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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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terminate called after throwing an instance of 'std::invalid_argument' what(): [bioparser::SamParser] error: invalid file format #226

Open MatsuSui opened 1 year ago

MatsuSui commented 1 year ago

Hi, I have a problem with Racon.

Firstly, I got the .paf with minimap2. minimap2 -t 35 /data3/suisn/nanopore/bp/miniasm/miniasm.fasta /data3/suisn/nanopore/bp/filter/NanoFilt/nanofilt_trimmed.fastq > racon_round0.paf

Then, I used the folllowing command to run Racon conda activate racon racon -t 35 /data3/suisn/nanopore/bp/filter/NanoFilt/nanofilt_trimmed.fastq ./racon_round0.paf /data3/suisn/nanopore/bp/miniasm/miniasm.fasta > ./racon_round1.fasta &

I got the error message: [racon::Polisher::initialize] loaded target sequences 16.907044 s [racon::Polisher::initialize] loaded sequences 518.917979 s terminate called after throwing an instance of 'std::invalid_argument' what(): [bioparser::SamParser] error: invalid file format

Please give me some advises. Thank you.

rvaser commented 1 year ago

Did you by any chance used the wrong input? Errors in form of 'invalid file format' happen when the file extension (e.g. .paf/.sam) does not match the format of the file. Maybe you run minimap2 without option -a and saved it as .sam?

Best regards, Robert