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ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
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Failed to evaluate input error when running pipeline #238

Open kmualim opened 2 years ago

kmualim commented 2 years ago

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

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 2 years ago

What is caper's version?

$ caper -v
kmualim commented 2 years ago

caper v1.6.3

leepc12 commented 2 years ago

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.