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An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.

License: Other

Perl 1.68% Shell 11.60% Julia 84.73% R 1.99%

trim-adapters ngs trimmer trimming quality illumina paired-end

atria's People

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jdeveloperw asan-emirsaleh arturoarciniega

atria's Issues

Error during initialization of module CHOLMOD

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

ERROR: UndefVarError: uncompressed_size1 not defined on gzipped single-end input

Running atria on gzipped single-end input gives me this error:
ERROR: UndefVarError: uncompressed_size1 not defined

Stacktrace:
 [1] (::Atria.Trimmer.var"#cycle_wrapper_single_end#31"{Array{UInt8,1},Int64,NTuple{60,Array{Atria.FqRecords.FqRecord,1}},Array{Bool,1},Array{Array{UInt8,1},1}})() at /home/jc/projects/atria/src/Trimmer/wrapper_single_end.jl:421
 [2] julia_wrapper_atria_single_end(::Array{String,1}; exit_after_help::Bool) at /home/jc/projects/atria/src/Trimmer/wrapper_single_end.jl:464
 [3] julia_wrapper_atria_single_end at /home/jc/projects/atria/src/Trimmer/wrapper_single_end.jl:6 [inlined]
 [4] julia_main() at /home/jc/projects/atria/src/Atria.jl:74
 [5] top-level scope at none:1

Looking at the location of the error (Trimmer/wrapper_single_end.jl:421), it appears to be the first use of uncompressed_size1 in that file. The only place where I see uncompressed_size1 being defined is by the chunk_sizes function in Trimmer/wrapper.jl which works on two input files, not one.

OSX Release?

Where do I find the .osx.tar.gz file? I only see files for the linux releases.

When running atria v3.2.2 with switch --stats, encounter error not seen in v3.2.1

Hi, just want to report what seems to be a bug.

When running atria v3.2.2 with switch --stats, I encounter the following error:

"nested task error: UndefVarError: is_concensused not defined"

When I remove --stats from my call to atria v3.2.2, the program runs fine. When I call atria v3.2.1 with --stats, the program runs fine.

I noticed a variable is_concensused used in wrapper.jl#L385 and a variable is_consensused in consensus.jl. Note the minor difference in spelling between the two variables: conc in is_concensused and cons is_consensused. I wonder if this is related to the error?

A minimal example to reproduce the error:

#!/bin/bash

threads=8
fq_1="SRR7939018_1.fastq.gz"
fq_2="SRR7939018_2.fastq.gz"
d_trim="."

#  Obtain relatively small fastqs for testing
curl "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR793/008/SRR7939018/${fq_1}" > "${fq_1}"
curl "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR793/008/SRR7939018/${fq_2}" > "${fq_2}"

#  Run v3.2.2 with --stats: Encounter error
alias atria="\${HOME}/path/to/Atria/app-3.2.2/bin/atria"  # Change path as appropriate
atria \
    -t "${threads}" \
    -r "${fq_1}" \
    -R "${fq_2}" \
    -o "${d_trim}" \
    --no-length-filtration \
    --stats

#  Run v3.2.2 without --stats: Runs fine
atria \
    -t "${threads}" \
    -r "${fq_1}" \
    -R "${fq_2}" \
    -o "${d_trim}" \
    --no-length-filtration

#  Run v3.2.1 with --stats: Runs fine
alias atria="\${HOME}/path/to/Atria/app-3.2.1/bin/atria"  # Change path as appropriate
atria \
    -t "${threads}" \
    -r "${fq_1}" \
    -R "${fq_2}" \
    -o "${d_trim}" \
    --no-length-filtration \
    --stats

#  Run v3.2.1 without --stats: Runs fine
atria \
    -t "${threads}" \
    -r "${fq_1}" \
    -R "${fq_2}" \
    -o "${d_trim}" \
    --no-length-filtration

Question about the necessity of read trimming when using local/soft-clipping aligners

