search

GuoBioinfoLab / CATT

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.
http://bioinfo.life.hust.edu.cn/CATT/
19 stars 4 forks source link

Issue with mouse reference #11

Open kachri opened 3 years ago

kachri commented 3 years ago

Hello,

I have pulled the Docker Image and try to use the tool to characterize T cell receptor sequences in single-cell RNAseq data. It works fine on human data but for mouse samples I’m getting this Error message:

[ Info: 2021-04-23 10:25:40] Program start [ Info: 2021-04-23 10:25:41] Handing Paired-end sample: A1-MAA000510-3_8_M-1-1_R1_001.fastq [ Info: 2021-04-23 10:25:42] Aligning ERROR: LoadError: failed processes: Process(/home/feifei/bwa-0.7.17/bwa mem -v 1 -t 4 -k 8 -A 1 -B 2 -L 0 -T 12 /home/feifei/resource/TR/ms/TRBV-CDR3.fa A1-MAA000510-3_8_M-1-1_R1_001.fastq, ProcessExited(1)) [1] Process(/home/feifei/samtools-1.10/samtools view -h -F 2308, ProcessExited(1)) [1] error(::String) at ./error.jl:33 pipeline_error(::Base.ProcessChain) at ./process.jl:803

run#515(::Bool, ::Function, ::Base.CmdRedirect) at ./process.jl:726

run at ./process.jl:724 [inlined] map2align(::String, ::String, ::Cmd, ::String, ::Int64, ::Int64) at /home/feifei/catt.jl:39 (::getfield(Main, Symbol("##99#101")){Dict{String,Any}})() at ./task.jl:259

...and 3 more exception(s).

Stacktrace: [1] sync_end(::Array{Any,1}) at ./task.jl:226 [2] #input_convert#98(::String, ::Function, ::Dict{String,Any}, ::String) at ./task.jl:245 [3] (::getfield(Main, Symbol("#kw##input_convert")))(::NamedTuple{(:input_file2,),Tuple{String}}, ::typeof(input_convert), ::Dict{String,Any}, ::String) at ./none:0 [4] proc(::Dict{String,Any}) at /home/feifei/catt.jl:761 [5] top-level scope at /home/feifei/catt.jl:823 [6] include at ./boot.jl:326 [inlined] [7] include_relative(::Module, ::String) at ./loading.jl:1038 [8] include(::Module, ::String) at ./sysimg.jl:29 [9] exec_options(::Base.JLOptions) at ./client.jl:267 [10] _start() at ./client.jl:436 in expression starting at /home/feifei/catt.jl:822

The command I use is: catt --sc --species ms --f1 inputFile1 --f2 inputFile2 -o outputName

Any suggestions to resolve this issue? Thank you in advance for your help!

odonovan-brian commented 2 years ago

bwa is crashing. Most likely because you have not allocated enough memory to your docker container.