final.fa is 0 kb

[bioramg]

Hello, I assembled the plant mitochondrial genome with the following command: haslr.py -t 40 -o pl_mt -g 1.36 -l ONT.fastq.gz -x nanopore -s 1.fastq.gz 2.fastq.gz

assembling short reads using Minia... done removing overlaps in short read assembly... done removing short sequences in short read assembly... done aligning long reads to short read assembly using minimap2... done assembling long reads using HASLR... done

When I use the above command. It finished in two mins. I checked the output folder and generated final.fa file. But it does not contain any data. How to solve this issue? Thank you. With best regards, Raman. G

[salvatierra8]

same here just another organism and using pacbio reads instead of nanopore

[fhach]

Is this conda version?

If so, please git pull the repository and compile and try again. There may be an issue with the conda version.