Jin wook Lee

You have irregular chromosomes (`chr20_GL383577v2_alt`), which is not covered our default chromosome sizes file, in your BAM file. Please use your own chromosome sizes file (define it with `-chrsz`) or...

@computbiolgeek Please post your input JSON for the new pipeline and command line for the old one.

No, both use the same default idr threshold (0.1). Please upload your input JSON file. It seems like you have `"atac.idr_thresh" : 0.05` in it. Jin On Thu, Sep 6,...

https://github.com/kundajelab/atac_dnase_pipelines#bigdatascript Did you add Java options to your ~/.bashrc?

You didn't specify `-species` and `-species_file` correctly. Please see README for details. Your species_file is wrong. It's pointing to a fasta file. It should be a text file (INI) containing...

`$ bds atac.bds` will just show help. Please check if you installed BDS (forked) correctly. https://github.com/kundajelab/atac_dnase_pipelines#bigdatascript Also, the pipeline itself https://github.com/kundajelab/atac_dnase_pipelines#pipeline

You can try removing trim-galore and change the version of bowtie2 in `requirements.txt`. Check available versions for MacOS here https://anaconda.org/bioconda/bowtie2/files. However, we strongly recommend to install docker and use our...

MacBook Pro doesn't have enough resources to run pipelines smoothly. Please try to add `"atac.bowtie2.cpu" : 1,` in your input JSON (see the resource section https://encode-dcc.github.io/wdl-pipelines/input_json_atac.html for details). Also try...

@llz-hiv : please take a look https://encode-dcc.github.io/wdl-pipelines/install.html#running-mysql-server-with-docker

It's a Google Cloud bucket permission problem. Go to the Google Cloud Project console and click on the vertical `...` at the right end of your bucket name and then...