/.nextflow/assets/nf-core/differentialabundance/nextflow.config
Mar-15 15:44:27.430 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: user1/.nextflow/assets/nf-core/differentialabundance/nextflow.config
Mar-15 15:44:27.440 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: rnaseq,docker
Mar-15 15:44:28.671 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [cfc_dev, uzl_omics, ifb_core, denbi_qbic, alice, mjolnir_globe, uppmax, incliva, ilifu, uge, rosalind_uge, lugh, unibe_ibu, vai, soft, test_soft, czbiohub_aws, jax, 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, ku_sund_dangpu, ccga_dx, crick, marvin, biohpc_gen, shifter, mana, mamba, york_viking, unc_lccc, wehi, awsbatch, wustl_htcf, imperial, maestro, software_license, utd_europa, 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, computerome, ucd_sonic, seg_globe, sanger, dkfz, pasteur, 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, self_hosted_runner, tufts, uw_hyak_pedslabs, utd_sysbio, debug, test_affy, genouest, cbe, phoenix, gitpod, seawulf, uod_hpc, fub_curta, uct_hpc, aws_tower, binac]
Mar-15 15:44:28.711 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Mar-15 15:44:28.711 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/nf-core/differentialabundance [magical_northcutt] DSL2 - revision: a3d664c [1.4.0]
Mar-15 15:44:28.712 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins declared=[nf-validation]
Mar-15 15:44:28.712 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Mar-15 15:44:28.712 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[nf-validation]
Mar-15 15:44:28.712 [main] DEBUG nextflow.plugin.PluginUpdater - Installing plugin nf-validation version: latest
Mar-15 15:44:28.822 [main] INFO org.pf4j.AbstractPluginManager - Plugin '[email protected]' resolved
Mar-15 15:44:28.822 [main] INFO org.pf4j.AbstractPluginManager - Start plugin '[email protected]'
Mar-15 15:44:28.840 [main] DEBUG nextflow.plugin.BasePlugin - Plugin started [email protected]
Mar-15 15:44:28.850 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: user1/.nextflow/secrets/store.json
Mar-15 15:44:28.853 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@6fcc0a1] - activable => nextflow.secret.LocalSecretsProvider@6fcc0a1
Mar-15 15:44:28.903 [main] DEBUG nextflow.Session - Session UUID: 3de3d34e-a1bb-4079-9827-22319e12cfd9
Mar-15 15:44:28.903 [main] DEBUG nextflow.Session - Run name: magical_northcutt
Mar-15 15:44:28.903 [main] DEBUG nextflow.Session - Executor pool size: 32
Mar-15 15:44:28.909 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Mar-15 15:44:28.934 [main] DEBUG nextflow.cli.CmdRun -
Version: 23.10.1 build 5891
Created: 12-01-2024 22:01 UTC (17:01 EDT)
System: Linux 4.14.322-244.536.amzn2.x86_64
Runtime: Groovy 3.0.19 on Java HotSpot(TM) 64-Bit Server VM 21.0.2+13-LTS-58
Encoding: UTF-8 (UTF-8)
Process: 24845@aff-linux-03 [10.100.6.50]
CPUs: 32 - Mem: 123.1 GB (115.7 GB) - Swap: 24 GB (24 GB) - Virtual threads ON
Mar-15 15:44:29.013 [main] DEBUG nextflow.Session - Work-dir: user1/running_nextflow/differentialabundance/work [nfs]
Mar-15 15:44:29.031 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Mar-15 15:44:29.042 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Mar-15 15:44:29.131 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Mar-15 15:44:29.139 [main] DEBUG nextflow.util.CustomPoolFactory - Creating virtual thread pool
Mar-15 15:44:29.374 [main] DEBUG nextflow.Session - Session start
Mar-15 15:44:29.378 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: user1/running_nextflow/differentialabundance/output_03_14_2024/pipeline_info/execution_trace_2024-03-15_15-44-28.txt
Mar-15 15:44:29.400 [main] DEBUG nextflow.Session - Using default localLib path: user1/.nextflow/assets/nf-core/differentialabundance/lib
Mar-15 15:44:29.404 [main] DEBUG nextflow.Session - Adding to the classpath library: user1/.nextflow/assets/nf-core/differentialabundance/lib
Mar-15 15:44:29.405 [main] DEBUG nextflow.Session - Adding to the classpath library: user1/.nextflow/assets/nf-core/differentialabundance/lib/nfcore_external_java_deps.jar
Mar-15 15:44:29.801 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Mar-15 15:44:29.819 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [validateParameters:validateParameters, paramsHelp:paramsHelp]; plugin Id: nf-validation
Mar-15 15:44:29.864 [main] DEBUG nextflow.validation.SchemaValidator - Starting parameters validation
Mar-15 15:44:30.026 [main] DEBUG nextflow.validation.SchemaValidator - Starting validation: 'input': 'user1/running_nextflow/differentialabundance/input_data/samplesheet_copy/samplesheet_RNASeq_v2.csv' with 'user1/.nextflow/assets/nf-core/differentialabundance/assets/schema_input.json'
Mar-15 15:44:30.071 [main] DEBUG nextflow.validation.SchemaValidator - Validation passed: 'input': 'user1/running_nextflow/differentialabundance/input_data/samplesheet_copy/samplesheet_RNASeq_v2.csv' with 'user1/.nextflow/assets/nf-core/differentialabundance/assets/schema_input.json'
Mar-15 15:44:30.071 [main] DEBUG nextflow.validation.SchemaValidator - Finishing parameters validation
Mar-15 15:44:30.986 [main] DEBUG nextflow.script.IncludeDef - Loading included plugin extensions with names: [paramsSummaryLog:paramsSummaryLog, paramsSummaryMap:paramsSummaryMap]; plugin Id: nf-validation
Mar-15 15:44:31.005 [main] INFO nextflow.Nextflow -

