NXF_VER=26.03.2-edge nextflow run <http://main.nf|main.nf> \

>     -profile test,singularity \

>     -c cluster.config \

>     --outdir results/ \

>     -resume

ERROR ~ Error executing process > ‘NFCORE_CRISPRCRISPR PIPELINEmapping_rna_pipeline:mappingscRNA (1)’ Caused by: Missing output file(s)

*_ks_transcripts_out/counts_unfiltered/adata.h5ad

expected by process

NFCORE_CRISPR:CRISPR_PIPELINE:mapping_rna_pipeline:mappingscRNA (1)

Command executed: echo “Processing A with IGVFFI1526NFSS.fastq.gz IGVFFI9278DMWO.fastq.gz” chemistry=$(extract_parsed_seqspec.py --file rna_parsed_seqSpec.txt) kb count -i transcriptome_index.idx -g transcriptome_t2g.txt --verbose -w barcode_file.txt \ --h5ad -x $chemistry -o A_ks_transcripts_out -t 8 \ IGVFFI1526NFSS.fastq.gz IGVFFI9278DMWO.fastq.gz --overwrite echo “scRNA KB mapping Complete” Command exit status: 0 Command output: Processing A with IGVFFI1526NFSS.fastq.gz IGVFFI9278DMWO.fastq.gz scRNA KB mapping Complete Command error: [progress] 59M reads processed (88.4% mapped) [progress] 60M reads processed (88.4% mapped) [progress] 61M reads processed (88.4% mapped) [progress] 62M reads processed (88.5% mapped) [progress] 63M reads processed (88.5% mapped) [progress] 65M reads processed (88.5% mapped) [progress] 66M reads processed (88.5% mapped) [progress] 67M reads processed (88.5% mapped) [progress] 68M reads processed (88.6% mapped) [progress] 69M reads processed (88.6% mapped) [progress] 70M reads processed (88.6% mapped) [progress] 71M reads processed (88.6% mapped) [progress] 72M reads processed (88.6% mapped) [progress] 73M reads processed (88.6% mapped) [progress] 74M reads processed (88.7% mapped) [progress] 75M reads processed (88.7% mapped) [progress] 76M reads processed (88.7% mapped) [progress] 77M reads processed (88.7% mapped) [progress] 78M reads processed (88.7% mapped) [progress] 79M reads processed (88.7% mapped) [progress] 80M reads processed (88.7% mapped) executor > local (10) [c2/10ac7d] NFCORE_CRISPRCRISPR PIPELINEseqSpecCheck_pipelineguideWorkflowseqSpecCheck [100%] 1 of 1 ✔️ [61/d03a9b] NFCORE_CRISPRCRISPR PIPELINEprepare_mapping_pipeline:prepare_covariate [100%] 1 of 1 ✔️ [cd/dfeddf] NFCORE_CRISPRCRISPR PIPELINEmapping_rna_pipeline:seqSpecParser [100%] 1 of 1 ✔️ [ca/211b3f] NFCORE_CRISPRCRISPR PIPELINEmapping_rna_pipeline:downloadReference [100%] 1 of 1 ✔️ [16/484e57] NFCORE_CRISPRCRISPR PIPELINEmapping_rna_pipeline:mappingscRNA (1) [ 0%] 0 of 1 ✘ [- ] NFCORE_CRISPRCRISPR PIPELINEmapping_rna_pipeline:anndata_concat - [57/d9d2c4] NFCORE_CRISPRCRISPR PIPELINEmapping_guide_pipeline:seqSpecParser [100%] 1 of 1 ✔️ [82/c95755] NFCORE_CRISPRCRISPR PIPELINEmapping_guide_pipeline:createGuideRef [100%] 1 of 1 ✔️ [e4/6d2b65] NFCORE_CRISPRCRISPR PIPELINEmapping_guide_pipeline:mappingGuide (A) [100%] 1 of 1 ✔️ [29/17ff03] NFCORE_CRISPRCRISPR PIPELINEmapping_guide_pipeline:anndata_concat [100%] 1 of 1 ✔️ [- ] NFCORE_CRISPRCRISPR PIPELINEpreprocessing_pipeline:PreprocessAnnData - [bd/b7d461] NFCORE_CRISPRCRISPR PIPELINEpreprocessing_pipeline:downloadGTF [100%] 1 of 1 ✔️ [- ] NFCORE_CRISPRCRISPR PIPELINECreateMuData - [- ] NFCORE_CRISPRCRISPR PIPELINEguide_assignment_pipeline:prepare_assignment - [- ] NFCORE_CRISPRCRISPR PIPELINEguide_assignment_pipeline:guide_assignment_sceptre - [- ] NFCORE_CRISPRCRISPR PIPELINEguide_assignment_pipeline:mudata_concat - [- ] NFCORE_CRISPRCRISPR PIPELINEinference_pipeline:prepare_guide_inference - [- ] NFCORE_CRISPRCRISPR PIPELINEinference_pipeline:sceptre_chunk_prepare - [- ] NFCORE_CRISPRCRISPR PIPELINEinference_pipeline:inference_sceptre - [- ] NFCORE_CRISPRCRISPR PIPELINEinference_pipeline:sceptre_chunk_merge - [- ] NFCORE_CRISPRCRISPR PIPELINEinference_pipeline:inference_perturbo - [- ] NFCORE_CRISPRCRISPR PIPELINEinference_pipeline:mergedResults - [- ] NFCORE_CRISPRCRISPR PIPELINEinference_pipeline:inference_perturbo_trans - [- ] NFCORE_CRISPRCRISPR PIPELINEinference_pipeline:mergeMudata - [- ] NFCORE_CRISPRCRISPR PIPELINEevaluation_pipeline:evaluation_plot - [- ] NFCORE_CRISPRCRISPR PIPELINEevaluation_pipeline:evaluation_controls - [- ] NFCORE_CRISPRCRISPR PIPELINEadditional_qc_plots - [- ] NFCORE_CRISPRCRISPR PIPELINEdashboard_pipeline:createDashboard_default - -[null] Pipeline completed with errors- ERROR ~ Error executing process > ‘NFCORE_CRISPRCRISPR PIPELINEmapping_rna_pipeline:mappingscRNA (1)’ Caused by: Missing output file(s)

