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sc-zhang / ALLHiC_components

Some components that speed up and reduce resource cost for original ALLHiC
BSD 3-Clause "New" or "Revised" License
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ALLHiC_prune #1

Closed wyim-pgl closed 1 year ago

wyim-pgl commented 2 years ago

Hi @sc-zhang! I am trying to use ALLHiC_prune. However, it kept generating "Segmentation fault (core dumped)" in "Getting contig pairs" step

I am using below version as environment.

gcc | 9.2.0
libgcc_mutex | 0.1
openmp_mutex | 4.5
bzip2 | 1.0.8
c-ares | 1.18.1
ca-certificates | 2021.10.26
htslib | 1.14
krb5 | 1.19.2
libcurl | 7.81.0
libdeflate | 1.9
libedit | 3.1.20210910
libev | 4.33
libgcc-ng | 11.2.0
libgomp | 11.2.0
libnghttp2 | 1.46.0
libssh2 | 1.10.0
libstdcxx-ng | 11.2.0
libzlib | 1.2.11
ncurses | 6.3
openssl | 1.1.1m
tk | 8.6.11
xz | 5.2.5
zlib | 1.2.11

image

Do you have any idea and recommendations? Also I found same error from ALLHiC repository.

Thanks Won

sc-zhang commented 2 years ago

It may caused by adding all reads name which need to be removed to an hash table. I modified it these days, and reduced the cost of memory, now the usage of memory just depends on how many contigs here. And you may try the newest version of ALLHiC_prune in the main branch of this repo.