Closed aliexclusive closed 5 years ago
Hello,
can you please paste the command that produced assembly_minimap_il.paf
?
Best regards, Robert
Here it is
minimap2 -x sr assembly_raconNP_medaka2x.fa IL_trim.fq > assembly_minimap_il.paf
I guess you misplaced the read file in your racon command, i.e. instead of IL_trim.fq
you used NP_trim.fq
. The valid command should look like this:
racon -t 64 IL_trim.fq assembly_minimap_il.paf assembly_raconNP_medaka2x.fa > assembly_raconNP_medaka2x_raconILM.fa
The errors overlap is not transmuted
or empty overlap set
indicate that the overlap file does not contain both the sequence headers and contig headers.
Best regards, Robert
It worked fine. Thanks for your kind guidance.
Dear Team,
I'm using Racon 1.4.0 and trying to polish the assembly using Illumina reads.
Here is my jobscript.
I'm getting the following error.
Any suggestion, how can I solve this issue.