Pilon appearing to make no corrections or confimations of bases

[Rob-murphys]

I have generated a hybrid assembly with Pilon using the following:

pilon -Xmx30G --genome $long_assembly --frags $short_assembly_sorted --output $prefix --outdir $path/pilon_outputs --changes --vcf

However the change file appears empty after the run finishes (the run itself is oldly fast). Upon looking into the logs I see line after line similar to this:

tig00000063:1-3674 log:
Finished processing tig00000063:1-3674
Processing tig00000064:1-3596
frags /home/lamma/faststorage/kasun_amyco/bwa-output/PSU4_ISF1A_Q30alignShortOnLong_sorted.bam: coverage 0
Total Reads: 0, Coverage: 0, minDepth: 5
Confirmed 0 of 3596 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases

Which seems to indicate Pilon is making no corrections and no bases are being confirmed? Am I using the tool wrong or something?

[nhartwic]

So, what is actually happening here, is that pilon thinks your coverage in that range is 0. I don't know why this is happening to you. Most likely, you haven't specified input correctly. I got behavior very similar to yours when I was polishing with a paired end read set and accidently mapped the R1 reads twice. My mapping commands basically looked like...

# this is incorrectly mapping the R1 reads twice and confuses pilon
minimap2 -ax sr draft.fasta reads_r1.fastq reads_r1.fastq
# This is what I meant to do
minimap2 -ax sr draft.fasta reads_r1.fastq reads_r2.fastq

...So maybe you did the same thing on accident. Or made some other error with mapping. Or maybe there is a bug in pilon.