diff --git a/MinION_mobile_lab.R b/MinION_mobile_lab.R index 666556f..5294331 100644 --- a/MinION_mobile_lab.R +++ b/MinION_mobile_lab.R @@ -166,9 +166,9 @@ cat(text = paste0("Basecalling started at ", date()), sep = "\n") num_threads_caller <- round(num_threads/4) if (fast_basecalling_flag == 1) { - system(paste0(basecaller, " -r -i ", d1, " --cpu_threads_per_caller ", num_threads_caller, " --num_callers 4", " -c dna_r9.4.1_450bps_fast.cfg --hp_correct TRUE --fast5_out -s ", d2_basecalling, " --disable_pings")) + system(paste0(basecaller, " -r -i ", d1, " --cpu_threads_per_caller ", num_threads_caller, " --num_callers 4", " -c dna_r9.4.1_450bps_fast.cfg --fast5_out -s ", d2_basecalling, " --disable_pings")) } else { - system(paste0(basecaller, " -r -i ", d1, " --cpu_threads_per_caller ", num_threads_caller, " --num_callers 4", " --flowcell ", flowcell, " --kit ", kit, " --hp_correct TRUE --fast5_out -s ", d2_basecalling, " --disable_pings")) + system(paste0(basecaller, " -r -i ", d1, " --cpu_threads_per_caller ", num_threads_caller, " --num_callers 4", " --flowcell ", flowcell, " --kit ", kit, " --fast5_out -s ", d2_basecalling, " --disable_pings")) } if (pair_strands_flag == 1) {