Error during initialization of module CHOLMOD

[jdm204]

Hi, thanks for the tool and maintaining it!

I just ran it for the first time, and it output trimmed reads, but the initial output contains this error:

┌ Error: Error during initialization of module CHOLMOD
│   exception =
│    could not load library "libcholmod"
│    libamd.so.2: cannot open shared object file: No such file or directory
│    Stacktrace:
│     [1] dlopen(s::String, flags::UInt32; throw_error::Bool)
│       @ Base.Libc.Libdl ./libdl.jl:117
│     [2] dlopen (repeats 2 times)
│       @ ./libdl.jl:116 [inlined]
│     [3] __init__()
│       @ SuiteSparse.CHOLMOD ~/scratch/atria/atria-4.0.3/share/julia/stdlib/v1.8/SuiteSparse/src/cholmod.jl:161
└ @ SuiteSparse.CHOLMOD /cache/build/default-amdci4-2/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/SuiteSparse/src/cholmod.jl:245

I'm not familiar with the code so unsure if this is a serious issue that will affect the output, as the tools did finish on my reads.

Here is the atria information:

pigz 2.8
┌ Info: ATRIA VERSIONS
│   atria = "v4.0.3"
└   julia = "v1.8.5"
┌ Info: ATRIA ARGUMENTS
└   command = `-t 4 --polyG -r LH20_blood_EKDN240004237-1A_2237NFLT4_L4_1.fq.gz -R LH20_blood_EKDN240004237-1A_2237NFLT4_L4_2.fq.gz`
┌ Info: ATRIA OUTPUT FILES
│   read1 = "/home/jdm204/scratch/atria/LH20_blood_EKDN240004237-1A_2237NFLT4_L4_1.atria.fq.gz"
└   read2 = "/home/jdm204/scratch/atria/LH20_blood_EKDN240004237-1A_2237NFLT4_L4_2.atria.fq.gz"
┌ Info: ATRIA TRIMMERS AND FILTERS
│   adapter_trimming = true
│   consensus_calling = true
│   hard_clip_3_end_r1 = false
│   hard_clip_3_end_r2 = false
│   hard_clip_5_end_r1 = false
│   hard_clip_5_end_r2 = false
│   quality_trimming = true
│   tail_N_trimming = true
│   max_N_filtering = true
└   length_filtering = true

[cihga39871]

Hello, thank you for your interest in Atria and report this issue!

I am sorry that you have been found this error. You are right, it does not affect any function of Atria.

It is fixed in the latest version. You can download in the release page or build from source to avoid this message.

The error was introduced by a third party package called 'PackageCompiler'. If you want to know some details, you can check this link.

Have a great day,
Eric