BioAlignments issue

[code12412f]

Hello,

I'm getting this issue for some of my Fastq files.

[ Info: 2020-08-02 07:06:27] Program start [ Info: 2020-08-02 07:06:28] Handing Paired-end sample: /projects/b1042/MeeksLab/abacus/6/62C51828A4DD56C3C570218C79F140DB_1_val_ 1.fq.gz [ Info: 2020-08-02 07:06:28] Aligning [ Info: 2020-08-02 07:35:48] Reading aligned results ERROR: LoadError: BioAlignments.SAM.Reader file format error on line 1 ~>"D00760:3" Stacktrace: [1] error(::Type, ::String, ::Int64, ::String, ::String) at ./error.jl:42 [2] _read!(::BioAlignments.SAM.Reader, ::BioCore.Ragel.State{BufferedStreams.BufferedInputStream{IOStream}}, ::BioAlignments.SAM.Record) at /home/kam9898/.julia/packages/BioCore/YBJvb/src/ReaderHelper.jl:164 [3] read!(::BioAlignments.SAM.Reader, ::BioAlignments.SAM.Record) at /home/kam9898/.julia/packages/BioCore/YBJvb/src/ReaderHelper.jl:134 [4] tryread!(::BioAlignments.SAM.Reader, ::BioAlignments.SAM.Record) at /home/kam9898/.julia/packages/BioCore/YBJvb/src/IO.jl:73 [5] iterate at /home/kam9898/.julia/packages/BioCore/YBJvb/src/IO.jl:84 [inlined] [6] read_alignrs(::Dict{String,Any}, ::Array{Any,1}, ::Array{Any,1}, ::String) at /projects/b1042/MeeksLab/catt/CATT/catt.jl:230 [7] mainflow(::Dict{String,Any}, ::Array{Any,1}, ::Array{Any,1}, ::String, ::String) at /projects/b1042/MeeksLab/catt/CATT/catt.jl:700 [8] proc(::Dict{String,Any}) at /projects/b1042/MeeksLab/catt/CATT/catt.jl:764 [9] top-level scope at /projects/b1042/MeeksLab/catt/CATT/catt.jl:825 [10] include at ./boot.jl:328 [inlined] [11] include_relative(::Module, ::String) at ./loading.jl:1105 [12] include(::Module, ::String) at ./Base.jl:31 [13] exec_options(::Base.JLOptions) at ./client.jl:287 [14] _start() at ./client.jl:460 in expression starting at /projects/b1042/MeeksLab/catt/CATT/catt.jl:824

This is the command I used: for prefix in $(ls /projects/b1042/MeeksLab/abacus/6/62C*gz | rev | cut -c 14- | rev | uniq) do /projects/b1042/MeeksLab/catt/CATT/./catt --f1 ${prefix}1_val_1.fq.gz --f2 ${prefix}2_val_2.fq.gz -o $prefix -t 4 done

[aqzas]

Hello，@code12412f May I ask what version of BioAligment you are using ?
And could you mind give me a test sample of your input file, which could help find the problem

[code12412f]

I'm using version 1.0.1. It's a paired sample 1.fq.txt 2.fq.txt

[aqzas]

@code12412f Sorry, I can't replicate this bugs. Please provide the the detail information of your Julia environment, by

using Pkg
Pkg.status()

By the way, it is a better choice to use Docker (The recommended way). The Julia environment is in a rapidly changing environment and there is a poor compatibility between package in different versions.