You can now use nextflow and nf-core pipeline on IFB core cluster with profile ifb_core
nf-core doc: https://github.com/nf-core/configs/blob/master/docs/ifb_core.md
7 « J'aime »
Bonjour,
J'ai essayé de suivre les instruction pour lancer un run test de la pipeline nf-core/rnaseq depuis mon espace. J'ai essayé les commandes suivantes:
srun --pty bash
module purge
module load nextflow/20.04.1
nextflow run nf-core/rnaseq -r 3.2 -profile test,ifb_core
Néanmoins, j'ai l'erreur suivante:
N E X T F L O W ~ version 20.04.1
Pulling nf-core/rnaseq ...
downloaded from https://github.com/nf-core/rnaseq.git
Launching `nf-core/rnaseq` [elegant_newton] - revision: b3ff92bc54 [3.2]
Unknown config attribute `params.projectDir` -- check config file: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/nextflow.config
Je suis bloquée, auriez-vous une idée pour m'aider?
Je vous colle ci-dessous le fichier nextflow.config crée, je ne trouve pas le attribut dont ils parlent.
Merci beaucoup d'avance pour toute aide ou suggestion!
Natalia.
/*
========================================================================================
nf-core/rnaseq Nextflow config file
========================================================================================
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
// References
genome = null
transcript_fasta = null
additional_fasta = null
splicesites = null
gtf_extra_attributes = 'gene_name'
gtf_group_features = 'gene_id'
featurecounts_feature_type = 'exon'
featurecounts_group_type = 'gene_biotype'
gencode = false
save_reference = false
// UMI handling
with_umi = false
umitools_extract_method = 'string'
umitools_bc_pattern = null
save_umi_intermeds = false
// Trimming
clip_r1 = null
clip_r2 = null
three_prime_clip_r1 = null
three_prime_clip_r2 = null
trim_nextseq = null
save_trimmed = false
skip_trimming = false
// Ribosomal RNA removal
remove_ribo_rna = false
save_non_ribo_reads = false
ribo_database_manifest = "${projectDir}/assets/rrna-db-defaults.txt"
// Alignment
aligner = 'star_salmon'
pseudo_aligner = null
seq_center = null
bam_csi_index = false
star_ignore_sjdbgtf = false
salmon_quant_libtype = null
hisat2_build_memory = '200.GB' // Amount of memory required to build HISAT2 index with splice sites
stringtie_ignore_gtf = false
min_mapped_reads = 5
save_merged_fastq = false
save_unaligned = false
save_align_intermeds = false
skip_markduplicates = false
skip_alignment = false
// QC
skip_qc = false
skip_bigwig = false
skip_stringtie = false
skip_fastqc = false
skip_preseq = false
skip_dupradar = false
skip_qualimap = false
skip_rseqc = false
skip_biotype_qc = false
skip_deseq2_qc = false
skip_multiqc = false
deseq2_vst = false
rseqc_modules = 'bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication'
// Boilerplate options
outdir = './results'
publish_dir_mode = 'copy'
multiqc_config = null
multiqc_title = null
email = null
email_on_fail = null
max_multiqc_email_size = '25.MB'
plaintext_email = false
monochrome_logs = false
help = false
igenomes_base = 's3://ngi-igenomes/igenomes'
tracedir = "${params.outdir}/pipeline_info"
igenomes_ignore = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes,modules'
enable_conda = false
singularity_pull_docker_container = false
// Config options
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
hostnames = [:]
config_profile_name = null
config_profile_description = null
config_profile_contact = null
config_profile_url = null
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/rnaseq custom config
try {
includeConfig "${params.custom_config_base}/pipeline/rnaseq.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config/rnaseq profiles: ${params.custom_config_base}/pipeline/rnaseq.config")
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
profiles {
debug { process.beforeScript = 'echo $HOSTNAME' }
conda {
params.enable_conda = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
}
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
}
manifest {
name = 'nf-core/rnaseq'
author = 'Phil Ewels, Rickard Hammarén'
homePage = 'https://github.com/nf-core/rnaseq'
description = 'Nextflow RNA-Seq analysis pipeline, part of the nf-core community.'
mainScript = 'main.nf'
nextflowVersion = '!>=21.04.0'
version = '3.2'
}
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}
Bonjour,
projectDir n'est effectivement pas un params, mais une variable interne à Nextflow devant normalement pointer vers la base du repo.