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,'
nf-core/differentialabundance v1.4.0-ga3d664c

Core Nextflow options
revision : 1.4.0
runName : magical_northcutt
containerEngine : docker
container : [RMARKDOWNNOTEBOOK:biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0]
launchDir : user1/running_nextflow/differentialabundance
workDir : user1/running_nextflow/differentialabundance/work
projectDir : user1/.nextflow/assets/nf-core/differentialabundance
userName : wami
profile : rnaseq,docker
configFiles :

Input/output options
input : user1/running_nextflow/differentialabundance/input_data/samplesheet_copy/samplesheet_RNASeq_v2.csv
contrasts : user1/running_nextflow/differentialabundance/input_data/contrasts_observations/contrasts_file.csv
outdir : user1/running_nextflow/differentialabundance/output_03_14_2024

Abundance values
matrix : user1/running_nextflow/differentialabundance/input_data/countmatrix/salmon.merged.gene_counts.tsv
affy_cel_files_archive : null
querygse : null

Affy input options
affy_cdfname : null

Proteus input options
proteus_round_digits : -1

Filtering
filtering_min_abundance : 1
filtering_min_samples : 1

Differential analysis
differential_min_fold_change: 2
differential_max_pval : 1

Limma specific options (microarray only)
limma_spacing : null
limma_block : null
limma_correlation : null
limma_p_value : 1

GSEA
gsea_gene_sets : null

Shiny app settings
shinyngs_shinyapps_account : null
shinyngs_shinyapps_app_name : null

Reporting options
report_file : user1/.nextflow/assets/nf-core/differentialabundance/assets/differentialabundance_report.Rmd
logo_file : user1/.nextflow/assets/nf-core/differentialabundance/docs/images/nf-core-differentialabundance_logo_light.png
css_file : user1/.nextflow/assets/nf-core/differentialabundance/assets/nf-core_style.css
citations_file : user1/.nextflow/assets/nf-core/differentialabundance/CITATIONS.md
report_title : null
report_author : null
report_description : null

Reference genome options
gtf : user1/running_nextflow/differentialabundance/input_data/gtf_annotation/gencode.v21.ATP.chr_patch_hapl_scaff.annotation.gtf

Institutional config options
config_profile_name : RNA-seq profile
config_profile_description : Settings for RNA-seq analysis

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/differentialabundance for your analysis please cite:

