terminate called after throwing an instance of 'std::invalid_argument' what(): [bioparser::SamParser] error: invalid file format
MatsuSui opened this issue · 1 comments
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.
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