On a normalement pas de soucis avec son utilisation, je vais me pencher sur la question.
Pouvez-vous joindre le fichier .nexflow.log ?
Bonjour @npinzonrestrepo
Avez-vous pu résoudre le problème ? Pouvez-vous nous joindre le fichier log de nextflow ( .nexflow.log) ?
Bonjour,
Désolée pour le délai. Je n'ai aps résolu le problème. Voic le fichier .log de nextflow
Jul-05 13:14:47.820 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/rnaseq -r 3.0 -profile test,ifb_core
Jul-05 13:14:47.920 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 20.04.1
Jul-05 13:14:48.581 [main] DEBUG nextflow.scm.AssetManager - Git config: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Jul-05 13:14:48.595 [main] DEBUG nextflow.scm.AssetManager - Git config: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Jul-05 13:14:48.982 [main] DEBUG nextflow.scm.AssetManager - Git config: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Jul-05 13:14:48.982 [main] INFO nextflow.cli.CmdRun - Launching `nf-core/rnaseq` [focused_kirch] - revision: 3643a94411 [3.0]
Jul-05 13:14:49.575 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/nextflow.config
Jul-05 13:14:49.575 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /shared/ifbstor1/home/npinzonrestrepo/nextflow.config
Jul-05 13:14:49.576 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/nextflow.config
Jul-05 13:14:49.576 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /shared/ifbstor1/home/npinzonrestrepo/nextflow.config
Jul-05 13:14:49.584 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,ifb_core`
Jul-05 13:14:50.281 [main] DEBUG nextflow.config.ConfigBuilder - In the following config object the attribute `params.projectDir` is empty:
input='https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/samplesheet.csv'
public_data_ids=''
skip_sra_fastq_download=false
genome=''
transcript_fasta='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/transcriptome.fasta'
additional_fasta='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/gfp.fa.gz'
splicesites=''
gtf_extra_attributes='gene_name'
gtf_group_features='gene_id'
gtf_count_type='exon'
gtf_group_features_type='gene_biotype'
gencode=false
save_reference=false
with_umi=false
umitools_extract_method='string'
umitools_bc_pattern='NNNN'
save_umi_intermeds=false
clip_r1=0
clip_r2=0
three_prime_clip_r1=0
three_prime_clip_r2=0
trim_nextseq=0
save_trimmed=false
skip_trimming=false
remove_ribo_rna=false
save_non_ribo_reads=false
ribo_database_manifest=[:]/assets/rrna-db-defaults.txt
aligner='star_salmon'
pseudo_aligner='salmon'
seq_center=''
star_ignore_sjdbgtf=false
hisat_build_memory=200
stringtie_ignore_gtf=false
min_mapped_reads=5
save_merged_fastq=false
save_unaligned=false
save_align_intermeds=false
skip_markduplicates=false
skip_alignment=false
skip_qc=false
skip_bigwig=false
skip_stringtie=false
skip_fastqc=false
skip_preseq=false
skip_dupradar=false
skip_qualimap=false
skip_rseqc=false
skip_biotype_qc=false
skip_deseq2_qc=false
skip_multiqc=false
deseq2_vst=false
rseqc_modules='bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication'
enable_conda=false
clusterOptions=''
outdir='./results'
publish_dir_mode='copy'
multiqc_config=''
multiqc_title=''
email=''
email_on_fail=''
max_multiqc_email_size='25.MB'
plaintext_email=false
monochrome_logs=false
help=false
igenomes_base='s3://ngi-igenomes/igenomes/'
tracedir=./results/pipeline_info
igenomes_ignore=true
singularity_pull_docker_container=false
custom_config_version='master'
custom_config_base=https://raw.githubusercontent.com/nf-core/configs/master
hostnames=['binac':['.binac.uni-tuebingen.de'], 'cbe':['.cbe.vbc.ac.at'], 'cfc':['.hpc.uni-tuebingen.de'], 'crick':['.thecrick.org'], 'icr_davros':['.davros.compute.estate'], 'imperial':['.hpc.ic.ac.uk'], 'imperial_mb':['.hpc.ic.ac.uk'], 'genotoul':['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], 'genouest':['.genouest.org'], 'uppmax':['.uppmax.uu.se'], 'utd_ganymede':['ganymede.utdallas.edu'], 'utd_sysbio':['sysbio.utdallas.edu']]
