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49 Open 127 Closed
49 Open 127 Closed
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Issues list

Insufficient peaks in pseudoreplicates resulting in chip.idr_ppr failure
#307 opened Sep 18, 2024 by nursyahr
Can chip-seq-pipeline2 run locally without internet?
#306 opened Jun 26, 2024 by cyz0315
1
Datasets for TF-target genes
#305 opened Mar 19, 2024 by yiqisu
pipeline stuck in call-macs2_signal_track_pooled
#302 opened Jan 11, 2024 by cmf1997
How do you resume ?
#301 opened Oct 27, 2023 by olechnwin
missing slurm qos parameter
#300 opened Oct 13, 2023 by giardine
2
how to create pseudo-replicate files
#299 opened Sep 22, 2023 by songxh1996
1
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 Sep 1, 2023 by ezioljj
2
signal track height is higher for input control
#297 opened May 20, 2023 by jamesaliba
1
no motif output
#296 opened May 20, 2023 by jamesaliba
The pipeline stops at Job chip.read_genome_tsv
#295 opened May 19, 2023 by peculiar97
10
Fixed peak size
#294 opened Apr 17, 2023 by kbattenb
1
”caper init local“ error
#293 opened Apr 5, 2023 by songxh1996
3
caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1
#292 opened Feb 23, 2023 by ritetsu
1
Changing MACS2 output from earlier pipeline version
#291 opened Jan 25, 2023 by clarabakker
2
Conflicts while running scripts/install_conda_env.sh
#285 opened Aug 17, 2022 by agduncan94
3
HELP: call-xcor fails with TEST command
#284 opened Jun 20, 2022 by yinyeya
3
Are adapter-trimmed FASTQs required?
#283 opened Jun 14, 2022 by benayang
3
Where are the peak files from MACS2 output stored?
#280 opened Jun 7, 2022 by gene-drive
Terra output missing metadata.json
#278 opened Apr 6, 2022 by elisadonnard
1
can this wdl pipeline be run with cromwell engine?
#277 opened Apr 6, 2022 by gudeqing
Pipeline stalls before IDR steps
#276 opened Apr 5, 2022 by gene-drive
3
Issue with running tf file
#272 opened Mar 6, 2022 by shirleytemples
6
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 Jan 12, 2022 by louisgevirtzman
8
pipeline fails trying to connect to auth.docker.io
#256 opened Jan 10, 2022 by GodloveD
8
ProTip! What’s not been updated in a month: updated:<2024-11-27.