Nextflow 26.04.0 is available - Please consider updating your version to it N E X T F L O W ~ version 25.10.5 Pulling xyz-tx/nf-sc-analysis ... downloaded from https://github.com/xyz-tx/nf-sc-analysis.git Downloading plugin nf-schema@2.5.1 Launching `https://github.com/xyz-tx/nf-sc-analysis` [distracted_kalam_24] DSL2 - revision: 43c4743bf9 [dev] ------------------------------------------------------ ,--./,-.  ___ __ __ __ ___ /,-._.--~'  |\ | |__ __ / ` / \ |__) |__ } {  | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,'  nf-core/scrnaseq 4.1.0 ------------------------------------------------------ Input/output options input_preprocess : input_downstream : outdir : Mandatory arguments aligner : cellranger Quality control options ambient_correction : cellbender Unify options unify_gene_symbols : true Celltype Annotation options celltypist_model : Adult_Mouse_Gut Generic options trace_report_suffix: 2026-05-09_04-38-47 Core Nextflow options revision : dev runName : distracted_kalam_24 launchDir : / workDir : /xyz-seqera-demo/scratch/54f2WwBuqCG2gV projectDir : /.nextflow/assets/xyz-tx/nf-sc-analysis userName : root profile : standard configFiles : /.nextflow/assets/xyz-tx/nf-sc-analysis/nextflow.config, /nextflow.config !! Only displaying parameters that differ from the pipeline defaults !! ------------------------------------------------------ * The pipeline https://doi.org/10.5281/zenodo.3568187 * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x * Software dependencies https://github.com/nf-core/scrnaseq/blob/master/CITATIONS.md WARN: The following invalid input values have been detected: * --celltypist_model: Adult_Mouse_Gut * --cellranger_include_introns: true * --ambient_correction: cellbender * --cellbender_epochs: 150 * --doublet_detection: scrublet * --unify_gene_symbols: true * --igenomes_ignore: true * --doublet_detection_threshold: 1 * --duplicate_var_resolution: sum * --cleanup_delay_ms: 15000 ╭─────────────────────────────────────────────────────────╮ │ Proceeding with downstream analysis: │ │ • Droplet removal │ │ • Ambient correction │ │ • Doublet detection │ │ • Cell type assignment │ ╰─────────────────────────────────────────────────────────╯ Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/orgs/xyz-Tx/workspaces/xyz-seqera-main/watch/3bP4YizeXG0dBy [e3/6989b9] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:GUNZIP_FASTA (Mus_musculus.GRCm39.dna.primary_assembly.fa.gz) [67/807f8a] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:GUNZIP_GTF (Mus_musculus.GRCm39.115.gtf.gz) [a1/7b81f7] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (Healthy2) [48/5911d9] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (Healthy1) [90/7246c5] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (Healthy3) [a8/1a3f1b] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (AcuteColitis1) [14/521401] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:GTF_GENE_FILTER (Mus_musculus.GRCm39.dna.primary_assembly.fa) [c5/19de77] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (AcuteColitis2) [37/38f5e9] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (AcuteColitis3) [a4/8e976f] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (ChronicColitis1) [43/3324b4] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_MKGTF (Mus_musculus.GRCm39.dna.primary_assembly_genes.gtf) [e3/f891b3] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (ChronicColitis2) [97/6c1282] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_MKREF (Mus_musculus.GRCm39.dna.primary_assembly.fa) [d6/3a90b6] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (ChronicColitis3) [c0/9630df] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:FASTQC_CHECK:FASTQC (ChronicColitis4) [fc/da699b] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (Healthy1) [db/72b313] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (Healthy2) [1f/cd8719] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD (Healthy1) [70/e54c08] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD (Healthy1) WARN: Sample 'Healthy1': Ambient correction step is skipped as CellBender performs both Empty Droplet Removal and Ambient RNA removal. [79/c436b3] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD (Healthy2) [e8/add544] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD (Healthy2) WARN: Sample 'Healthy2': Ambient correction step is skipped as CellBender performs both Empty Droplet Removal and Ambient RNA removal. [92/353b6e] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:QUALITY_CONTROL:GET_UNFILTERED_SIZE (Healthy2) [bf/f3ebd9] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:QUALITY_CONTROL:GET_UNFILTERED_SIZE (Healthy1) [de/0bf9bc] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:QUALITY_CONTROL:EMPTY_DROPLET_REMOVAL:CELLBENDER_REMOVEBACKGROUND (Healthy1) [df/7e929a] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:QUALITY_CONTROL:EMPTY_DROPLET_REMOVAL:CELLBENDER_REMOVEBACKGROUND (Healthy2) [b7/444dad] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (Healthy3) [e7/ee11d0] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (AcuteColitis1) [32/1bbc9b] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD (Healthy3) [e8/6f5009] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD (Healthy3) WARN: Sample 'Healthy3': Ambient correction step is skipped as CellBender performs both Empty Droplet Removal and Ambient RNA removal. [4a/910ff4] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:QUALITY_CONTROL:GET_UNFILTERED_SIZE (Healthy3) [ff/9adb1e] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD (AcuteColitis1) [f9/d60643] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:MTX_TO_H5AD (AcuteColitis1) WARN: Sample 'AcuteColitis1': Ambient correction step is skipped as CellBender performs both Empty Droplet Removal and Ambient RNA removal. [9c/e2fa95] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:QUALITY_CONTROL:GET_UNFILTERED_SIZE (AcuteColitis1) [13/5be907] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:QUALITY_CONTROL:EMPTY_DROPLET_REMOVAL:CELLBENDER_REMOVEBACKGROUND (Healthy3) [24/5903c0] Submitted process > NFCORE_SCRNASEQ:SCRNASEQ:QUALITY_CONTROL:EMPTY_DROPLET_REMOVAL:CELLBENDER_REMOVEBACKGROUND (AcuteColitis1) ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:QUALITY_CONTROL:EMPTY_DROPLET_REMOVAL:CELLBENDER_REMOVEBACKGROUND (Healthy1)' Caused by: Essential container in task exited Command executed: TMPDIR=. cellbender remove-background --epochs 150 --cpu-threads 6 --cuda --input Healthy1_raw_matrix.h5ad --output Healthy1_cellbender.h5 cat <<-END_VERSIONS > versions.yml "NFCORE_SCRNASEQ:SCRNASEQ:QUALITY_CONTROL:EMPTY_DROPLET_REMOVAL:CELLBENDER_REMOVEBACKGROUND": cellbender: $(cellbender --version) END_VERSIONS Command exit status: 1 Command output: (empty) Command error: /usr/bin/fusion-gpu-tracer: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (required by /usr/bin/fusion-gpu-tracer) /usr/bin/fusion-gpu-tracer: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /usr/bin/fusion-gpu-tracer) 4:44AM WRN [seqera-fusion] GPU tracer failed error="exit status 1" /opt/conda/lib/python3.7/site-packages/torch/cuda/__init__.py:88: UserWarning: CUDA initialization: Unexpected error from cudaGetDeviceCount(). Did you run some cuda functions before calling NumCudaDevices() that might have already set an error? Error 803: system has unsupported display driver / cuda driver combination (Triggered internally at ../c10/cuda/CUDAFunctions.cpp:109.) return torch._C._cuda_getDeviceCount() > 0 Traceback (most recent call last): File "/opt/conda/bin/cellbender", line 8, in sys.exit(main()) File "/opt/conda/lib/python3.7/site-packages/cellbender/base_cli.py", line 115, in main args = cli_dict[args.tool].validate_args(args) File "/opt/conda/lib/python3.7/site-packages/cellbender/remove_background/cli.py", line 80, in validate_args assert torch.cuda.is_available(), "Trying to use CUDA, " \ AssertionError: Trying to use CUDA, but CUDA is not available. FUSION_GPU_USED=false Fusion Info: fusion_version: 2.4.21-a2fba53 clone_namespace: false kernel_version: 6.1 disk_cache_size: 837Gb max_open_files: 1048576 Work dir: s3://xyz-seqera-demo/scratch/54f2WwBuqCG2gV/de/0bf9bc283de31b5ffe8e6897048ae0 Container: wave.seqera.io/wt/bc5da19e29ce/us.gcr.io/broad-dsde-methods/cellbender:0.3.2 Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out` -- Check 'nf-3bP4YizeXG0dBy.log' file for details Execution cancelled -- Finishing pending tasks before exit WARN: Unable to upload nextflow out file: nf-3bP4YizeXG0dBy.txt — reason: Thread was interrupted WARN: Unable to upload nextflow log file: nf-3bP4YizeXG0dBy.log — reason: Thread was interrupted WARN: Unable to upload tower reprts file: nf-3bP4YizeXG0dBy-reports.tsv — reason: Thread was interrupted ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check 'nf-3bP4YizeXG0dBy.log' file for details [6c/d233a5] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (AcuteColitis2) [e9/228fdd] Cached process > NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT (AcuteColitis3) [onComplete] Pipeline did not complete successfully — skipping cleanup. -[nf-core/scrnaseq] Pipeline completed with errors- WARN: Seqera Platform request field `workflow.errorMessage` exceeds expected size | offending value: `/usr/bin/fusion-gpu-tracer: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.32' not found (require(truncated)`, size: 1425 (max: 255)