ENCODE-DCC/chip-seq-pipeline2

Issues

• conda list ucsc-twobittofa

  #308 opened 2 months ago by YasaminRaziee
  2

• Insufficient peaks in pseudoreplicates resulting in chip.idr_ppr failure

  #307 opened 3 months ago by nursyahr
  0

• pipeline fails trying to connect to auth.docker.io

  #256 opened 3 years ago by GodloveD
  8

• Can chip-seq-pipeline2 run locally without internet?

  #306 opened 6 months ago by cyz0315
  1

• signal track height is higher for input control

  #297 opened 2 years ago by jamesaliba
  1

• Datasets for TF-target genes

  #305 opened 9 months ago by yiqisu
  0

• pipeline stuck in call-macs2_signal_track_pooled

  #302 opened a year ago by cmf1997
  0

• Error in Alignment process : Call input and runtime attributes evaluation failed for align: Failed to evaluate input 'tmp_fastqs' (reason 1 of 1): transpose requires all collections have the same size

  #290 opened 2 years ago by cafri1105
  2

• missing slurm qos parameter

  #300 opened a year ago by giardine
  2

• how to create pseudo-replicate files

  #299 opened a year ago by songxh1996
  1

• How do you resume ?

  #301 opened a year ago by olechnwin
  0

• The pipeline stops at Job chip.read_genome_tsv

  #295 opened 2 years ago by peculiar97
  10

• Does the calculation of sval in encode_task_macs2_signal_track_chip.py take into account the difference between single-end and paired-end data?

  #298 opened a year ago by ezioljj
  2

• no motif output

  #296 opened 2 years ago by jamesaliba
  0

• Fixed peak size

  #294 opened 2 years ago by kbattenb
  1

• ”caper init local“ error

  #293 opened 2 years ago by songxh1996
  3

• Are adapter-trimmed FASTQs required?

  #283 opened 3 years ago by benayang
  3

• caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1

  #292 opened 2 years ago by ritetsu
  1

• Changing MACS2 output from earlier pipeline version

  #291 opened 2 years ago by clarabakker
  2

• Problem about build_genome_data.sh

  #279 opened 2 years ago by Mozillian1
  2

• No peak call output from "TF" pipeline

  #289 opened 2 years ago by jsemple19
  4

• caper.wdl_parser|ERROR| Failed to parse WDL with miniwdl.

  #288 opened 2 years ago by wbszhu
  2

• Conflicts while running scripts/install_conda_env.sh

  #285 opened 2 years ago by agduncan94
  3

• Terra output missing metadata.json

  #278 opened 3 years ago by elisadonnard
  1

• HELP: call-xcor fails with TEST command

  #284 opened 2 years ago by yinyeya
  3

• Where are the peak files from MACS2 output stored?

  #280 opened 3 years ago by gene-drive
  0

• Pipeline stalls before IDR steps

  #276 opened 3 years ago by gene-drive
  3

• can this wdl pipeline be run with cromwell engine?

  #277 opened 3 years ago by gudeqing
  0

• Advice on output folders/files

  #273 opened 3 years ago by gene-drive
  1

• Issue with running tf file

  #272 opened 3 years ago by shirleytemples
  6

• |ERROR| Failed to parse WDL with miniwdl, |ERROR| Conda environment name not found in WDL metadata

  #271 opened 3 years ago by shirleytemples
  1

• Run gives error

  #266 opened 3 years ago by shirleytemples
  12

• Unable to run caper on windows

  #258 opened 3 years ago by silentsilencee
  3

• parrallel proccessing with spp

  #268 opened 3 years ago by louisgevirtzman
  2

• TEST run gave an error. Please help!

  #265 opened 3 years ago by yingsun-ucsd
  6

• chip-seq-pipeline2 run with conda on linux with ERROR

  #242 opened 3 years ago by yingsun-ucsd
  5

• call-xcor fails before peak calling

  #261 opened 3 years ago by wx2022
  4

• cc.plot.png, cc.fraglen, no such file or directory

  #259 opened 3 years ago by shirleytemples
  5

• A question about the use of fragment length estimated from cross-correlation analysis.

  #260 opened 3 years ago by yr-gh
  0

• caper.caper_workflow_opts|INFO| Conda environment name not found in WDL metadata. wdl=/net/waterston/vol2/home/gevirl/chip-seq-pipeline2-2.1.2/chip.wdl

  #257 opened 3 years ago by louisgevirtzman
  8

• bedClip: command not found,Fail to run chip.call_peak workflow when test example

  #250 opened 3 years ago by ckfromCN
  4

• An error occurs when running the process with test data

  #253 opened 3 years ago by tyewaichung
  3

• libreadline.so.6: cannot open shared object file: No such file or directory

  #254 opened 3 years ago by tyewaichung
  1

• Job chip.spp_pooled:NA:1 exited with return code 1

  #249 opened 3 years ago by jkanbar
  0

• Error in chip.align tasks (Failed to evaluate job outputs)

  #226 opened 4 years ago by sqreb
  5

• Failed to evaluate input error when running pipeline

  #238 opened 3 years ago by kmualim
  3

• Example Chip-seq JSON not working

  #240 opened 3 years ago by grevetjd
  2

• Can I run chip-seq-pipeline without input files?

  #236 opened 3 years ago by Reemann
  3

• inquiry about reproducibility results

  #237 opened 3 years ago by monnneee
  0

• Example JSON not working

  #235 opened 3 years ago by lcamillo
  3