Description
Operating System
Other Linux (please specify below)
Other Linux
Red Hat Enterprise Linux 8.8 (Ootpa)
Workflow Version
v3.0.0
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
nextflow run software_packages/wf-single-cell
--expected_cells 10000
--fastq gene_expression/library_2_reads_merged
--kit 3prime:v3
--ref_genome_dir data/RefGenome/
-profile standard
--out_dir runs/run5
Workflow Execution - CLI Execution Profile
singularity
What happened?
Setup:
kit: 3prime:v3
executor: singularity
environment: computing cluster
RAM: 128GB
cores: 12
Current Behaviour:
I am trying to run the Epi2me workflow on our Single Cell sequencing reads.
The pipeline runs fine, but then it skips over the assign_features, create_matrix, process_matrix and merge_transcriptome steps without any logs on why the steps did not run.
The output folder does not contain any outputs except the nextflow reports, and the config.json and whitelist.tsv files
Expected Behaviour:
The pipeline runs fine without any issues and gives out the results matrix
Relevant log output
> executor > local (129)
> [f9/6eb465] fastcat (1) | 1 of 1 ✔
> [a7/9df511] parse_kit_metadata (1) | 1 of 1 ✔
> [e6/e0d557] pipeline:getVersions | 1 of 1 ✔
> [e5/7a59f1] pipeline:getParams | 1 of 1 ✔
> [ce/678ffb] pip…e:preprocess:call_paftools | 1 of 1 ✔
> [8b/9be766] pip…rocess:build_minimap_index | 1 of 1 ✔
> [0f/b51f74] pip…cess:call_adapter_scan (2) | 11 of 11 ✔
> [46/8c3c49] pip…ummarize_adapter_table (1) | 1 of 1 ✔
> [46/83fdb4] pip…s_bams:split_gtf_by_chroms | 1 of 1 ✔
> [ba/cf6351] pip…ams:generate_whitelist (1) | 1 of 1 ✔
> [c9/29dfdf] pip…_bams:assign_barcodes (10) | 11 of 11 ✔
> [ba/d5c2d2] pip…:merge_and_publish_tsv (1) | 1 of 1 ✔
> [be/fc085a] pip…bams:cat_tags_by_chrom (1) | 1 of 1 ✔
> [e8/b1d1f8] pip…rocess_bams:merge_bams (1) | 1 of 1 ✔
> [77/c5c8b7] pip…rocess_bams:stringtie (43) | 47 of 47 ✔
> [83/920b13] pip…lign_to_transcriptome (47) | 47 of 47 ✔
> [- ] pip…ocess_bams:assign_features -
> [- ] pip…process_bams:create_matrix -
> [- ] pip…rocess_bams:process_matrix -
> [- ] pip…s_bams:merge_transcriptome -
> [4e/8ec1ed] pip…ocess_bams:pack_images (1) | 1 of 1 ✔
> Plus 5 more processes waiting for tasks…
> Completed at: 26-Feb-2025 19:04:54
> Duration : 4h 31m 40s
> CPU hours : 38.4
> Succeeded : 129Application activity log entry
Were you able to successfully run the latest version of the workflow with the demo data?
yes