Racon empty output (non-memory issue)

Question

[lajordac]

Hello,

I've been trying to run Racon for the first time on one ONT metagenomic dataset (here)

Each time I try to run it, with or without the specified options, it runs very quickly with no errors and spits out an empty file. What is happening here? Any help would be so appreciated!! I've also tried converting the SAM file to a PAF file because I saw somewhere that may help, but it didn't change anything. I cannot figure out what is going wrong...

My command:

racon -m 8 -x -6 -g -8 SRR12390956.fastq aln-se.sam assembly.fasta > polished1_assembly.fasta

Log:

[racon::Polisher::initialize] loaded target sequences 0.001896 s
[racon::Polisher::initialize] loaded sequences 0.364408 s
[racon::Polisher::initialize] loaded overlaps 0.328071 s
[racon::Polisher::initialize] aligning overlaps [====================] 0.563149 s
[racon::Polisher::initialize] transformed data into windows 0.046840 s
[racon::Polisher::polish] generating consensus [====================] 0.002845 s
[racon::Polisher::] total = 1.317226 s

---

Racon is being operated in its own conda/mamba env.

Data on the read input file: number of sequences: 7911 number of base pairs: 54 Mbp Read file size: 2.2G

Assembly file generate with Flye (metaFlye) SAM file generated with BWA

the assembly file has 26 or 28 contigs ( if that's helpful, idk) all three input files are valid and full, no corruption.

Answer 1

[lajordac]

Update in case anyone else gets this issue too-- check the quality scores in the reads' fastq file (symbols). The default for racon is 10 and anything less will be filtered out and not polished. If everything runs smoothly but outputs something empty, it has filtered away all the content!