config_profile_description='Minimal test dataset to check pipeline function'
config_profile_contact='https://community.france-bioinformatique.fr'
config_profile_url='https://www.france-bioinformatique.fr/'
max_memory=6 GB
max_cpus=2
max_time=2d
modules {
sra_ids_to_runinfo {
publish_dir='public_data'
publish_files=['tsv':'runinfo']
}
sra_runinfo_to_ftp {
publish_dir='public_data'
publish_files=['tsv':'runinfo']
}
sra_fastq_ftp {
publish_dir='public_data'
publish_files=['fastq.gz':'', 'md5':'md5']
}
sra_to_samplesheet {
publish_dir='public_data'
publish_files=false
}
sra_merge_samplesheet.publish_dir='public_data'
gffread {
args='--keep-exon-attrs -F -T'
publish_dir='genome'
}
cat_fastq.publish_dir='fastq'
fastqc.args='--quiet'
trimgalore {
args='--fastqc'
publish_files=['txt':'', 'html':'fastqc', 'zip':'fastqc']
}
umitools_extract {
args=''
publish_files=['log':'']
}
sortmerna {
args='--num_alignments 1 --fastx -v'
publish_files=['log':'']
}
star_genomegenerate.publish_dir='genome/index'
star_align {
args='--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend'
publish_dir=star_salmon
publish_files=['out':'log', 'tab':'log']
}
star_salmon_quant.publish_dir=star_salmon
star_salmon_tximport {
publish_dir=star_salmon
publish_by_id=true
}
star_salmon_merge_counts.publish_dir=star_salmon
hisat2_build.publish_dir='genome/index'
hisat2_align {
args='--met-stderr --new-summary --dta'
publish_files=['log':'log']
}
rsem_preparereference {
args='--star'
publish_dir='genome/index'
args2='--genomeSAindexNbases 7'
}
rsem_calculateexpression {
args='--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1'
publish_files=['log':'log', 'stat':'', 'results':'']
publish_dir=star_salmon
}
rsem_merge_counts.publish_dir=star_salmon
samtools_sort {
suffix='.sorted'
publish_files=['stats':'samtools_stats', 'flagstat':'samtools_stats', 'idxstats':'samtools_stats']
publish_dir=star_salmon
}
salmon_index {
args=''
publish_dir='genome/index'
}
salmon_quant.args=''
salmon_tximport.publish_by_id=true
salmon_merge_counts.publish_dir=
preseq_lcextrap {
args='-verbose -bam -seed 1 -seg_len 100000000'
publish_files=['txt':'', 'log':'log']
publish_dir=star_salmon/preseq
}
umitools_dedup {
publish_files=['tsv':'umitools']
suffix='.umi_dedup.sorted'
publish_dir=star_salmon
}
picard_markduplicates {
args='ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp'
suffix='.markdup.sorted'
publish_files=['bam':'', 'metrics.txt':'picard_metrics']
publish_dir=star_salmon
}
picard_markduplicates_samtools {
suffix='.markdup.sorted'
publish_files=['bai':'', 'stats':'samtools_stats', 'flagstat':'samtools_stats', 'idxstats':'samtools_stats']
publish_dir=star_salmon
}
stringtie {
args='-v'
publish_dir=star_salmon/stringtie
}
subread_featurecounts {
args='-B -C'
publish_dir=star_salmon/featurecounts
}
multiqc_custom_biotype.publish_dir=star_salmon/featurecounts
bedtools_genomecov.publish_files=false
ucsc_bedclip {
suffix='.clip'
publish_files=false
}
ucsc_bedgraphtobigwig.publish_dir=star_salmon/bigwig
deseq2_qc {
args='--id_col 1 --sample_suffix \'\' --outprefix deseq2'
publish_files=['RData':'', 'pca.vals.txt':'', 'plots.pdf':'', 'sample.dists.txt':'', 'size_factors':'', 'log':'']
publish_dir=star_salmon/deseq2_qc
}
qualimap_rnaseq.publish_dir=star_salmon/qualimap
dupradar {
publish_files=['Dens.pdf':'scatter_plot', 'Boxplot.pdf':'box_plot', 'Hist.pdf':'histogram', 'Matrix.txt':'gene_data', 'slope.txt':'intercepts_slope']
publish_dir=star_salmon/dupradar
}
rseqc_bamstat.publish_dir=star_salmon/rseqc/bam_stat
rseqc_innerdistance {
publish_files=['txt':'txt', 'pdf':'pdf', '.r':'rscript']
publish_dir=star_salmon/rseqc/inner_distance
}