Mar-15 15:44:33.190 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE
Mar-15 15:44:33.193 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:GTF_TO_TABLE matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE
Mar-15 15:44:33.200 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.201 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.205 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Mar-15 15:44:33.211 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=32; memory=123.1 GB; capacity=32; pollInterval=100ms; dumpInterval=5m
Mar-15 15:44:33.213 [main] DEBUG n.processor.TaskPollingMonitor - >>> barrier register (monitor: local)
Mar-15 15:44:33.294 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR
Mar-15 15:44:33.294 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:VALIDATOR matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR
Mar-15 15:44:33.296 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.296 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.306 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER
Mar-15 15:44:33.306 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:CUSTOM_MATRIXFILTER matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER
Mar-15 15:44:33.307 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.307 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.318 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM
Mar-15 15:44:33.318 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DESEQ2_DIFFERENTIAL matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM
Mar-15 15:44:33.319 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DESEQ2_NORM matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM
Mar-15 15:44:33.320 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.320 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.325 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL
Mar-15 15:44:33.325 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DESEQ2_DIFFERENTIAL matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL
Mar-15 15:44:33.326 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.326 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.354 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY
Mar-15 15:44:33.355 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:PLOT_EXPLORATORY matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY
Mar-15 15:44:33.356 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.356 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.362 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL
Mar-15 15:44:33.362 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:PLOT_DIFFERENTIAL matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL
Mar-15 15:44:33.363 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.363 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.398 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS
Mar-15 15:44:33.398 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:CUSTOM_DUMPSOFTWAREVERSIONS matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS
Mar-15 15:44:33.400 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.400 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.451 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP
Mar-15 15:44:33.451 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:SHINYNGS_APP matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP
Mar-15 15:44:33.452 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.452 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.462 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK
Mar-15 15:44:33.462 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:RMARKDOWNNOTEBOOK matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK
Mar-15 15:44:33.463 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.463 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.470 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_single matches labels process_single for process with name NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE
Mar-15 15:44:33.470 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:MAKE_REPORT_BUNDLE matches process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE
Mar-15 15:44:33.471 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Mar-15 15:44:33.471 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Mar-15 15:44:33.474 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: ZIP, VALIDATOR, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER, CUSTOM_TABULARTOGSEAGCT, ATLASGENEANNOTATIONMANIPULATION_GTF2FEATUREANNOTATION, MAKE_REPORT_BUNDLE, PLOT_DIFFERENTIAL, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM, GSEA_GSEA, SHINYNGS_VALIDATEFOMCOMPONENTS, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP, GUNZIP_GTF, AFFY_JUSTRMA, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS, CUSTOM_TABULARTOGSEACLS, TABULAR_TO_GSEA_CHIP, GUNZIP, SHINYNGS_STATICDIFFERENTIAL, UNTAR, AFFY_JUSTRMA_RAW, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK, GEOQUERY_GETGEO, GTF_TO_TABLE, PROTEUS_READPROTEINGROUPS, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE, DESEQ2_DIFFERENTIAL, SHINYNGS_STATICEXPLORATORY, DESEQ2_NORM, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL, RMARKDOWNNOTEBOOK, LIMMA_DIFFERENTIAL, SHINYNGS_APP, CUSTOM_DUMPSOFTWAREVERSIONS, CUSTOM_MATRIXFILTER, PLOT_EXPLORATORY, PROTEUS, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY, AFFY_JUSTRMA_NORM, NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL
Mar-15 15:44:33.477 [main] DEBUG nextflow.Session - Igniting dataflow network (19)
Mar-15 15:44:33.478 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE
Mar-15 15:44:33.479 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR
Mar-15 15:44:33.479 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER
Mar-15 15:44:33.479 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM
Mar-15 15:44:33.480 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL
Mar-15 15:44:33.480 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY
Mar-15 15:44:33.480 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL
Mar-15 15:44:33.480 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS
Mar-15 15:44:33.481 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP
Mar-15 15:44:33.482 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK
Mar-15 15:44:33.482 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE
Mar-15 15:44:33.482 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_736359fe28427d7c: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/main.nf
Script_0b2b547b5bd8d72f: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/deseq2/differential/main.nf
Script_8258fa18ec202f1e: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/geoquery/getgeo/main.nf
Script_bd162165863945c5: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/shinyngs/validatefomcomponents/main.nf
Script_fd29bcfb844eda4d: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/limma/differential/main.nf
Script_e11ffbac6afe36ec: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/gsea/gsea/main.nf
Script_c3c7f0ae80cda0cc: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/shinyngs/staticexploratory/main.nf
Script_66ffa6df5b55d922: user1/.nextflow/assets/nf-core/differentialabundance/main.nf
Script_f291caf4f7573aca: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/custom/tabulartogseagct/main.nf
Script_af0fb319323fde68: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/affy/justrma/main.nf
Script_61045595cd57fdfa: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/custom/tabulartogseacls/main.nf
Script_a9670c657bdfaa03: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/local/tabular_to_gsea_chip.nf
Script_cb1a92e48950cb6f: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/shinyngs/app/main.nf
Script_36fafb73beaa89a0: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/rmarkdownnotebook/main.nf
Script_1a6661f1fced92e0: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/rmarkdownnotebook/./parametrize.nf
Script_980ffca4de0b9bc8: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/shinyngs/staticdifferential/main.nf
Script_c901260d3c3d641a: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/custom/matrixfilter/main.nf
Script_777604ec37a36f79: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/custom/dumpsoftwareversions/main.nf
Script_66471300492dce16: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/differentialabundance.nf
Script_7002cd4537b0f229: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/proteus/readproteingroups/main.nf
Script_079385570c0cda9d: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/untar/main.nf
Script_b4abc93ac1f4bba3: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/zip/main.nf
Script_a71c717f63173976: user1/.nextflow/assets/nf-core/differentialabundance/./workflows/../modules/nf-core/gunzip/main.nf
Mar-15 15:44:33.482 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Mar-15 15:44:33.482 [main] DEBUG nextflow.Session - Session await
Mar-15 15:44:33.670 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
Mar-15 15:44:33.671 [Task submitter] INFO nextflow.Session - [4e/d2b80a] Submitted process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode)
Mar-15 15:44:36.668 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode); status: COMPLETED; exit: 125; error: -; workDir: user1/running_nextflow/differentialabundance/work/4e/d2b80aa5a32f2e96b04e5e9e0edc49]
Mar-15 15:44:36.671 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
task: name=NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode); work-dir=user1/running_nextflow/differentialabundance/work/4e/d2b80aa5a32f2e96b04e5e9e0edc49
error [nextflow.exception.ProcessFailedException]: Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode) terminated with an error exit status (125)
Mar-15 15:44:36.685 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode)'

