Issue with mouse reference

[kachri]

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]

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