Open gbloeb opened 2 years ago
does anyone has an update on this issue? encounter the same problem. Thanks.
I am also having this issue
The issue seems to persist. I am also having this issue. @donaldcampbelljr Could you do me a favor to solve the issue?Thanks!
@ljmills Did you ever find a solution? Thanks!
Ran a project with reference peaks, but I am unable to generate a count table for the reference peaks: When the project is run: 1) peaks are still called for each sample individually 2) Each sample/peak_calling_mm10 directory contains both: GLIS3_Ctrl_1_S2_ref_peaks_coverage.bed corresponding to the reference peaks and GLIS3_Ctrl_1_S2_peaks_coverage.bed.gz corresponding to the called peaks
When I run the project processing pipeline, consensus peaks are still generated and the count table is generated with the consensus peaks with the warning: Warning message: In PEPATACr::peakCounts(sample_table, summary_dir, argv$results, : Peak coverage files are not derived from a singular reference peak set.
My config:
a sample log file: PEPATAC_log.md
project log file: `### Pipeline run code and environment:
/wynton/protected/home/reiter/gloeb/pepatac/pipelines/pepatac_collator.py --config /wynton/protected/home/reiter/gloeb/pepatac/220126_GLIS_ATAC_IMCD3/config_GLIS_doxpctrl_shift.bed_nolambda_q0.0000001_sh-30_peaks.yaml -O /wynton/protected/home/reiter/gloeb/group/bulk_atac/220126_GLIS_ATAC_IMCD3/GLIS3_nolambda_qe-7_sh-30_peaks/pepatac_results -P 1 -M 16G -n GLIS3_ATAC_nolambda_qe-7_sh-30_peaks -r /wynton/protected/home/reiter/gloeb/group/bulk_atac/220126_GLIS_ATAC_IMCD3/GLIS3_nolambda_qe-7_sh-30_peaks/pepatac_results/results_pipeline
Version log:
/wynton/protected/home/reiter/gloeb/miniconda3/envs/pepatac/lib/python3.9/site-packages/pypiper
/wynton/protected/home/reiter/gloeb/pepatac/pipelines
Arguments passed to pipeline:
config_file
:/wynton/protected/home/reiter/gloeb/pepatac/220126_GLIS_ATAC_IMCD3/config_GLIS_doxpctrl_shift.bed_nolambda_q0.0000001_sh-30_peaks.yaml
cores
:1
cutoff
:2
dirty
:False
force_follow
:False
logdev
:False
mem
:16G
min_olap
:1
min_score
:5
name
:GLIS3_ATAC_nolambda_qe-7_sh-30_peaks
new_start
:False
normalized
:False
output_parent
:/wynton/protected/home/reiter/gloeb/group/bulk_atac/220126_GLIS_ATAC_IMCD3/GLIS3_nolambda_qe-7_sh-30_peaks/pepatac_results
poverlap
:False
recover
:False
results
:/wynton/protected/home/reiter/gloeb/group/bulk_atac/220126_GLIS_ATAC_IMCD3/GLIS3_nolambda_qe-7_sh-30_peaks/pepatac_results/results_pipeline
silent
:False
skip_consensus
:False
skip_table
:False
testmode
:False
verbosity
:None
Target to produce:
/wynton/protected/home/reiter/gloeb/group/bulk_atac/220126_GLIS_ATAC_IMCD3/GLIS3_nolambda_qe-7_sh-30_peaks/pepatac_results/summary/GLIS3_ATAC_nolambda_qe-7_sh-30_peaks_libComplexity.pdf
,/wynton/protected/home/reiter/gloeb/group/bulk_atac/220126_GLIS_ATAC_IMCD3/GLIS3_nolambda_qe-7_sh-30_peaks/pepatac_results/summary/GLIS3_ATAC_nolambda_qe-7_sh-30_peaks_*_consensusPeaks.narrowPeak
,/wynton/protected/home/reiter/gloeb/group/bulk_atac/220126_GLIS_ATAC_IMCD3/GLIS3_nolambda_qe-7_sh-30_peaks/pepatac_results/summary/GLIS3_ATAC_nolambda_qe-7_sh-30_peaks_peaks_coverage.tsv
WARNING: y-max value changed from default 139.24586665 to the max real data 201.6892724 Successfully produced project summary plots.
Calculating mm10 consensus peak set from 4 samples... Consensus peak set: /wynton/protected/home/reiter/gloeb/group/bulk_atac/220126_GLIS_ATAC_IMCD3/GLIS3_nolambda_qe-7_sh-30_peaks/pepatac_results/summary/GLIS3_ATAC_nolambda_qe-7_sh-30_peaks_mm10_consensusPeaks.narrowPeak
Calculating mm10 peak counts for 4 samples... Counts table: /wynton/protected/home/reiter/gloeb/group/bulk_atac/220126_GLIS_ATAC_IMCD3/GLIS3_nolambda_qe-7_sh-30_peaks/pepatac_results/summary/GLIS3_ATAC_nolambda_qe-7_sh-30_peaks_mm10_peaks_coverage.tsv
Counts table: /wynton/protected/home/reiter/gloeb/group/bulk_atac/220126_GLIS_ATAC_IMCD3/GLIS3_nolambda_qe-7_sh-30_peaks/pepatac_results/summary/GLIS3_ATAC_nolambda_qe-7_sh-30_peaks_mm10_peaks_coverage.tsv
Warning message: In PEPATACr::peakCounts(sample_table, summary_dir, argv$results, : Peak coverage files are not derived from a singular reference peak set. Command completed. Elapsed time: 0:00:57. Running peak memory: 0.91GB. PID: 9429; Command: Rscript; Return code: 0; Memory used: 0.91GB
Pipeline completed. Epilogue
`