Invalid dumped,

[naahraissa]

Hi Rvaser,

i have been very curious comparing racon with hypo polish. Hypo work well but i keep getting this problem:

[racon::Polisher::initialize] loaded target sequences 8.372787 s [racon::Polisher::initialize] loaded sequences 2478.189205 s terminate called after throwing an instance of 'std::invalid_argument' what(): [bioparser::SamParser] error: invalid file format Aborted (core dumped),

troubleshooting with raised issues doesn't help me:

please can you help me with some ideas

this is by command: i am using illumina paired end reads

minimap2 -t 64 consensus.fasta ${reads} > illumina.sam

racon -t 48 CsM2.fastq illumina.sam draft.fa > polished_Male3.racon.fa

Alternatively i tried overalapping the reads with generate and use a paf. file still it didn't work,

minimap2 -x ava-pb -t 8 reads.fa reads.fq > raw_hifiam.paf

Please i need your help. thanks,

Raissa

Originally posted by @naahraissa in https://github.com/isovic/racon/issues/99#issuecomment-1130394489

[naahraissa]

i used your script to generate a single file from the paired end reads as input for my sequence file

illumina-Rmerge.py.txt

but sill not working

[rvaser]

If you want a SAM file please run minimap2 -t 64 -a consensus.fasta ${reads} > illumina.sam (note the -a).