Problem with refgenie

[peculiar97]

**I am trying to run pepatac tutorial based on this instruction .

After running looper in dry mode, I get this error:**

`Looper version: 1.3.2

Command: run [1 of 2] sample: tutorial1; pipeline: PEPATAC Calling pre-submit function: refgenconf.looper_refgenie_populate Attributes in namespaces (project, looper, pipeline, compute, sample, refgenie) missing for the following template: '{pipeline.path} --output-parent { looper.results_subdir } --cores { compute.cores } --mem { compute.mem } --sample-name { sample.sample_name } --input { sample.read1 } {% if sample.read2 is defined %} --input2 { sample.read2 } {% endif %} --single-or-paired { sample.read_type } --genome { sample.genome } {% if sample.chrom_sizes is defined %} --chrom-sizes { sample.chrom_sizes } {% elif refgenie[sample.genome].fasta is defined %} --chrom-sizes { refgenie[sample.genome].fasta.chrom_sizes } {% endif %} {% if sample.TSS_name is defined %} --TSS-name { sample.TSS_name } {% elif refgenie[sample.genome].refgene_anno is defined %} --TSS-name { refgenie[sample.genome].refgene_anno.refgene_tss } {% endif %} {% if sample.blacklist is defined %} --blacklist { sample.blacklist } {% elif refgenie[sample.genome].blacklist is defined %} --blacklist { refgenie[sample.genome].blacklist.blacklist } {% endif %} {% if sample.anno_name is defined %} --anno-name { sample.anno_name } {% elif refgenie[sample.genome].feat_annotation is defined %} --anno-name { refgenie[sample.genome].feat_annotation.feat_annotation } {% endif %} {% if sample.trimmer is defined %} --trimmer { sample.trimmer } {% else %} --trimmer "skewer" {% endif %} {% if sample.aligner is defined %} --aligner { sample.aligner } {% set aligner = sample.aligner %} {% else %} --aligner "bowtie2" {% set aligner = "bowtie2" %} {% endif %} {% if aligner == "bowtie2" or sample.aligner == "bowtie2" %} {% if sample.genome_index is defined %} --genome-index { sample.genome_index } {% elif refgenie[sample.genome].bowtie2_index is defined %} --genome-index { refgenie[sample.genome].bowtie2_index.dir } {% endif %} {% else %} {% if sample.genome_index is defined %} --genome-index { sample.genome_index } {% elif refgenie[sample.genome].bwa_index is defined %} --genome-index { refgenie[sample.genome].bwa_index.dir } {% endif %} {% endif %} {% if sample.prealignment_index is defined %} --prealignment-index { sample.prealignment_index } {% endif %} {% if sample.prealignment_names is defined %} {% if aligner == "bowtie2" or sample.aligner == "bowtie2" %} --prealignment-index {% for p in sample.prealignment_names %} { p ~ '=' ~ refgenie[p].bowtie2_index.dir } {% endfor %} {% else %} --prealignment-index {% for p in sample.prealignment_names %} { p ~ '=' ~ refgenie[p].bwa_index.dir } {% endfor %} {% endif %} {% endif %} {% if sample.deduplicator is defined %} --deduplicator { sample.deduplicator } {% endif %} {% if sample.peak_caller is defined %} --peak-caller { sample.peak_caller } {% else %} --peak-caller "macs2" {% endif %} {% if sample.peak_type is defined %} --peak-type { sample.peak_type } {% else %} --peak-type "fixed" {% endif %} {% if sample.extend is defined %} --extend { sample.extend } {% else %} --extend 250 {% endif %} {% if sample.genome_size is defined %} --genome-size { sample.genome_size } {% else %} --genome-size "2.7e9" {% endif %} {% if sample.frip_ref_peaks is defined %} --frip-ref-peaks { sample.frip_ref_peaks } {% endif %} {% if sample.motif is defined %} --motif {% endif %} {% if sample.sob is defined %} --sob {% endif %} {% if sample.sob is defined %} {% if refgenie[sample.genome].tallymer_index is defined %} --search-file { refgenie[sample.genome].tallymer_index.search_file } {% endif %} {% endif %} {% if sample.sob is defined %} {% if refgenie[sample.genome].fasta is defined %} --fasta { refgenie[sample.genome].fasta.fasta } {% endif %} {% endif %} {% if sample.fasta is defined %} --fasta { sample.fasta } {% elif refgenie[sample.genome].fasta is defined %} --fasta { refgenie[sample.genome].fasta.fasta } {% endif %} {% if sample.no_scale is defined %} --no-scale {% endif %} {% if sample.prioritize is defined %} --prioritize {% endif %} {% if sample.keep is defined %} --keep {% endif %} {% if sample.no_fifo is defined %} --noFIFO {% endif %} {% if sample.lite is defined %} --lite {% endif %} {% if sample.skipqc is defined %} --skipqc {% endif %} {%- if sample.command_extra is defined %} {sample.command_extra} {% endif -%}'

Not submitted: attmap.attmap.AttMap object has no attribute 'rCRSd'

`

The following yaml code is used for running:

`name: PEPATAC_tutorial

pep_version: 2.0.0 sample_table: tutorial.csv

looper: output_dir: "${TUTORIAL}/processed/" pipeline_interfaces: ["${TUTORIAL}/tools/pepatac/project_pipeline_interface.yaml"]

sample_modifiers: append: pipeline_interfaces: ["${TUTORIAL}/tools/pepatac/sample_pipeline_interface.yaml"] derive: attributes: [read1, read2] sources:

Obtain tutorial data from http://big.databio.org/pepatac/ then set

  # path to your local saved files
  R1: "${TUTORIAL}/data/{sample_name}_r1.fastq.gz"
  R2: "${TUTORIAL}/data/{sample_name}_r2.fastq.gz"

imply:

• if: organism: ["human", "Homo sapiens", "Human", "Homo_sapiens"] then: genome: hg38 prealignment_names: ["rCRSd"] deduplicator: samblaster # Default. [options: picard] trimmer: skewer # Default. [options: pyadapt, trimmomatic] peak_type: fixed # Default. [options: variable] extend: "250" # Default. For fixed-width peaks, extend this distance up- and down-stream. frip_ref_peaks: None # Default. Use an external reference set of peaks instead of the peaks called from this run`

[peculiar97]

Update: The problem was solved by providing the right parameters for the refgenie.

[Ruthwww]

Update: The problem was solved by providing the right parameters for the refgenie.

Would u like to tell me more information on solving the problem by setting the parameters, thank you so much！