Hi Eric,

I have a quick question about the necessity of read trimming when using local/soft-clipping aligners. Historically, I've trimmed reads prior to alignment (both local and end-to-end) regardless of the downstream analysis (e.g., transcriptome assembly, differential binding from ChIP-seq, etc.) However, I've seen in search engine results and in some publications the following opinions (e.g., taken from here):

For counting applications such as differential gene expression (DGE), RNA-seq analysis, ChIP-seq, or ATAC-seq, read trimming is generally not required anymore when using modern aligners. For such studies local aligners or pseudo-aligners should be used. Modern “local aligners” like STAR, BWA-MEM, HISAT2, will “soft-clip” non-matching sequences. Pseudo-aligners like Kallisto or Salmon will also not have any problem with reads containing adapter sequences.

However, if the data are used for variant analyses, genome annotation or genome or transcriptome assembly purposes, we recommend read trimming, including both adapter and quality trimming.

I wanted to ask for your perspective on this, if you have anything to share, given your expertise and the development of Atria.

Thank you,
Kris

Multiple adapter specifying

Hello!
Amazing job! Thank you a lot for you this tool to create!

I have a question on specifying multiple adapter.
While doing round with --detect-adapter, the result would contain four strings for each direction. The are much shorter than default adapter sequences and several bases are different. Do I have to specify them all? How to specify multiple adapter seqs?

Best regards
Asan

More benchmark against existing tools

Thanks a lot for your tool! BBDuk can also do paired end adapter trimming, and I'm curious about how this tool compares against it. Could you also include BBDuk in your benchmark?

GC.safepoint

Add GC.safepoint() in codes.

Inserts a point in the program where garbage collection may run. This can be useful in rare cases in multi-threaded programs where some threads are allocating memory (and hence may need to run GC) but other threads are doing only simple operations (no allocation, task switches, or I/O). Calling this function periodically in non-allocating threads allows garbage collection to run.

Benchmarking against establishing trimming tools

Interesting paper. Would it be possible to add “cutadapt” or “scythe” to the benchmarking results? Given these are both established tools in the field specifically for adapter trimming I think performance comparisons to these could be quite informative.

command not found issue

Hello, I installed Atria on Mac as guided.
However, when I try to execute the command, it keeps showing command not found
as below:

Last login: Wed Dec 7 09:49:48 on ttys001
(base) ryu@Ryu ~ % cd atria
(base) ryu@Ryu atria % ls
2nd_2_Control_1.fastq.gz app-3.2.1
3rd_2_Control_1.fastq.gz app-3.2.1_2022-12-07T09-50
CHANGELOG.md benchmark
LICENSE.md build_atria.jl
Manifest.toml docs
Project.toml src
README.md test
adapter.known.txt
(base) ryu@Ryu atria % atria -h
zsh: command not found: atria
(base) ryu@Ryu atria %

can anybody have an idea on how to solve this?
I am not familiar with programming, so I think I am missing something or may be wrong working directory?

Thanks in advance,
Ryu

Trimming after adapter detection

Using the --detect-adapter flag does detect the adapters, but does not start trimming of the fastq files. The adapter sequences have to be copy-pasted into another atria command. Any way to automate this process? Thanks.

Too many arguments error

Hello @cihga39871
I have been trying to use atria for the first time but everytime I try to run it I get the too many arguments error as follows:
Running script:

#!/usr/bin/env bash

#Data locations
workDir="/media/geokit/Extreme SSD/Eugene"
echo 'work directory is' $workDir
ls "$workDir"
##Data1
Read1_1='/media/geokit/Extreme SSD/Eugene/S1_S1_L001_R1_001.fastq.gz'
Read1_2='/media/geokit/Extreme SSD/Eugene/S1_S1_L001_R2_001.fastq.gz'

##Data2
Read2_1='/media/geokit/Extreme SSD/Eugene/S2_S1_L001_R1_001.fastq.gz'
Read2_2='/media/geokit/Extreme SSD/Eugene/S2_S1_L001_R2_001.fastq.gz'

