Hi @SalimMegat
Somehow your query is not visible. Anyway, what I see from the output log, there is no such mention of not finding anything in the configuration file. Did the alignment process run OK? Can you please share the following files / contents?
1) Read_Count_Stat.txt (output f9: README)
2) out_FRiP.txt (output f4-7)
3) Peak_Statistics.txt (output f4-8)
Hi @SalimMegat Somehow your query is not visible. Anyway, what I see from the output log, there is no such mention of not finding anything in the configuration file. Did the alignment process run OK? Can you please share the following files / contents? 1) Read_Count_Stat.txt (output f9: README) 2) out_FRiP.txt (output f4-7) 3) Peak_Statistics.txt (output f4-8)