Comments (3)
We just bypass this issue by splitting chromsomes/scaffolds. Maybe you can consider similar way to fix this bug.
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I am having the same problem:
effective genome size = 3.60e+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: 1000 bps and 10000 bps
Broad region calling is off
Paired-End mode is off
MACS will save fragment pileup signal per million reads
INFO @ Fri, 11 Jan 2019 11:37:33: #1 read tag files...
INFO @ Fri, 11 Jan 2019 11:37:33: #1 read treatment tags...
INFO @ Fri, 11 Jan 2019 11:37:37: 1000000
INFO @ Fri, 11 Jan 2019 11:37:41: 2000000
INFO @ Fri, 11 Jan 2019 11:37:45: 3000000
INFO @ Fri, 11 Jan 2019 11:37:49: 4000000
INFO @ Fri, 11 Jan 2019 11:37:53: 5000000
INFO @ Fri, 11 Jan 2019 11:37:57: 6000000
INFO @ Fri, 11 Jan 2019 11:38:01: 7000000
INFO @ Fri, 11 Jan 2019 11:38:05: 8000000
INFO @ Fri, 11 Jan 2019 11:38:10: 9000000
INFO @ Fri, 11 Jan 2019 11:38:15: 10000000
INFO @ Fri, 11 Jan 2019 11:38:21: 11000000
INFO @ Fri, 11 Jan 2019 11:38:28: 12000000
INFO @ Fri, 11 Jan 2019 11:38:32: 13000000
INFO @ Fri, 11 Jan 2019 11:38:36: 14000000
INFO @ Fri, 11 Jan 2019 11:38:40: 15000000
INFO @ Fri, 11 Jan 2019 11:38:45: 16000000
INFO @ Fri, 11 Jan 2019 11:38:49: 17000000
INFO @ Fri, 11 Jan 2019 11:38:54: 18000000
INFO @ Fri, 11 Jan 2019 11:38:59: 19000000
INFO @ Fri, 11 Jan 2019 11:39:02: 20000000
Killed
I was using 80GB. Is this a memory issue?
from macs.
Closing years old issues. Please reopen if you are still interested.
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Related Issues (20)
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- What is the difference between "absolute peak summit" and "summit position" in narrowPeak format? HOT 1
- Q: conversion of output files to UCSC track hub format? HOT 1
- Feat: Enhanced clarification of the specific definition of BEDPE as used by MACS HOT 1
- Feat: Reduction of memory consumption HOT 3
- Q: HMMRATAC output and options for _summit.bed HOT 1
- Feat: Built-in scoring for HMMRATAC HOT 1
- Q: HMMRATAC producing too many peaks HOT 10
- Bug: undefined symbol: __pow_finite HOT 3
- Q: HMMRATAC reproducibility HOT 2
- Q: how to use MACS3 for ATAC seq with "himmratac" option? HOT 2
- Bug: Callvar throws an error when run on broadPeak file HOT 15
- Q: impact of sequencing throughput on peak calling HOT 4
- Setting cut-off when using logFE bigWig files from bdgcmp
- Q: How to use HMMRATAC to give us a narrow peak file and have signalValue, p and q-value ? HOT 1
- Bug: OverflowError when running hmmratac
- Number of de-duplicated reads indicated by filterdup log does not match number of lines in output BED file.
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