error running ABC model with averaged Hi-C files

[cmlakhan]

I am trying to run the ABC model on my data. I have a tsv file like this

biosample   DHS ATAC    H3K27ac default_accessibility_feature   HiC_file    HiC_type    HiC_resolution  alt_TSS alt_genes
microglia       /gpfs/commons/groups/knowles_lab/data/ADSP_reguloML/annotations/brain_all/glass_lab_fastq/processed_files/ABC_data/ATAC_HMG063_NS004_Microglia.sorted.tagAlign.bgz  /gpfs/commons/groups/knowles_lab/data/ADSP_reguloML/annotations/brain_all/glass_lab_fastq/processed_files/ABC_data/H3K27ac_HMG063_NS004_Microglia.sorted.bam    ATAC    /gpfs/commons/groups/knowles_lab/data/ADSP_reguloML/annotations/brain_all/glass_lab_fastq/processed_files/ABC_data/hic_extract/AvgHiC   avg 5000

which I processed as suggested in your documentation but I received this error and I can't understand why this might be the case. I was able to run the power law version by removing all of the Hi-C arguments so it seems to be related to an issue with the tsv file or I have messed one of the arguments.

usage: run.neighborhoods.py [-h] --candidate_enhancer_regions
                            CANDIDATE_ENHANCER_REGIONS --outdir OUTDIR --genes
                            GENES
                            [--genes_for_class_assignment GENES_FOR_CLASS_ASSIGNMENT]
                            [--ubiquitously_expressed_genes UBIQUITOUSLY_EXPRESSED_GENES]
                            [--gene_name_annotations GENE_NAME_ANNOTATIONS]
                            [--primary_gene_identifier PRIMARY_GENE_IDENTIFIER]
                            [--skip_gene_counts] [--H3K27ac [H3K27AC]]
                            [--DHS [DHS]] [--ATAC [ATAC]]
                            [--default_accessibility_feature [DEFAULT_ACCESSIBILITY_FEATURE]]
                            [--expression_table [EXPRESSION_TABLE]]
                            [--qnorm QNORM]
                            [--tss_slop_for_class_assignment TSS_SLOP_FOR_CLASS_ASSIGNMENT]
                            [--skip_rpkm_quantile]
                            [--use_secondary_counting_method] --chrom_sizes
                            CHROM_SIZES --chrom_sizes_bed CHROM_SIZES_BED
                            [--enhancer_class_override ENHANCER_CLASS_OVERRIDE]
                            [--supplementary_features SUPPLEMENTARY_FEATURES]
                            [--cellType CELLTYPE]
run.neighborhoods.py: error: unrecognized arguments: /gpfs/commons/groups/knowles_lab/data/ADSP_reguloML/annotations/brain_all/glass_lab_fastq/processed_files/ABC_data/hic_extract/AvgHiC avg 5000
[Wed Nov 27 17:26:09 2024]
Error in rule create_neighborhoods:

[cmlakhan]

Never mind, it was a formatting issue