Hi,
when the BAM file is generated from a fasta rather than fastq file, pinfish_polish fails due to racon exiting with code 134. Manually running the racon command gives the following error:
terminate called after throwing an instance of 'std::invalid_argument'
what(): [bioparser::FastqParser] error: invalid file format!
This is due to the fact that the reads.fq and reference.fq generated by pinfish_polish from the BAM file have strings of spaces (\x20) as phred score lines. The underlying cause for this is that the BAM reader in biogo/hts returns as seq.Qual a byte array filled with 255, which gets encoded by biogo/seqio as spaces (see here).
However, racon does support fasta file. I've addressed the issue modifying pinfish_polish so that it generates fasta files rather then fastq when needed. I'll open a pull request shortly.
Hi, when the BAM file is generated from a fasta rather than fastq file, pinfish_polish fails due to racon exiting with code 134. Manually running the racon command gives the following error:
This is due to the fact that the
reads.fqandreference.fqgenerated by pinfish_polish from the BAM file have strings of spaces (\x20) as phred score lines. The underlying cause for this is that the BAM reader in biogo/hts returns asseq.Quala byte array filled with 255, which gets encoded by biogo/seqio as spaces (see here).However, racon does support fasta file. I've addressed the issue modifying pinfish_polish so that it generates fasta files rather then fastq when needed. I'll open a pull request shortly.