*_ks_transcripts_out/counts_unfiltered/adata.h5ad

expected by process

NFCORE_CRISPR:CRISPR_PIPELINE:mapping_rna_pipeline:mappingscRNA (1)

Command executed: echo “Processing A with IGVFFI1526NFSS.fastq.gz IGVFFI9278DMWO.fastq.gz” chemistry=$(extract_parsed_seqspec.py --file rna_parsed_seqSpec.txt) kb count -i transcriptome_index.idx -g transcriptome_t2g.txt --verbose -w barcode_file.txt \ --h5ad -x $chemistry -o A_ks_transcripts_out -t 8 \ IGVFFI1526NFSS.fastq.gz IGVFFI9278DMWO.fastq.gz --overwrite echo “scRNA KB mapping Complete” Command exit status: 0 Command output: Processing A with IGVFFI1526NFSS.fastq.gz IGVFFI9278DMWO.fastq.gz scRNA KB mapping Complete Command error: [progress] 59M reads processed (88.4% mapped) [progress] 60M reads processed (88.4% mapped) [progress] 61M reads processed (88.4% mapped) [progress] 62M reads processed (88.5% mapped) [progress] 63M reads processed (88.5% mapped) [progress] 65M reads processed (88.5% mapped) [progress] 66M reads processed (88.5% mapped) [progress] 67M reads processed (88.5% mapped) [progress] 68M reads processed (88.6% mapped) [progress] 69M reads processed (88.6% mapped) [progress] 70M reads processed (88.6% mapped) [progress] 71M reads processed (88.6% mapped) [progress] 72M reads processed (88.6% mapped) [progress] 73M reads processed (88.6% mapped) [progress] 74M reads processed (88.7% mapped) [progress] 75M reads processed (88.7% mapped) [progress] 76M reads processed (88.7% mapped) [progress] 77M reads processed (88.7% mapped) [progress] 78M reads processed (88.7% mapped) [progress] 79M reads processed (88.7% mapped) [progress] 80M reads processed (88.7% mapped) [progress] 81M reads processed (88.8% mapped) [progress] 82M reads processed (88.8% mapped) [progress] 83M reads processed (88.8% mapped) [progress] 84M reads processed (88.8% mapped) [progress] 85M reads processed (88.8% mapped) [progress] 87M reads processed (88.8% mapped) [progress] 88M reads processed (88.8% mapped) [progress] 89M reads processed (88.8% mapped) [2026-04-29 163504,009] ERROR [main] An exception occurred Traceback (most recent call last): File “/opt/conda/envs/nfenv/lib/python3.11/site-packages/kb_python/main.py”, line 1933, in main COMMAND_TO_FUNCTION[args.command](parser, args, temp_dir=temp_dir) File “/opt/conda/envs/nfenv/lib/python3.11/site-packages/kb_python/main.py”, line 715, in parse_count count( File “/opt/conda/envs/nfenv/lib/python3.11/site-packages/ngs_tools/logging.py”, line 62, in inner return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File “/opt/conda/envs/nfenv/lib/python3.11/site-packages/kb_python/count.py”, line 1350, in count bus_result = kallisto_bus( ^^^^^^^^^^^^^ File “/opt/conda/envs/nfenv/lib/python3.11/site-packages/kb_python/count.py”, line 244, in kallisto_bus run_executable(command) File “/opt/conda/envs/nfenv/lib/python3.11/site-packages/kb_python/dry/__init__.py”, line 25, in inner return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File “/opt/conda/envs/nfenv/lib/python3.11/site-packages/kb_python/utils.py”, line 203, in run_executable raise sp.CalledProcessError(p.returncode, ' ‘.join(command)) subprocess.CalledProcessError: Command ‘/opt/conda/envs/nfenv/lib/python3.11/site-packages/kb_python/bins/linux/kallisto/kallisto bus -i transcriptome_index.idx -o A_ks_transcripts_out -x 0,0,160,16,261,0,92 -t 8 IGVFFI1526NFSS.fastq.gz IGVFFI9278DMWO.fastq.gz’ died with <Signals.SIGKILL: 9>. [2026-04-29 163504,020] DEBUG [main] Removing

A_ks_transcripts_out/tmp

directory Work dir: /Chris/CRISPR_Pipeline/work/16/484e57f0be298a98233a53f1bad09f Container: /Chris/CRISPR_Pipeline/work/singularity/ghcr.io-pinellolab-crispr_pipeline-conda-docker-latest.img Tip: you can replicate the issue by changing to the process work dir and entering the command

bash .command.run

-- Check ‘.nextflow.log’ file for details