Bad_alloc for deep Hi-C dataset

[jimwry]

Hi,

I've been trying to use chromap for Hi-C data. It is very convenient and super fast!

I have no problem for most Hi-C dataset, however I encountered an "bad_alloc" issue for ultra-deep Hi-C. (more than 1 billion reads). I attached my command line and log below, do you have any idea about solving this issue? Many thanks Jim

CPU： 80 threads, memory: 125GB.

command: chromap --preset hic -x chromap-mm10 -r mm10.fa -1 SRR9906313_GSM4010832_HiC_Retina_Adult-Rep1_Mus_musculus_Hi-C_1.fastq.gz -2 SRR9906313_GSM4010832_HiC_Retina_Adult-Rep1_Mus_musculus_Hi-C_2.fastq.gz -o SRR9906313_HiC_Retina_Adult-Rep1_Hi-C.chromap.pairs -t 64 log : "Mapped all reads in 6054.02s. Number of reads: 2866604954. Number of mapped reads: 2582847256. Number of uniquely mapped reads: 2315287482. Number of reads have multi-mappings: 267559774. Number of candidates: 109967150601. Number of mappings: 2582847256. Number of uni-mappings: 2315287482. Number of multi-mappings: 267559774. terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc"

[haowenz]

Sorry for the late reply. You are right. It seems that there are just too many reads. We will try to fix this soon. Thanks for trying the tool.

[jimwry]

Hi Haowen,

No worries, I have split the reads into smaller input, and run it separately. And it worked well.

Thanks for your attention.

[yuzhenpeng]

Hi Haowen,

No worries, I have split the reads into smaller input, and run it separately. And it worked well.

Thanks for your attention.

How to split the paired reads

[yuzhenpeng]

some one solved this problem?

[jimwry]

You could use fastqsplitter(https://fastqsplitter.readthedocs.io/en/stable/)

[yuzhenpeng]

You could use fastqsplitter(https://fastqsplitter.readthedocs.io/en/stable/)

thank you.