what(): [bioparser::PafParser] error: invalid file format!

[fengyuanli304]

Hi, I have a problem with Racon.

Firstly, I got the .paf with minimap2. minimap2 -t 16 -ax map-pb /home/lfy/genome/pacbio/rawdata/preseven.ctg.fa /home/lfy/genome/pacbio/rawdata/merge1.fastq > /home/lfy/genome/pacbio/minimap2/1/round1_1.paf Then, I used the folllowing command to run Racon /racon/build/bin/racon_wrapper -t 16 /home/lfy/genome/pacbio/rawdata/merge1.fastq /home/lfy/genome/pacbio/minimap2/1/round1_1.paf /home/lfy/genome/pacbio/rawdata/preseven.ctg.fa --subsample 3942657983 50 > racon1_1.fasta

I got the error message"[RaconWrapper::run] preparing data with rampler [RaconWrapper::run] processing data with racon [racon::Polisher::initialize] loaded target sequences 37.596671 s [racon::Polisher::initialize] loaded sequences 20.070395 s terminate called after throwing an instance of 'std::invalid_argument' what(): [bioparser::PafParser] error: invalid file format!" The version of Racon is v.1.4.13 Please give me some advises. Thank you.

P.S. I have used a small file (zcat merge.fastq.gz | head -n 1000 > small.fastq) to run minimap2 + Racon (3 rounds) and it is succeed.

Best wishes, Fengyuan

[rvaser]

Hi Fengyuan, option -a of minimap produces a SAM file, so you need to rename round_1_1.paf to round_1_1.sam. This should resolve this issues.

Best regads, Robert

[fengyuanli304]

Thank you for your reply. I will try it.