N E X T F L O W ~ version 23.10.1 Pulling nf-core/rnasplice ... downloaded from https://github.com/nf-core/rnasplice.git Launching `https://github.com/nf-core/rnasplice` [RNASplice-Samplesheet-S2-tno1-ContrastSheet_tno2-20240311-Run03] DSL2 - revision: 2b7adfa697 [1.0.3] Downloading plugin nf-validation@1.1.3 ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/rnasplice v1.0.3-g2b7adfa ------------------------------------------------------ Core Nextflow options revision : 1.0.3 runName : RNASplice-Samplesheet-S2-tno1-ContrastSheet_tno2-20240311-Run03 launchDir : /mnt/batch/tasks/workitems/nf-workflow-34jf5Ff9QibjIK/job-1/nf-workflow-34jf5Ff9QibjIK/wd workDir : /workdir001/scratch/34jf5Ff9QibjIK projectDir : /.nextflow/assets/nf-core/rnasplice userName : root profile : standard configFiles :  Input/output options input : https://api.tower.nf/workspaces/238400348310534/datasets/3bBM0FZ6RcEjasipMZ8d8E/v/1/n/RNASplice-Samplesheet-S2-tno1.csv contrasts : https://mystorage.com/RNASplice-ContrastSamplesheet-try2.csv outdir : az://myoutdir Reference genome options genome : GRCh38 fasta : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa gtf : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf star_index : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/ igenomes_base : s3://ngi-igenomes/igenomes/ Alignment options aligner : star_salmon rMATS options rmats : true DEXSeq DEU options dexseq_exon : true edgeR DEU options edger_exon : true DEXSeq DTU options dexseq_dtu : true min_samps_gene_expr : 4 min_samps_feature_expr: 2 min_samps_feature_prop: 2 Miso sashimi_plot : true miso_genes : ENSG00000004961, ENSG00000005302, ENSG00000147403 miso_genes_file : null !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ If you use nf-core/rnasplice for your analysis please cite: * The pipeline https://doi.org/10.5281/zenodo.8424632 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/rnasplice/blob/master/CITATIONS.md WARN: ============================================================================= When using '--genome GRCh38' the assembly is from the NCBI and NOT Ensembl. Biotype QC will be skipped to circumvent the issue below: https://github.com/nf-core/rnaseq/issues/460 If you would like to use the soft-masked Ensembl assembly instead please see: https://github.com/nf-core/rnaseq/issues/159#issuecomment-501184312 =================================================================================== WARN: Both --aligner=star_salmon and --pseudo_aligner=salmon specified. Downstream analyses will be performed on both salmon output files. Uploading local `bin` scripts folder to az://workdir001/scratch/34jf5Ff9QibjIK/tmp/37/4235bb1f6d28780a13d9db98ea5799/bin WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition Monitor the execution with Nextflow Tower using this URL: https://tower.nf/orgs/myorg/workspaces/workspace1/watch/34jf5Ff9QibjIK [e7/2e9ae6] Submitted process > NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK (RNASplice-ContrastSamplesheet-S2-tno2.csv) [61/14e663] Submitted process > NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK (RNASplice-Samplesheet-S2-tno1.csv) Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa [58/1e37fd] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (genes.gtf) [1a/43040e] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (genes.gtf) [8a/43c2e2] Submitted process > NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3 [51/ae4f23] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (genes.gtf) [85/f0745f] Submitted process > NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_STAR_SALMON:GFFREAD_TX2GENE (genes.gtf) [d1/3169a7] Submitted process > NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_SALMON:GFFREAD_TX2GENE (genes.gtf) [3f/b9ace6] Submitted process > NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (genes.gtf) [74/e5a58a] Submitted process > NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:SUBREAD_FLATTENGTF (genes.gtf) [c4/8fe05a] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (genes.gtf) [49/5ec845] Submitted process > NFCORE_RNASPLICE:RNASPLICE:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SAGCFN_24_00002) [13/79650e] Submitted process > NFCORE_RNASPLICE:RNASPLICE:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SAGCFN_24_00001) [88/75a66b] Submitted process > NFCORE_RNASPLICE:RNASPLICE:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SAGCFN_24_00001) [f5/349a85] Submitted process > NFCORE_RNASPLICE:RNASPLICE:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SAGCFN_24_00002) [a2/8a3f3b] Submitted process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa) [d4/1f9a50] Submitted process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:GTF_GENE_FILTER (genome.fa) [49/ceb5c6] Submitted process > NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_INDEX [1a/245fe6] Submitted process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genome.fa) [ab/3c15eb] Submitted process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:SALMON_INDEX (genome.transcripts.fa) [d2/5516cc] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SALMON_QUANT_SALMON (SAGCFN_24_00002) Staging foreign file: s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex [fa/edbfdc] Submitted process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN_IGENOMES (SAGCFN_24_00002) [c0/7ecf24] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SALMON_QUANT_SALMON (SAGCFN_24_00001) [e0/f2ed5f] Submitted process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN_IGENOMES (SAGCFN_24_00001) [cc/d94e58] Submitted process > NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_SALMON:TXIMPORT (genes.tx2gene.tsv) [8e/dc9b0d] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:PSIPEREVENT (suppa_tpm.txt) [e3/051fe8] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:SPLIT_FILES_TPM (suppa_tpm.txt) [81/1b0ddf] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:PSIPERISOFORM (suppa_tpm.txt) [06/352d98] Submitted process > NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1) [93/710752] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:SPLIT_FILES_IOE (suppa_local.psi) [06/352d98] NOTE: Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)` terminated with an error exit status (1) -- Execution is retried (1) [71/382d24] Re-submitted process > NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1) [95/06d6e5] Submitted process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:SPLIT_FILES_IOI (suppa_isoform.psi) [71/382d24] NOTE: Process `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)` terminated with an error exit status (1) -- Execution is retried (2) [dc/1bef3d] Re-submitted process > NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1) 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 RNASplice-Samplesheet-S2-tno1.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: 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: -> -> .local -> stopifnot Execution halted Work dir: az://workdir001/scratch/34jf5Ff9QibjIK/dc/1bef3d946f43b7335060f6f3f870dc Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run` -- Check 'nf-34jf5Ff9QibjIK.log' file for details WARN: Failed to publish file: az://workdir001/scratch/34jf5Ff9QibjIK/49/ceb5c608581a97469676270495f141/index; to: az://myoutdir/misopy/index [copy] -- See log file for details -[nf-core/rnasplice] Pipeline completed with errors- WARN: Killing running tasks (2) WARN: Tower request field `workflow.errorMessage` exceeds expected size | offending value: ` 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: -> -> .local -> stopifnot Execution halted`, size: 281 (max: 255)