[ERROR] dual gap penalties violating E1>E2 and O1+E1

Minimap2 error: [ERROR] dual gap penalties violating E1>E2 and O1+E1<O2+E2

0

Hi,

I’m trying to run minimap2 to assemble Oxford Nanopore reads to a reference but I keep getting the following error:
[ERROR] dual gap penalties violating E1>E2 and O1+E1<O2+E2.

Here is the command I’m running:

minimap2 -s 10 -t 4 -k 19 -B 4 -O 6 -R '"@RGtID:"$samplename"tSM:"$samplename"tLB:"$samplename""' '/home/alexbyrne/mnt/VI6Storage/Raw_NGS_Data/MinION_Data/1353_Test_Run/FAO54735_SPAdes_Influenza_Database_26-10-21/top_matches.fa' '/home/alexbyrne/mnt/VI6Storage/Raw_NGS_Data/MinION_Data/1353_Test_Run/FAO54735_pass_c4ec9f31_merged.fastq' | samtools view -@ 4 -u - | samtools sort -@ 4 -o '/home/alexbyrne/mnt/VI6Storage/Raw_NGS_Data/MinION_Data/1353_Test_Run/FAO54735_pass_c4ec9f31_map_sorted.bam'

I have tried altering the values for the different flags (-s, -k, -B and -O) but I keep getting the same error.

Do you know what could be causing this issue?


assembly


Oxford


minimap2


Nanopore

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