ENCODE-DCC/chip-seq-pipeline2

Failed to evaluate input error when running pipeline

kmualim opened this issue · 3 comments

kmualim commented

Describe the bug

I can't seem to run the pipeline, it keeps saying Failed to evaluate input 'fastqs_rep1_R1' (reason 1 of 1): No coercion defined from '"/oak/stanford/groups/akundaje/kmualim/06062021_ChromModelling/fastq/ENCFF680HKS.fastq.gz"' of type 'spray.json.JsString' to 'Array[File]'.

OS/Platform

  • OS/Platform: Stanford Sherlock
  • Conda version: conda 4.10.3
  • Pipeline version: v1.9.0
  • Caper version: running caper --version takes forever for some reason.

Input JSON file

{
    "chip.ctl_fastqs_rep1_R1": [ "/oak/stanford/groups/akundaje/kmualim/06062021_ChromModelling/fastq/ENCFF884PXT.fastq.gz"],
    "chip.ctl_fastqs_rep2_R1": [ "/oak/stanford/groups/akundaje/kmualim/06062021_ChromModelling/fastq/ENCFF884PXT.fastq.gz"],
    "chip.enable_idr": "true",
    "chip.fastqs_rep1_R1": [ "/oak/stanford/groups/akundaje/kmualim/06062021_ChromModelling/fastq/ENCFF247YSO.fastq.gz"],
    "chip.fastqs_rep2_R1": [ "/oak/stanford/groups/akundaje/kmualim/06062021_ChromModelling/fastq/ENCFF453TXD.fastq.gz"],
    "chip.genome.tsv": "https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v3/hg38.tsv",
    "chip.idr_thresh": 0.05,
    "chip.paired_end": "false",
    "chip.peak_caller": "macs2",
    "chip.pipeline_type": "tf",
    "chip.title": "AKAP8-human_HepG2"
}

Troubleshooting result

Unfortunately, because the Caper server dies, I am unable to use caper troubleshoot to diagnose. cromwell.out is empty since I'm assuming the workflow doesn't start due to the failure in evaluating the input above.

leepc12 commented

What is caper's version?

$ caper -v
kmualim commented

caper v1.6.3

leepc12 commented

Please check your java version with module avail java.
You need Java >=11.
Btw I will be releasing new stable caper + new atac/chip pipelines soon by end of this week.
That will fix all dependency/singularity/slurm problems.