##Data3
Read3_1="$workDir/D_1.fastq.gz"
Read3_2="$workDir/D_2.fastq.gz"

#Atria analysis
##Data3
atria \
-r "$Read3_1"	\
-R "$Read3_2" \
-o $workDir/atria_trimming \
--detect-adapter --no-quality-trim \
-t 3 --no-tail-n-trim --max-n=-1 --no-length-filtration

Error:

work directory is /media/geokit/Extreme SSD/Eugene
atria_trimming	   D_1.fastq.gz  prtn-g.fasta  S1_S1_L001_R1_001.fastq	S2_S1_L001_R1_001.fastq.gz
atria_trimming.sh  D_2.fastq.gz  prtn-m.fasta  S1_S1_L001_R2_001.fastq	S2_S1_L001_R2_001.fastq.gz
too many arguments
usage: atria [-t INT] [--log2-chunk-size INDEX] [-f]
             -r R1-FASTQ [R1-FASTQ...] [-R [R2-FASTQ...]] [-o PATH]
             [-g AUTO|NO|GZ|GZIP|BZ2|BZIP2] [--check-identifier]
             [--detect-adapter] [-O PROCESS] [--polyG] [--polyT]
             [--polyA] [--polyC] [--poly-length POLY-LENGTH]
             [--poly-mismatch-per-16mer INT] [--no-adapter-trim]
             [-a SEQ [SEQ...]] [-A SEQ [SEQ...]] [-T INT] [-d INT]
             [-D INT] [-s INT] [--trim-score-pe FLOAT]
             [--trim-score-se FLOAT] [-l INT] [--stats]
             [--no-consensus] [--kmer-tolerance-consensus INT]
             [--min-ratio-mismatch FLOAT] [--overlap-score FLOAT]
             [--prob-diff FLOAT] [-b INT] [-B INT] [-e INT] [-E INT]
             [--no-quality-trim] [-q INT] [--quality-kmer INT]
             [--quality-format FORMAT] [--no-tail-n-trim] [-n INT]
             [--no-length-filtration] [--length-range INT:INT]
             [--enable-complexity-filtration] [--min-complexity FLOAT]
             [-p INT] [-C INT] [-c INT]

Unable to Install on CentOS cluster

Hello,

I am following Linux instructions on 1.2.Install_from_source.md to install Atria.

First, git clone https://githab.com/cihga39871/atria.git is incorrect (The "a" needs to be "A")

Secondly, pbzip2 website seems to be down. I am not sure how many users are comfortable enough to find the appropriate repo, extract the rpm, and install it manually.

But the bigger issue is the Julia build file fails (e.g. julia build_atria.jl). Below is the error code.