Caused by:
Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode) terminated with an error exit status (125)

Command executed:

gtf2featureAnnotation.R
--gtf-file gencode.v21.ATP.chr_patch_hapl_scaff.annotation.gtf
--output-file gencode.anno.tsv

--feature-type 'transcript' --first-field 'gene_id'

cat <<-END_VERSIONS > versions.yml
"NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE":
r-base: $(echo $(R --version 2>&1) | sed 's/^.R version //; s/ .$//')
atlas-gene-annotation-manipulation: 1.1.0
END_VERSIONS

Command exit status:
125

Command output:
(empty)

Command error:
Unable to find image 'quay.io/biocontainers/atlas-gene-annotation-manipulation:1.1.0--hdfd78af_0' locally
1.1.0--hdfd78af_0: Pulling from biocontainers/atlas-gene-annotation-manipulation
c1a16a04cedd: Pulling fs layer
4ca545ee6d5d: Pulling fs layer
4e62a07e3f97: Pulling fs layer
4ca545ee6d5d: Verifying Checksum
4ca545ee6d5d: Download complete
c1a16a04cedd: Download complete
4e62a07e3f97: Verifying Checksum
4e62a07e3f97: Download complete
docker: failed to register layer: rename /docker/image/overlay2/layerdb/tmp/write-set-2818107168 /docker/image/overlay2/layerdb/sha256/968f331861f0ab0535ba337d320dac4aaca7ee4b11048be407a4dbd4915004f5: file exists.
See 'docker run --help'.

Work dir:
user1/running_nextflow/differentialabundance/work/4e/d2b80aa5a32f2e96b04e5e9e0edc49

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
Mar-15 15:44:36.700 [Actor Thread 177] DEBUG nextflow.file.SortFileCollector - FileCollector temp dir not removed: null
Mar-15 15:44:36.701 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Mar-15 15:44:36.703 [main] DEBUG nextflow.Session - Session await > all processes finished
Mar-15 15:44:36.716 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: local) - terminating tasks monitor poll loop
Mar-15 15:44:36.716 [main] DEBUG nextflow.Session - Session await > all barriers passed
Mar-15 15:44:36.772 [main] INFO nextflow.Nextflow - -[nf-core/differentialabundance] Pipeline completed with errors-
Mar-15 15:44:36.776 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=2.9s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=1; peakCpus=1; peakMemory=6 GB; ]
Mar-15 15:44:36.776 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Mar-15 15:44:36.778 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Mar-15 15:44:37.548 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Mar-15 15:44:37.813 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Mar-15 15:44:37.813 [main] INFO org.pf4j.AbstractPluginManager - Stop plugin '[email protected]'
Mar-15 15:44:37.814 [main] DEBUG nextflow.plugin.BasePlugin - Plugin stopped nf-validation
Mar-15 15:44:37.877 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Mar-15 15:44:37.878 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System information

Nextflow version 23.10.1
Hardware AWS EC2 instance
Executor local
Container engine: Docker, Singularity, Conda
OS CentOS
Version of nf-core/differentialabundance 1.4.0
@dgoswamia dgoswamia added the bug Something isn't working label Mar 15, 2024
@dgoswamia
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dgoswamia commented Mar 16, 2024 •
edited
Loading

change profile to
profile : rnaseq,conda

still a similar error with atlas gene annotation manipulation package

N E X T F L O W ~ version 23.10.1
Launching https://github.com/nf-core/differentialabundance [friendly_heyrovsky] DSL2 - revision: a3d664c [master]
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
There is a problem with your Conda configuration!

