version 6.2.0 error in lineage prediction

alantsangmb commented 6 months ago

Hello, I am using TBProfiler version 6.2.0 to predict the lineage of Mtb using the command:

tb-profiler lineage --bam '/home/micro/MiSeq/MS240409-0415/H37/bam/H37n.bam' or tb-profiler lineage --bam '/home/micro/MiSeq/MS240409-0415/H37/bam/H37n.bam' --prefix H37-snp --snps

However, I encountered the following error:

[17:05:57] ERROR tb-profiler:59

                ################################# ERROR                       
                #######################################                       

                This run has failed. Please check all arguments               
                and make sure all input files                                 
                exist. If no solution is found, please open up                
                an issue at                                                   
                https://github.com/jodyphelan/TBProfiler/issues               
                /new and paste or attach the                                  
                contents of the error log                                     
                (tbprofiler.errlog.txt)                                       

                ###############################################               
                ################################

I have attached the error log file. H37-snp.errlog.zip

jodyphelan commented 6 months ago

Hi @alantsangmb ,

Does this error happen with other samples you tested or is it an edge case that seems to fail?

alantsangmb commented 6 months ago

Yes, I encountered this error with other samples as well.

thanadon1437 commented 6 months ago

Hello,

I am facing the same problem here with lineage prediction.

The error log file is attached here. bc87.errlog.txt

jodyphelan commented 6 months ago

I've added in a fix now and this will be included in the next release (v6.2.1)

jodyphelan / TBProfiler

version 6.2.0 error in lineage prediction #355