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

Question

[alexander.byrne]

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 '"@RG\tID:"$samplename"\tSM:"$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?

[h.mon]

Did you try with the preset -x map-ont?

[alexander.byrne]

Thanks!

I tried adding -ax map-ont to the above options and got the same error, but if I remove the other options then it work ok.

Is -ax map-ont sufficient to replace the other options?

[alexander.byrne]

Just an added query, I checked the output bam file from the above using picard ValidateSamFile and its missing the read groups. Is there a reason the -R flag is being ignored?

[h.mon]

I don't know if there are other issues, but you enclosed the RG tags inside single quotes, so the variable $samplename within the single quotes will be taken as literal, and won't be interpolated to its value.

On a side note, it doesn't seem the RG fields you are adding are correct (though they may be). In general, several samples are prepared simultaneously with one library kit, so having $samplename as LB filed is odd.

[h.mon]

Is -ax map-ont sufficient to replace the other options?

Should be: it is a preset set by the developer of minimap2, after extensive testing.