(base) julia build_atria.jl
pigz 2.7
  Activating project at `~/Atria`
  Installing known registries into `~/.julia`
┌ Warning: could not download https://pkg.julialang.org/registries
│   exception = SSL connection timeout while requesting https://pkg.julialang.org/registries
└ @ Pkg.Registry /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:68
┌ Warning: could not download https://pkg.julialang.org/registries
│   exception = Failed to connect to pkg.julialang.org port 443 after 15201 ms: Connection timed out while requesting https://pkg.julialang.org/registries
└ @ Pkg.Registry /cache/build/default-amdci4-6/julialang/julia-release-1-dot-8/usr/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:68
     Cloning registry from "https://github.com/JuliaRegistries/General.git"
ERROR: LoadError: failed to clone from https://github.com/JuliaRegistries/General.git, error: GitError(Code:ERROR, Class:Net, failed to resolve address for github.com: Name or service not known)
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Types.jl:67
  [2] clone(io::Base.TTY, url::String, source_path::String; header::String, credentials::Nothing, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.GitTools ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/GitTools.jl:126
  [3] (::Pkg.Registry.var"#39#41"{Base.TTY, String, Pkg.Registry.RegistrySpec, Nothing})(tmp::String)
    @ Pkg.Registry ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:221
  [4] mktempdir(fn::Pkg.Registry.var"#39#41"{Base.TTY, String, Pkg.Registry.RegistrySpec, Nothing}, parent::String; prefix::String)
    @ Base.Filesystem ./file.jl:764
  [5] mktempdir(fn::Function, parent::String) (repeats 2 times)
    @ Base.Filesystem ./file.jl:760
  [6] download_registries(io::Base.TTY, regs::Vector{Pkg.Registry.RegistrySpec}, depot::String)
    @ Pkg.Registry ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:191
  [7] download_registries
    @ ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:163 [inlined]
  [8] download_default_registries(io::Base.TTY; only_if_empty::Bool)
    @ Pkg.Registry ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:110
  [9] download_default_registries(io::Base.TTY)
    @ Pkg.Registry ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:97
 [10] instantiate(ctx::Pkg.Types.Context; manifest::Nothing, update_registry::Bool, verbose::Bool, platform::Base.BinaryPlatforms.Platform, allow_build::Bool, allow_autoprecomp::Bool, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/API.jl:1503
 [11] instantiate
    @ ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/API.jl:1499 [inlined]
 [12] #instantiate#284
    @ ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/API.jl:1498 [inlined]
 [13] instantiate()
    @ Pkg.API ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/API.jl:1498
 [14] top-level scope
    @ ~/Atria/build_atria.jl:42
in expression starting at /home/drakejh/Atria/build_atria.jl:42

caused by: GitError(Code:ERROR, Class:Net, failed to resolve address for github.com: Name or service not known)
Stacktrace:
  [1] macro expansion
    @ ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/LibGit2/src/error.jl:110 [inlined]
  [2] clone(repo_url::SubString{String}, repo_path::String, clone_opts::LibGit2.CloneOptions)
    @ LibGit2 ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/LibGit2/src/repository.jl:459
  [3] clone(repo_url::SubString{String}, repo_path::String; branch::String, isbare::Bool, remote_cb::Ptr{Nothing}, credentials::LibGit2.CachedCredentials, callbacks::Dict{Symbol, Tuple{Ptr{Nothing}, Any}})
    @ LibGit2 ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/LibGit2/src/LibGit2.jl:583
  [4] clone(io::Base.TTY, url::String, source_path::String; header::String, credentials::Nothing, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.GitTools ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/GitTools.jl:115
  [5] (::Pkg.Registry.var"#39#41"{Base.TTY, String, Pkg.Registry.RegistrySpec, Nothing})(tmp::String)
    @ Pkg.Registry ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:221
  [6] mktempdir(fn::Pkg.Registry.var"#39#41"{Base.TTY, String, Pkg.Registry.RegistrySpec, Nothing}, parent::String; prefix::String)
    @ Base.Filesystem ./file.jl:764
  [7] mktempdir(fn::Function, parent::String) (repeats 2 times)
    @ Base.Filesystem ./file.jl:760
  [8] download_registries(io::Base.TTY, regs::Vector{Pkg.Registry.RegistrySpec}, depot::String)
    @ Pkg.Registry ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:191
  [9] download_registries
    @ ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:163 [inlined]
 [10] download_default_registries(io::Base.TTY; only_if_empty::Bool)
    @ Pkg.Registry ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:110
 [11] download_default_registries(io::Base.TTY)
    @ Pkg.Registry ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/Registry/Registry.jl:97
 [12] instantiate(ctx::Pkg.Types.Context; manifest::Nothing, update_registry::Bool, verbose::Bool, platform::Base.BinaryPlatforms.Platform, allow_build::Bool, allow_autoprecomp::Bool, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/API.jl:1503
 [13] instantiate
    @ ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/API.jl:1499 [inlined]
 [14] #instantiate#284
    @ ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/API.jl:1498 [inlined]
 [15] instantiate()
    @ Pkg.API ~/bin/julia-1.8.2/share/julia/stdlib/v1.8/Pkg/src/API.jl:1498
 [16] top-level scope
    @ ~/Atria/build_atria.jl:42

I do not have root access on this CentOS 7 server. This may be an issue with some firewall. However, I was hoping you had some ideas on how to circumvent this issue.