rseqc_inferexperiment.publish_dir=star_salmon/rseqc/infer_experiment
rseqc_junctionannotation {
publish_files=['pdf':'pdf', '.r':'rscript', 'bed':'bed', 'xls':'xls', 'log':'log']
publish_dir=star_salmon/rseqc/junction_annotation
}
rseqc_junctionsaturation {
publish_files=['pdf':'pdf', '.r':'rscript']
publish_dir=star_salmon/rseqc/junction_saturation
}
rseqc_readdistribution.publish_dir=star_salmon/rseqc/read_distribution
rseqc_readduplication {
publish_files=['pdf':'pdf', '.r':'rscript', 'xls':'xls']
publish_dir=star_salmon/rseqc/read_duplication
}
multiqc {
args=''
publish_dir=multiqc/star_salmon
}
}
genomes=[:]
config_profile_name='Test profile'
fasta='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
gtf='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz'
gff='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff.gz'
hisat2_index='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/hisat2.tar.gz'
star_index='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/star.tar.gz'
salmon_index='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/salmon.tar.gz'
rsem_index='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/rsem.tar.gz'
Jul-05 13:14:50.286 [main] ERROR nextflow.cli.Launcher - Unknown config attribute `params.projectDir` -- check config file: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/nextflow.config
nextflow.exception.ConfigParseException: Unknown config attribute `params.projectDir` -- check config file: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/nextflow.config
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80)
at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:74)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:237)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:249)
at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:405)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:184)
at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:407)
at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
at nextflow.config.ConfigBuilder.merge0(ConfigBuilder.groovy:372)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:184)
at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:321)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
at nextflow.config.ConfigBuilder.buildGivenFiles(ConfigBuilder.groovy:287)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:168)
at nextflow.config.ConfigBuilder.buildConfigObject(ConfigBuilder.groovy:659)
at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:672)
at nextflow.script.ScriptRunner.<init>(ScriptRunner.groovy:84)
at nextflow.cli.CmdRun.run(CmdRun.groovy:254)
at nextflow.cli.Launcher.run(Launcher.groovy:460)
at nextflow.cli.Launcher.main(Launcher.groovy:642)
Bonjour Natalia,
Comme discuté sur ce post: https://community.france-bioinformatique.fr/t/erreur-lancement-nf-core-rnaseq/, en palliatif, pouvez-vous essayer en exportant la variable d'environnement projectDir:
export projectDir=/shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/
Et/Ou avec la version 21.04 de NextFlow:
export JAVA_LD_LIBRARY_PATH=/shared/ifbstor1/software/miniconda/envs/nextflow-21.04.0/lib/server
export JAVA_HOME=/shared/ifbstor1/software/miniconda/envs/nextflow-21.04.0
module load nextflow/21.04.0
Bonjour dbenaben,
Merci beaucoup! J'ai eu le même résultat que dans le post https://community.france-bioinformatique.fr/t/erreur-lancement-nf-core-rnaseq/
Avec la version 20.04.1 j'obtiens ceci:
N E X T F L O W ~ version 20.04.1
Launching `nf-core/rnaseq` [clever_boyd] - revision: b3ff92bc54 [3.2]
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
No such variable: enable
-- Check script '/shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/main.nf' at line: 12 or see '.nextflow.log' file for more details
En chargenat les variables d'environnement et la version 21.04 de Nextflow, la pipeline test tourne.
