Chip-seq RSEG deadzone

Nino

Member

Join Date: Mar 2013

Posts: 27
- Share
- Tweet
#1

Chip-seq RSEG deadzone

12-15-2014, 12:37 PM

Hello,

I am currently using RSEG to do my broad peak calls on my chip-seq data (human). It requires a deadzone bed file based off of the read length of the bam file. I am currently running the command below and getting the error.

[compute-055 /amber3/feinbergLab/personal/sramazan/Chip-seq/test_kit]$ /home/jhmi/xinli/bin/deadzones -s fa -k 50 -p 4 -v -o deadzones-hg19-k50.bed /amber3/feinbergLab/personal/sramazan/hg19/
[IDENTIFYING CHROMS] [DONE]
chromosome files found (approx size):
/amber3/feinbergLab/personal/sramazan/hg19/hg19.fa (3200Mbp)

[READING SEQUENCE FILES]
ERROR: could not allocate memory

I tried a second solution to read in the chr's split:

[compute-055 /amber3/feinbergLab/personal/sramazan/Chip-seq/test_kit]$ /home/jhmi/xinli/bin/deadzones -s fa -k 50 -p 4 -v -o deadzones-hg19-k50.bed /home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/
[IDENTIFYING CHROMS] [DONE]
chromosome files found (approx size):
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr7.fa (162Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr13.fa (117Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/lambda.fa (0Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr12.fa (137Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr6.fa (175Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr4.fa (195Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr10.fa (138Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr11.fa (138Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr5.fa (185Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr15.fa (105Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr1.fa (254Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr14.fa (109Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr16.fa (92Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr2.fa (248Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/zymo.fa (0Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr3.fa (202Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr17.fa (83Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chrX.fa (158Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chrY.fa (61Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/ecoli.fa (5Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chrM.fa (0Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr9.fa (144Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr8.fa (149Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr18.fa (80Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr20.fa (64Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr21.fa (49Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr19.fa (60Mbp)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr22.fa (52Mbp)

[READING SEQUENCE FILES]
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr7.fa (SEQS: 1)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr13.fa (SEQS: 1)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/lambda.fa (SEQS: 1)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr12.fa (SEQS: 1)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr6.fa (SEQS: 1)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr4.fa (SEQS: 1)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr10.fa (SEQS: 1)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr11.fa (SEQS: 1)
/home/jhmi/xinli/amber3/no_back_up/data/genome/Homo_sapiens/UCSC/hg19/Sequence/Chromosomes/chr5.fa (SEQS: 1)
ERROR: could not allocate memory

Still I get the same error.

I have contacted the author who recommended for the -p or -prefix to be set to 4 but as you can see above still same error. If anyone has a solution to this problem I would appreciate the help.

Thanks,
Nino
Tags: None

Previous template Next

Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by GATTACAT

Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
- Channel: Articles
07-01-2026, 11:43 AM
Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by SEQadmin2

I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

Here are nine questions we think about, in roughly the order they matter, before...
- Channel: Articles
06-18-2026, 07:11 AM

Topics	Statistics	Last Post
High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2 Started by SEQadmin2, 07-02-2026, 11:08 AM	0 responses 16 views 0 reactions	Last Post by SEQadmin2 07-02-2026, 11:08 AM
New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2 Started by SEQadmin2, 06-30-2026, 05:37 AM	0 responses 17 views 0 reactions	Last Post by SEQadmin2 06-30-2026, 05:37 AM
Large-Scale Protein Screen Uncovers Hidden Regulators of Alternative Polyadenylation by SEQadmin2 Started by SEQadmin2, 06-26-2026, 11:10 AM	0 responses 21 views 0 reactions	Last Post by SEQadmin2 06-26-2026, 11:10 AM
Whole-Genome Sequencing Traces Faroe Islands Ancestry to a North Atlantic Founder Population by SEQadmin2 Started by SEQadmin2, 06-17-2026, 06:09 AM	0 responses 54 views 0 reactions	Last Post by SEQadmin2 06-17-2026, 06:09 AM

Unconfigured Ad

Chip-seq RSEG deadzone

Latest Articles

ad_right_rmr

News