Jin wook Lee

There are many template input JSON files in `/examples/` (for each platform, pick up any JSON in `/examples/klab/` for local pipeline running). `bandend.conf` is in `/backends/`. We strongly recommend that...

New pipeline repo is https://github.com/ENCODE-DCC/atac-seq-pipeline/

FRIP scores should be on the report.html. Can you upload your `report.html` it here so that I can take a look?

It looks like you are looking at old pipeline? Pipeline no longer uses BEDPE to make pseudo replicates for paired end data sets. Please take a look at `spr_tag_PE()` in...

If you don't explicitly specify output directory with `-out_dir [SOMEWHERE]` then `out/` will be generated on the working directory where you ran the pipeline command. Also skip `-gensz mm`. it's...

Did you specify species (hg38, mm10, ...) by `-species [SPECIES]`? Did you install genome data correctly? Did you see a "success" message at the end of the genome data installation...

Please post a full log (including `Bowtie2 index (-bwt2_idx) doesn't exists!`) for debugging info. Also, what is the full command line that you used for running a pipeline?

Please do the following for more info: ``` $ cat /homes/reham/ATAC-Seq/atac_dnase_pipelines/default.env $ ls -l /homes/reham/ATAC-Seq/genomes/mm10 $ ls -l /homes/reham/ATAC-Seq/genomes ``` Jin ``` On Mon, Jul 2, 2018 at 8:22 AM,...

Please just post them here On Mon, Jul 2, 2018 at 9:04 AM, rehamFatima wrote: > Thanks Jin, > > should I send you the output for these ? >...

Please add `-species_file /nfs/nobackup/ensembl/reham_ens/genome/bds_atac_species.conf` to the command line and try again.