Cependant, elle s'arrête à cause d'une erreur dans le processus DESEQ2_QC_SALMON. Si je vais dans le répertoire de travail, dans le command.log, l'information sur l'erreur produite est:
Error in validObject(.Object) :
invalid class "DESeqDataSet" object: superclass "RectangularData" not defined in the environment of the object's class
Auriez-vous peut-être une suggestion?
Voici ce que dit le .nextflow.log:
Jul-23 15:17:44.130 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON` terminated with an error exit status (1)
Command executed:
deseq2_qc.r \
--count_file salmon.merged.gene_counts_length_scaled.tsv \
--outdir ./ \
--cores 2 \
--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3
if [ -f "R_sessionInfo.log" ]; then
sed "s/deseq2_pca/salmon_deseq2_pca/g" <deseq2_pca_header.txt >tmp.txt
sed -i -e "s/DESeq2 PCA/SALMON DESeq2 PCA/g" tmp.txt
cat tmp.txt *.pca.vals.txt > salmon.pca.vals_mqc.tsv
sed "s/deseq2_clustering/salmon_deseq2_clustering/g" <deseq2_clustering_header.txt >tmp.txt
sed -i -e "s/DESeq2 sample/SALMON DESeq2 sample/g" tmp.txt
cat tmp.txt *.sample.dists.txt > salmon.sample.dists_mqc.tsv
fi
Rscript -e "library(DESeq2); write(x=as.character(packageVersion('DESeq2')), file='deseq2.version.txt')"
Command exit status:
1
Command output:
(empty)
Command error:
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Je dois avouer que cela me dépasse.
Peut-être que la @team.workflow aura plus d'idées ?
@npinzonrestrepo Pas de soucis de mon coté quand je reproduis le test.
Pourriez-vous créer une issue sur GitHub: Issues · nf-core/rnaseq · GitHub
En specifiant les profils utilisés, la version de Nextflow, et joindre les fichiers .command.log .command.err du repertoire de travail, ainsi que le fichier .nextflow.log ?
Je pense que les devs du pipeline seront plus à même de pouvoir réagir à ce bug.
merci @maxulysse et @dbenaben !
Je vais faire ça, mais avant, je constate qu'il y a ce warning sur mon .command.err:
[33mWARNING:[0m Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Il y aurait peut-être un conflit sur, peut-être, la version de singularity dans mon cas?
[33mWARNING:[0m Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
converting counts to integer mode
Error in validObject(.Object) :
invalid class "DESeqDataSet" object: superclass "RectangularData" not defined in the environment of the object's class
Calls: DESeqDataSetFromMatrix ... DESeqDataSet -> new -> initialize -> initialize -> validObject
Execution halted
Le WARNING est pour moi sans conséquence et n'est probablement pas lié à l'erreur invalid class "DESeqDataSet".
Je pense comme @dbenaben
Merci beaucoup @maxulysse et @dbenaben !!
J'ai demandé l'aide du dev principal sur l'issue (error running nf-core rnaseq test pipeline · Issue #679 · nf-core/rnaseq · GitHub)
1 « J'aime »
Bonjour @maxulysse et @dbenaben, j'ai finalement résolue le problème.
J'ai caché mon ~/R et maintenant ça tourne bien. Apparamment la pipeline allait le chercher 
.
Merci encore pour votre aide!