jma1991
commented
5 months ago Hi @SergioManzano10
Please provide your command, nextflow config, and log file of your run.
Closed SergioManzano10 closed 5 months ago
jma1991
commented
5 months ago Hi @SergioManzano10
Please provide your command, nextflow config, and log file of your run.
SergioManzano10
commented
5 months ago I have also atached two screenshots regarding to the contrast sheet and sample sheet (in this last one, there are control samples that are not shown in the image)
Command: cmd="nextflow run nf-core/rnasplice --input $samples --contrasts $contrasts --outdir $outdir --fasta $genome --gtf $gtf --miso_genes ENSG00000185379.21 --edger_exon -profile singularity -c nextflow.config -resume"
Nextflow config:
params {
config_profile_description = 'bioinfo config'
config_profile_contact = 'Sergio Manzano sergiomanzano@vhio.net'
config_profile_url = "tobecopiedingithub"
}
singularity {
enabled = true
autoMounts = true
cacheDir="cache/"
}
executor {
name = "slurm"
queueSize = 12
}
process {
executor = 'slurm'
queue = { task.time <= 5.h && task.memory <= 10.GB ? 'short': (task.memory <= 70.GB ? 'long' : 'highmem')}
withName: 'SAMTOOLS_SORT' {
memory = 250.GB
cpus = 24 }
}
params {
max_memory = 175.GB
max_cpus = 24
max_time = 240.h
}Log file:
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)` terminated with an error exit status (1)
Command executed:
run_dexseq_dtu.R samples.tsv Contrast_sheet_rnasplice.csv counts.tsv 10
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU":
r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
bioconductor-dexseq: $(Rscript -e "library(DEXSeq); cat(as.character(packageVersion('DEXSeq')))")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
anyMissing, rowMedians
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: DESeq2
Loading required package: AnnotationDbi
Loading required package: RColorBrewer
converting counts to integer mode
Warning message:
In DESeqDataSet(rse, design, ignoreRank = TRUE) :
some variables in design formula are characters, converting to factors
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA) :
replacement has 1 row, data has 0
Calls: mapply ... colData<- -> makeBigModelFrame -> $<- -> $<-.data.frame
Execution halted
jma1991
commented
5 months ago Is that your full nextflow.config file?
SergioManzano10
commented
5 months ago No, sorry. The global one is this:
// Global default params, used in configs
params {
// Input options
input = null
contrasts = null
source = 'fastq'
// References
genome = null
transcript_fasta = null
gtf_extra_attributes = 'gene_name'
gtf_group_features = 'gene_id'
gencode = false
save_reference = false
igenomes_base = 's3://ngi-igenomes/igenomes'
igenomes_ignore = 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
skip_trimgalore_fastqc = false
min_trimmed_reads = 10000
// Alignment
aligner = 'star_salmon'
pseudo_aligner = 'salmon'
bam_csi_index = false
seq_center = null
salmon_quant_libtype = null
star_ignore_sjdbgtf = false
skip_alignment = false
save_unaligned = false
save_align_intermeds = false
save_merged_fastq = false
// QC
skip_bigwig = true
skip_fastqc = false
// rMATs
rmats = true
rmats_splice_diff_cutoff = 0.0001
rmats_paired_stats = true
rmats_read_len = 40
rmats_novel_splice_site = false
rmats_min_intron_len = 50
rmats_max_exon_len = 500
// DEXSeq DEU
dexseq_exon = true
save_dexseq_annotation = false
gff_dexseq = null
alignment_quality = 10
aggregation = true
save_dexseq_plot = true
n_dexseq_plot = 10
// edgeR DEU
edger_exon = true
save_edger_plot = true
n_edger_plot = 10
// DEXSeq DTU
dexseq_dtu = true
dtu_txi = 'dtuScaledTPM'
// Miso
sashimi_plot = true
miso_genes = 'ENSG00000004961, ENSG00000005302, ENSG00000147403'
miso_genes_file = null
miso_read_len = 75
fig_width = 7
fig_height = 7
// DRIMSeq Filtering
min_samps_feature_expr = 2
min_samps_feature_prop = 2
min_samps_gene_expr = 4
min_feature_expr = 10
min_feature_prop = 0.1
min_gene_expr = 10
// SUPPA options
suppa = true
suppa_per_local_event = true
suppa_per_isoform = true
suppa_tpm = null
// SUPPA Generate events options
generateevents_pool_genes = true
generateevents_event_type = 'SE SS MX RI FL'
generateevents_boundary = 'S'
generateevents_threshold = 10
