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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
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broadpeak calling is off #114

Closed fanying2015 closed 6 years ago

fanying2015 commented 6 years ago

The pipeline seems to be working fine generally, but I can't get any broadpeaks or gapped peaks after finishing the whole pipeline.

--------------------Stderr-------------------- INFO @ Wed, 09 May 2018 06:23:35:

Command line: callpeak -t /pbtech_mounts/khuranalab_scratch_athena/fta2001/Flow/Flow/ATAC_ENCODE_Pipeline_mouse/1/out/align/rep1/Chr3164_EYFP-1_AT_A12_TGCTGGGT_IGO_08155_3_S34_R1_001.trim.PE2SE.nodup.tn5.tagAlign.gz -f BED -n /pbtech_mounts/khuranalab_scratch_athena/fta2001/Flow/Flow/ATAC_ENCODE_Pipeline_mouse/1/out/peak/macs2/rep1/Chr3164_EYFP-1_AT_A12_TGCTGGGT_IGO_08155_3_S34_R1_001.trim.PE2SE.nodup.tn5.pf -g mm -p 0.01 --nomodel --shift -75 --extsize 150 -B --SPMR --keep-dup all --call-summits

ARGUMENTS LIST:

name = /pbtech_mounts/khuranalab_scratch_athena/fta2001/Flow/Flow/ATAC_ENCODE_Pipeline_mouse/1/out/peak/macs2/rep1/Chr3164_EYFP-1_AT_A12_TGCTGGGT_IGO_08155_3_S34_R1_001.trim.PE2SE.nodup.tn5.pf

format = BED

ChIP-seq file = ['/pbtech_mounts/khuranalab_scratch_athena/fta2001/Flow/Flow/ATAC_ENCODE_Pipeline_mouse/1/out/align/rep1/Chr3164_EYFP-1_AT_A12_TGCTGGGT_IGO_08155_3_S34_R1_001.trim.PE2SE.nodup.tn5.tagAlign.gz']

control file = None

effective genome size = 1.87e+09

band width = 300

model fold = [5, 50]

pvalue cutoff = 1.00e-02

qvalue will not be calculated and reported as -1 in the final output.

Larger dataset will be scaled towards smaller dataset.

Range for calculating regional lambda is: 10000 bps

Broad region calling is off

Paired-End mode is off

Searching for subpeak summits is on

MACS will save fragment pileup signal per million reads

  I've ran some debugged codes as suggested in other issues. The result is attached.

Thanks!!

screen shot 2018-05-14 at 12 37 33 am
fanying2015 commented 6 years ago

The StdErr message of the whole pipeline is attached here. Thanks! ATAC_ENCODE_Pipeline_mouse.1.bsub.txt

akundaje commented 6 years ago

This is by design. The broad and gapped peak implementation is very flawed in MACS2 and gives incoherent results. So we don't support it any more.

We will be providing another strategy to call broad peaks in the near future.

Anshul.

On May 13, 2018 9:48 PM, "fanying2015" notifications@github.com wrote:

The StdErr message of the whole pipeline is attached here. Thanks! ATAC_ENCODE_Pipeline_mouse.1.bsub.txt https://github.com/kundajelab/atac_dnase_pipelines/files/1999388/ATAC_ENCODE_Pipeline_mouse.1.bsub.txt

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fanying2015 commented 6 years ago

Thank you for the quick response, Anshul!