Jin wook Lee

Please try with `-Dbackend.provider.google.config.root=gs://YOUR_BUCKET_NAME`. Your bucket name should start with `gs://`. You don't need to make your own genome data buckets. Pick a genome TSV file under `gs://encode-pipeline-genome-data/`. This bucket...

@llz-hiv, that dxWDL thing is a known issue. For the latest dxWDL, you need to add `-project [NAME_OF_YOUR_DNANEXUS_PRJ]` to the command line. About the bucket permission problem... Does `gsutil cp...

As described in the instruction web page, did you run the following to store Google Cloud credential information on your computer? ``` $ gcloud auth login --no-launch-browser $ gcloud auth...

FYI, `/cromwell_root/` is a directory for localized files in an instance. For every sub-task, cromwell copies files on buckets into an instance on this directory. I created a new google...

Can you increase memory for MACS2 (by adding `-mem_macs2 20G` to the command line) and try again? some references: https://github.com/JuliaLang/julia/issues/14807 https://stackoverflow.com/questions/27825280/change-the-rlimit-nproc-in-linux

The latest atac-seq-pipeline does not have `conda/install_genome_data.sh`. Are you guys using an old version? The latest one has `conda/build_genome_data.sh`

Please post a full log. `-nth 16` means total number of threads for the pipeline. You have 3 replicates so 16 threads are distributed to these threads according to the...

This is a disk space problem. Please check disk space on 1) your working directory where you ran the pipeline command line. 2) your pipeline git directory (`/home/$USER` usually have...

We no longer maintain this pipeline. Please try with a new one at https://github.com/ENCODE-DCC/atac-seq-pipeline

https://encode-dcc.github.io/wdl-pipelines/install.html#local-computer-with-docker @raboul101: We are sorry about that, we wanted to have a unified documentation for all pipelines but that made users confusing. We will update the documentation. Until then, please...