generateevents_exon_length = 100
psiperevent_total_filter = 0
// SUPPA Diffsplice options
diffsplice_local_event = true
diffsplice_isoform = true
diffsplice_method = 'empirical'
diffsplice_area = 1000
diffsplice_lower_bound = 0
diffsplice_gene_correction = true
diffsplice_paired = true
diffsplice_alpha = 0.05
diffsplice_median = false
diffsplice_tpm_threshold = 0
diffsplice_nan_threshold = 0
// SUPPA Cluster options
clusterevents_local_event = true
clusterevents_isoform = true
clusterevents_sigthreshold = null
clusterevents_dpsithreshold= 0.05
clusterevents_eps = 0.05
clusterevents_metric = 'euclidean'
clusterevents_separation = null
clusterevents_min_pts = 20
clusterevents_method = 'DBSCAN'
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.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: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/rnasplice custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/rnasplice.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/rnasplice profiles: ${params.custom_config_base}/pipeline/rnasplice.config")
// }
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
docker.userEmulation = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_edger { includeConfig 'conf/test_edger.config' }
test_rmats { includeConfig 'conf/test_rmats.config' }
test_dexseq { includeConfig 'conf/test_dexseq.config' }
test_suppa { includeConfig 'conf/test_suppa.config' }
test_fastq { includeConfig 'conf/test_fastq.config' }
test_genome_bam { includeConfig 'conf/test_genome_bam.config' }
test_transcriptome_bam { includeConfig 'conf/test_transcriptome_bam.config' }
test_salmon_results { includeConfig 'conf/test_salmon_results.config' }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
// Nextflow plugins
plugins {
id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'nf-core/rnasplice'
author = """Ben Southgate, James Ashmore"""
homePage = 'https://github.com/nf-core/rnasplice'
description = """Alternative splicing analysis using RNA-seq."""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.0.1'
doi = '10.5281/zenodo.8424632'
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// 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
}
}
}By default, the workflow executes all available downstream analysis tools. In the complete nextflow.config file, each tool is controlled by a variable that determines whether it runs (e.g., rmats = true). Your command line argument sets edger_exon to true, which is the default setting. However, since you're using all the settings defined in nextflow.config, all other tools will also run. To run only the specific tool you’re interested in, you should set all other tools to false in the config file.
SergioManzano10
commented
5 months ago Okay, thank you!
However, I am facing a new problem that I have seen that is not previously solved:
ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)'
Caused by:
Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)` terminated with an error exit status (1)
Command executed:
run_drimseq_filter.R salmon.merged.txi.dtu.rds tximport.tx2gene.tsv prueba_sample_sheet_rnasplice.csv \
4 \
2 \
2 \
10 \
0.1 \
10
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER":
r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
bioconductor-drimseq: $(Rscript -e "library(DRIMSeq); cat(as.character(packageVersion('DRIMSeq')))")
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Attaching package: 'DRIMSeq'
The following object is masked from 'package:base':
proportions
Error in .local(x, ...) :
min_samps_gene_expr >= 0 && min_samps_gene_expr <= ncol(x@counts) is not TRUE
Calls: <Anonymous> -> <Anonymous> -> .local -> stopifnot
Execution haltedThis new problem looks to be a copy of #126 - I will close this issue as your original problem has been solved. Please monitor the other thread for updates.
Description of the bug
I am trying to apply RNA splicing pipeline for DEU approach. However, I get this error which refers to some DTU approach, which I don't want to do so far (I will do it later).
Therefore, I don't understand what the pipeline is trying to do or how I could solve it.
Thank you.
Command used and terminal output
Relevant files
No response
System information
No response