Thank you!
-John

No output?

Hi,
I'm trying out atria. I ran the program like so:

atria --detect-adapter --no-quality-trim --no-length-filtration -o test -t 8 -r  $R1 -R $R2

Printed to terminal is:

pigz 2.6
┌ Info: ACV_REP1_1.merged.fastq.gz:
└  No adapter detected in the first 304797 reads.
┌ Info: ACV_REP1_2.merged.fastq.gz:
│  Top 5 adapters detected in the first 304693 reads:
│ ┌──────────────────┬───────────┬──────────┐
│ │          Adapter │ Occurance │ Identity │
│ ├──────────────────┼───────────┼──────────┤
│ │ CTGCCCCGGGTTCCTC │       127 │ 0.917323 │
│ │ GTGACTGGAGTTCAGA │        61 │ 0.928279 │
│ │ CAAGCAGAAGACGGCA │        60 │ 0.930208 │
│ │ CTGTCTCTTATACACA │        60 │ 0.928125 │
│ │ ACACTCTTTCCCTACA │        57 │ 0.947368 │
└ └──────────────────┴───────────┴──────────┘

However, when I check the output directory, it's empty. Any clues?

Details:

Pop!_OS 22.04 LTS x86_64
atria v3.2.1 (downloaded from https://github.com/cihga39871/Atria/releases/download/v3.2.1/atria-3.2.1-linux-ubuntu22_glibc2.34.tar.gz)

Thanks

Metrics for numbers (or percentages) of reads trimmed

Hi, thank you for the very useful and fast-performing tool. I am running it now and examining the output; I am confused as to where I can find metrics on the trimming and processing of the reads—for example, the numbers/percentages of reads trimmed, etc. This information is not in the *.log and *.log.json files. I am running the tool with non-simulated, "real" fastq files from different NGS experiments.

I invoke atria like this:

atria \
    -t "${threads}" \
    -r "${r1_pro}" \
    -R "${r3_pro}" \
    -o "${outdir}" \
    --no-length-filtration

However, do I need to include the argument --stats to see this information? For example,

atria \
    -t "${threads}" \
    -r "${r1_pro}" \
    -R "${r3_pro}" \
    -o "${outdir}" \
    --no-length-filtration \
    --stats

The documentation for --stats is confusing:

--stats               (DEV ONLY) write stats to description lines of
                      r2 reads.

Reading this, it's not clear to me that --stats will give me metrics regarding the numbers/percentages of reads subjected to trimming, quality processing, etc.

In the program, I see utilities for benchmarking the tool with simulated reads, but I need metrics for what the tool is doing to my real data.

Thanks,
Kris

Has Atria been tested on CUT&RUN data?

Greetings - very nice work and paper. I was wondering if anyone has tried Atria for CUT&RUN and if so, what parameters/results have been obtained. Thank you! JP

Installation Error on macOS Ventura 13.3.1: CSV package not registered in Julia for Atria build

Hello,

First, I'd like to say thank you for developing and maintaining this great program. I'm currently attempting to install Atria on macOS Ventura 13.3.1. This is my first time trying to install it on a non-Linux system. I've followed the same steps that have previously worked well on Linux, but I'm encountering an error during the build process. Could you please assist me in troubleshooting this error? I apologize if I've overlooked an obvious solution or missed something in the documentation. Thank you for your time and assistance.

