nrhorner
commented
1 year ago Hi @theheking
I can see from your log that you were running with the default standard profile (which uses docker)
Could you try using -profile singularity
Thanks
Closed theheking closed 1 year ago
nrhorner
commented
1 year ago Hi @theheking
I can see from your log that you were running with the default standard profile (which uses docker)
Could you try using -profile singularity
Thanks
theheking
commented
1 year ago Thank you! Did not see the profile flag on help/man pages. Cheers
|||||||||| _____ ____ ___ ____ __ __ _____ _ _
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||||| | _| | |_) | | __) | |\/| | _| _____| |/ _` | '_ \/ __|
||||| | |___| __/| | / __/| | | | |__|_____| | (_| | |_) \__ \
|||||||||| |_____|_| |___|_____|_| |_|_____| |_|\__,_|_.__/|___/
|||||||||| wf-single-cell v0.2.0
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Typical pipeline command:
nextflow run epi2me-labs/wf-single-cell \
--fastq test_data/reads.fastq.gz
Input Options
--fastq [string] FASTQ files to use in the analysis.
--ref_genome_dir [string] The path to the 10x reference directory
--kit_config [string] A file defining the configurations associated with the various supported 10x kits.
--merge_bam [boolean] Merge BAM alignment files into a single BAM file per sample
--kit_name [string] 10x kit name [default: 3prime]
--kit_version [string] 10x kit version [default: v3]
--expected_cells [integer] Number of expected cells. [default: 500]
Sample Options
--single_cell_sample_sheet [string] An optional CSV file used to assign library metadata to samples. If all samples have the same library metadata, this
can be supplied instead by using the parameters (kit_name, kit_version, expected cells)
--sample_sheet [string] A CSV file used to map barcodes to sample aliases. The sample sheet can be provided when the input data is a
directory containing sub-directories with FASTQ files.
--sample [string] A single sample name for non-multiplexed data. Permissible if passing a single .fastq(.gz) file or directory of
.fastq(.gz) files.
Output Options
--out_dir [string] Directory for output of all workflow results. [default: output]
Advanced options
--max_threads [integer] This is used to control how many threads the following multithread-capable processes can use: combine_chrom_bams(max
8 threads), stringtie(max_threads/4), align_to_transcriptome(max_threads/2) .It is also used as the number of parts
to chunk the fastq data into before processing. [default: 4]
--read_structure_batch_size [integer] Batch size when processing reads using adapter_scan_vsearch.py (changing not recommended). [default: 40000]
--barcode_adapter1_suff_length [integer] Suffix length of the read1 adapter to use in creating the probe sequence for identifying barcode/UMI bases.
[default: 10]
--barcode_min_quality [integer] Minimum allowed nucleotide-level quality score in the extracted/uncorrected barcode sequence [default: 15]
--barcode_max_ed [integer] Maximum allowable edit distance between uncorrected barcode and the best matching corrected barcode from the sample
whitelist. [default: 2]
--barcode_min_ed_diff [integer] Minimum allowable edit distance difference between whitelist barcode candidates. [default: 2]
--gene_assigns_minqv [integer] Minimum alignment qscore allowed for a read to be assigned to a gene or genomic region. [default: 60]
--umi_genomic_interval [integer] Size of genomic window (bp) to assign to a read if alignment falls outside of an annotated gene. [default:
1000]
--umi_cell_gene_max_reads [integer] Maximum number of reads to cluster for a particular barcode/gene combination. [default: 20000]
--umi_cluster_max_threads [integer] Maximum number of threads to use per-chromosome in UMI clustering step. [default: 4]
--matrix_min_genes [integer] Filter cells from the gene expression matrix if they contain fewer than <matrix_min_genes> genes. [default:
25]
--matrix_min_cells [integer] Filter genes from the gene expression matrix that are observed in fewer than <matrix_min_cells> cells. [default:
3]
--matrix_max_mito [integer] Filter cells from the gene expression matrix if more than <matrix_max_mito> percent of UMI counts come from
mitochondrial genes. [default: 20]
--matrix_norm_count [integer] Normalize expression matrix to <matrix_norm_count> counts per cell. [default: 10000]
--umap_plot_genes [string] File containing a list of gene symbols (one symbol per line) to annotate with expression values in the UMAP
projections.
--resources_mm2_max_threads [integer] Maximum allowed threads for the minimap2 stage. [default: 4]
--resources_mm2_flags [string] Optional flags for the minimap2 stage. [default: -I 16G]
--mito_prefix [string] Gene name prefix to identify for mitochondrial genes. [default: MT-]
Miscellaneous Options
--disable_ping [boolean] Enable to prevent sending a workflow ping.
--help [boolean] Display help text.
--version [boolean] Display version and exit.
Other parameters
--process_label [string] The main process label for template processes to use by default [default: singlecell]
--aws_image_prefix [string] null
--aws_queue [string] null
--monochrome_logs [boolean] null
--validate_params [boolean] null [default: true]
--show_hidden_params [boolean] null
What happened?
I am currently trying to run wf-single-cell-demo via singularity but coming up with this error. Is there a workaround for not using docker and only having singularity installed as I do not have sudo privileges. Thank you in advance,
Operating System
ubuntu 20.04
Workflow Execution
Command line
Workflow Execution - EPI2ME Labs Versions
wf-single-cell-demo
Workflow Execution - CLI Execution Profile
Singularity
Workflow Version
wf-single-cell v0.2.0-g539c102
Relevant log output