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-Run01_11] 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-Run01_11 launchDir : /mnt/batch/tasks/workitems/nf-workflow-5CWNFDrQ0MiUuI/job-1/nf-workflow-5CWNFDrQ0MiUuI/wd workDir : /workdir001/scratch/2LdoQdhfsZRgy 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-try1.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 :  !! 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/2LdoQdhfsZRgy/tmp/ff/830ffd79149363cecc831281db084c/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/5CWNFDrQ0MiUuI [94/fb3074] Cached process > NFCORE_RNASPLICE:RNASPLICE:CONTRASTS_CHECK:CONTRASTSHEET_CHECK (RNASplice-ContrastSamplesheet-try1.csv) [a1/603259] Cached process > NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_ANNOTATION (genes.gtf) [07/e4a1a3] Cached process > NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:SUBREAD_FLATTENGTF (genes.gtf) [5c/f22f94] Cached process > NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:GTF_2_GFF3 [b3/b254a0] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOI (genes.gtf) [ab/c00ea5] Cached process > NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_SALMON:GFFREAD_TX2GENE (genes.gtf) [50/1d9335] Cached process > NFCORE_RNASPLICE:RNASPLICE:INPUT_CHECK:SAMPLESHEET_CHECK (RNASplice-Samplesheet-S2-tno1.csv) [ab/4d0479] Cached process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:GTF_GENE_FILTER (genome.fa) [05/6826bd] Cached process > NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_STAR_SALMON:GFFREAD_TX2GENE (genes.gtf) [38/05066c] Cached process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fa) [2a/823a2d] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOI (genes.gtf) [5c/89b76e] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:GENERATE_EVENTS_IOE (genes.gtf) [83/c65b80] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:GENERATE_EVENTS_IOE (genes.gtf) [10/3cd081] Cached process > NFCORE_RNASPLICE:RNASPLICE:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SAGCFN_24_00002) [a5/71f5bf] Cached process > NFCORE_RNASPLICE:RNASPLICE:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SAGCFN_24_00001) [55/f5aa2f] Cached process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genome.fa) [45/cbc39b] Cached process > NFCORE_RNASPLICE:RNASPLICE:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SAGCFN_24_00002) [bd/a10acf] Cached process > NFCORE_RNASPLICE:RNASPLICE:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (SAGCFN_24_00001) [34/4e387c] Cached process > NFCORE_RNASPLICE:RNASPLICE:PREPARE_GENOME:SALMON_INDEX (genome.transcripts.fa) [88/c5c4b2] Cached process > NFCORE_RNASPLICE:RNASPLICE:SALMON_QUANT_SALMON (SAGCFN_24_00001) [e9/49f923] Cached process > NFCORE_RNASPLICE:RNASPLICE:SALMON_QUANT_SALMON (SAGCFN_24_00002) [fc/c1820a] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN_IGENOMES (SAGCFN_24_00002) [a5/937f8f] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN_IGENOMES (SAGCFN_24_00001) [91/4c86a1] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (SAGCFN_24_00002) [c2/c86d7e] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (SAGCFN_24_00001) [8c/0576a4] Cached process > NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_COUNT (SAGCFN_24_00002) [96/952ffd] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (SAGCFN_24_00002) [7c/a2e4ae] Cached process > NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_COUNT (SAGCFN_24_00001) [ef/62f75e] Cached process > NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:SUBREAD_FEATURECOUNTS (SAGCFN_24_00002) [35/140469] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (SAGCFN_24_00001) [77/73e474] Cached process > NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:SUBREAD_FEATURECOUNTS (SAGCFN_24_00001) [f8/ad75f9] Cached process > NFCORE_RNASPLICE:RNASPLICE:SALMON_QUANT_STAR (SAGCFN_24_00001) [2e/6bfd15] Cached process > NFCORE_RNASPLICE:RNASPLICE:SALMON_QUANT_STAR (SAGCFN_24_00002) [06/a2f9b4] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SAGCFN_24_00001) [43/94fc65] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SAGCFN_24_00001) [bc/bd54da] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (SAGCFN_24_00002) [86/2cd7ba] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (SAGCFN_24_00002) [c4/cf37ac] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SAGCFN_24_00001) [1f/34c9c8] Cached process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (SAGCFN_24_00002) [1e/e82a7a] Cached process > NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_SALMON:TXIMPORT (genes.tx2gene.tsv) [10/971420] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:PSIPEREVENT (suppa_tpm.txt) [5c/35e3de] Submitted process > NFCORE_RNASPLICE:RNASPLICE:DEXSEQ_DEU:DEXSEQ_EXON (1) [19/58fbb3] Submitted process > NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:EDGER_EXON (RNASplice-Samplesheet-S2-tno1.csv) [3c/705522] Cached process > NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_STAR_SALMON:TXIMPORT (genes.tx2gene.tsv) [19/8250da] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:PSIPEREVENT (suppa_tpm.txt) [63/ef064f] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:PSIPERISOFORM (suppa_tpm.txt) [25/202d31] Submitted process > NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1) [e2/5cb01b] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:SPLIT_FILES_TPM (suppa_tpm.txt) [bf/15d544] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:SPLIT_FILES_IOE (suppa_local.psi) [ce/90adf9] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:PSIPERISOFORM (suppa_tpm.txt) [b1/d97b1f] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:SPLIT_FILES_TPM (suppa_tpm.txt) [21/b64f24] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:SPLIT_FILES_IOE (suppa_local.psi) [24/aea0ff] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_SALMON:SPLIT_FILES_IOI (suppa_isoform.psi) [70/c05a52] Submitted process > NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_STAR_SALMON:DRIMSEQ_FILTER (1) [0a/b2a5fa] Cached process > NFCORE_RNASPLICE:RNASPLICE:SUPPA_STAR_SALMON:SPLIT_FILES_IOI (suppa_isoform.psi) [f0/35eecc] Cached process > NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_INDEX [c9/c647a4] Cached process > NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_RUN (1) [05/fdc176] Cached process > NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_RUN (2) [3c/0b3570] Cached process > NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SETTINGS [24/5b23be] Submitted process > NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (2) [78/255284] Submitted process > NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (1) [90/7330d1] Submitted process > NFCORE_RNASPLICE:RNASPLICE:VISUALISE_MISO:MISO_SASHIMI (3) ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:EDGER_EXON (RNASplice-Samplesheet-S2-tno1.csv)' Caused by: Process `NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:EDGER_EXON (RNASplice-Samplesheet-S2-tno1.csv)` terminated with an error exit status (1) Command executed: run_edger_exon.R featurecounts RNASplice-Samplesheet-S2-tno1.csv RNASplice-ContrastSamplesheet-try1.csv 10 cat <<-END_VERSIONS > versions.yml "NFCORE_RNASPLICE:RNASPLICE:EDGER_DEU:EDGER_EXON": r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//') bioconductor-edger: $(Rscript -e "library(edgeR); cat(as.character(packageVersion('edgeR')))") END_VERSIONS Command exit status: 1 Command output: (empty) Command error: Loading required package: limma Error in eval(ej, envir = levelsenv) : object 'GBR' not found Calls: makeContrasts -> eval -> eval Execution halted Work dir: az://workdir001/scratch/2LdoQdhfsZRgy/19/58fbb34666f3dc8d40b329f1dd730a Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check 'nf-5CWNFDrQ0MiUuI.log' file for details Execution cancelled -- Finishing pending tasks before exit Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to complete (1 files) Waiting for file transfers to 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transfers to complete (1 files) Waiting for file transfers to complete (1 files) -[nf-core/rnasplice] Pipeline completed with errors-