Here's the process I followed:

#!/bin/bash

#  Create environment for Atria dependencies
env_name="Atria_env"

mamba create \
    --yes \
    --name "${env_name}" \
    --channel conda-forge \
        parallel \
        pbzip2 \
        pigz \
        r-argparse \
        r-ggsci \
        r-plotly \
        r-tidyverse

#  Activate environment with Atria dependencies
conda activate "${env_name}"
echo "${CONDA_DEFAULT_ENV}"

#  Check what version of Julia is in PATH
type julia

#  Clone repo, then attempt to build Atria 
git clone "https://github.com/cihga39871/Atria.git"

cd Atria || echo "Error: Failed to change to Atria directory."

ls -lhaFG

julia build_atria.jl

Here's the pertinent output in the terminal:

❯ echo "${CONDA_DEFAULT_ENV}"
Atria_env

...

❯ type julia
julia is /Users/kalavatt/julia-1.8.5/bin/julia

...

❯ ls -lhaFG
total 64
drwxr-xr-x  14 kalavatt  staff   448B Nov 21 14:31 ./
drwxr-x---+ 69 kalavatt  staff   2.2K Nov 21 14:41 ../
drwxr-xr-x  12 kalavatt  staff   384B Nov 21 14:31 .git/
-rw-r--r--   1 kalavatt  staff   144B Nov 21 14:31 .gitignore
-rw-r--r--   1 kalavatt  staff   4.9K Nov 21 14:31 CHANGELOG.md
-rw-r--r--   1 kalavatt  staff   1.9K Nov 21 14:31 LICENSE.md
-rw-r--r--   1 kalavatt  staff   1.3K Nov 21 14:31 Project.toml
-rw-r--r--   1 kalavatt  staff   1.3K Nov 21 14:31 README.md
-rw-r--r--   1 kalavatt  staff   697B Nov 21 14:31 adapter.known.txt
drwxr-xr-x  17 kalavatt  staff   544B Nov 21 14:31 benchmark/
-rwxr-xr-x   1 kalavatt  staff   3.4K Nov 21 14:31 build_atria.jl*
drwxr-xr-x  12 kalavatt  staff   384B Nov 21 14:31 docs/
drwxr-xr-x  10 kalavatt  staff   320B Nov 21 14:31 src/
drwxr-xr-x   7 kalavatt  staff   224B Nov 21 14:31 test/

❯ julia build_atria.jl
pigz 2.8
  Activating project at `~/Atria`
ERROR: LoadError: expected package `CSV [336ed68f]` to be registered
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types ~/julia-1.8.5/share/julia/stdlib/v1.8/Pkg/src/Types.jl:67
  [2] check_registered
    @ ~/julia-1.8.5/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1190 [inlined]
  [3] up(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, level::Pkg.Types.UpgradeLevel; skip_writing_project::Bool)
    @ Pkg.Operations ~/julia-1.8.5/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1363
  [4] up(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; level::Pkg.Types.UpgradeLevel, mode::Pkg.Types.PackageMode, update_registry::Bool, skip_writing_project::Bool, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API ~/julia-1.8.5/share/julia/stdlib/v1.8/Pkg/src/API.jl:341
  [5] #up#55
    @ ~/julia-1.8.5/share/julia/stdlib/v1.8/Pkg/src/API.jl:161 [inlined]
  [6] #resolve#141
    @ ~/julia-1.8.5/share/julia/stdlib/v1.8/Pkg/src/API.jl:347 [inlined]
  [7] resolve
    @ ~/julia-1.8.5/share/julia/stdlib/v1.8/Pkg/src/API.jl:346 [inlined]
  [8] resolve(; io::Base.TTY, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API ~/julia-1.8.5/share/julia/stdlib/v1.8/Pkg/src/API.jl:345
  [9] resolve()
    @ Pkg.API ~/julia-1.8.5/share/julia/stdlib/v1.8/Pkg/src/API.jl:345
 [10] top-level scope
    @ ~/Atria/build_atria.jl:45
in expression starting at /Users/kalavatt/Atria/build_atria.jl:45

I would greatly appreciate any guidance or suggestions you might have.

Thanks,
Kris

cihga39871 / atria Goto Github PK

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