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  • #1

    Chip-seq RSEG deadzone

    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
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