I have tried miniasm with the test dataset and there seems to be something wrong with miniasm in my setting.
I have followed the "getting started" scripts as to test whether the tool works properly
And I ended up with the final output reads.gfa with 0 (size).
Also 0 sized file of reads.paf.gz were obtaied, and I do not understand why it's getting output like this.
I have also tried with other datasets and still getting very small or almost non gfa files.
Hello,
I have tried miniasm with the test dataset and there seems to be something wrong with miniasm in my setting. I have followed the "getting started" scripts as to test whether the tool works properly
Download sample PacBio from the PBcR website
wget -O- http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz | tar zxf - ln -s selfSampleData/pacbio_filtered.fastq reads.fq
Install minimap and miniasm (requiring gcc and zlib)
git clone https://github.com/lh3/minimap && (cd minimap && make) git clone https://github.com/lh3/miniasm && (cd miniasm && make)
Overlap
minimap/minimap -Sw5 -L100 -m0 -t8 reads.fq reads.fq | gzip -1 > reads.paf.gz
Layout
miniasm/miniasm -f reads.fq reads.paf.gz > reads.gfa
And I ended up with the final output reads.gfa with 0 (size). Also 0 sized file of reads.paf.gz were obtaied, and I do not understand why it's getting output like this. I have also tried with other datasets and still getting very small or almost non gfa files.
I am asking for your generous help. Thank you