You will need to set-up the conda-forge and bioconda channels correctly.
Please refer to https://bioconda.github.io/
The observed channel order is
[defaults]
but the following channel order is required:
[conda-forge, bioconda, defaults]



------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/differentialabundance v1.4.0-ga3d664c
------------------------------------------------------
Core Nextflow options
  revision                    : master
  runName                     : friendly_heyrovsky
  container                   : [RMARKDOWNNOTEBOOK:biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0]
  launchDir                   : /user1/running_nextflow/differentialabundance
  workDir                     : /user1/running_nextflow/differentialabundance/work
  projectDir                  : /user1/.nextflow/assets/nf-core/differentialabundance
  userName                    : wami
  profile                     : rnaseq,conda
  configFiles                 : 

Input/output options
  input                       : input_data/samplesheet_copy/samplesheet_RNASeq_v2.csv
  contrasts                   : input_data/contrasts_observations/contrasts_file.csv
  outdir                      : input_data/output_03_14_2024

Abundance values
  matrix                      : input_data/countmatrix/salmon.merged.gene_counts.tsv
  affy_cel_files_archive      : null
  querygse                    : null

Affy input options
  affy_cdfname                : null

Proteus input options
  proteus_round_digits        : -1

Filtering
  filtering_min_abundance     : 1
  filtering_min_samples       : 1

Differential analysis
  differential_min_fold_change: 2
  differential_max_pval       : 1

Limma specific options (microarray only)
  limma_spacing               : null
  limma_block                 : null
  limma_correlation           : null
  limma_p_value               : 1

GSEA
  gsea_gene_sets              : null

Shiny app settings
  shinyngs_shinyapps_account  : null
  shinyngs_shinyapps_app_name : null

Reporting options
  report_file                 : /user1/.nextflow/assets/nf-core/differentialabundance/assets/differentialabundance_report.Rmd
  logo_file                   : /user1/.nextflow/assets/nf-core/differentialabundance/docs/images/nf-core-differentialabundance_logo_light.png
  css_file                    : /user1/.nextflow/assets/nf-core/differentialabundance/assets/nf-core_style.css
  citations_file              : /user1/.nextflow/assets/nf-core/differentialabundance/CITATIONS.md
  report_title                : null
  report_author               : null
  report_description          : null

Reference genome options
  gtf                         : input_data/gtf_annotation/gencode.v21.chr_patch_hapl_scaff.annotation.gtf

Institutional config options
  config_profile_name         : RNA-seq profile
  config_profile_description  : Settings for RNA-seq analysis

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/differentialabundance for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.7568000

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/differentialabundance/blob/master/CITATIONS.md

[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE -

[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE                -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR                   -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER         -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM                 -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL         -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY            -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL           -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP                -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK           -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE          -

[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE                -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR                   -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER         -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM                 -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL         -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY            -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL           -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP                -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK           -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE          -
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE'

Caused by:
  Conda environment file does not exist: modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml


 -- Check '.nextflow.log' file for details
-[nf-core/differentialabundance] Pipeline completed with errors-

[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE                -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR                   -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER         -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_NORM                 -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:DESEQ2_DIFFERENTIAL         -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY            -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL           -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_DUMPSOFTWAREVERSIONS -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP                -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK           -
[-        ] process > NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE          -
ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE'

Caused by:
  Conda environment file does not exist: modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml

@WackerO
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WackerO commented Mar 18, 2024

Hello @dgoswamia, this seems to be not a pipeline problem, but an issue with docker. Not sure how much I can help with this, but you could try pruning your docker images?

@dgoswamia
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dgoswamia commented Mar 18, 2024 •
edited
Loading

Hello @WackerO , Thank you for your quick input,
After running: docker image prune -a
I able to run the whole nf-core/differentialabundance analysis pipeline. no issue.
Thanks again !!
Please close the ticket

@dgoswamia
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Thanks to @WackerO for quick comment

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@WackerO @dgoswamia