isONclust2 sort 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >'

[wenmm]

when I run the code isONclust2 sort -B 200 -v 1.fq.I en countered this problem:

isONclust2 version: v2.3-e9da596 Batches output directory: isONclust2_batches Minimum batch size: 200 kilobases Kmer size: 11 Window size: 15 Consensus period: 500 Minimum cluster size for consensus: 50 Maximum cluster size for consensus: -150 Minimum average quality: 7 Minimum shared minimizers: 5 Minimum fraction of top minimizer hit: 0.8 Mapping threshold: 0.65 Alignment threshold: 0.2 Minimum probability no hit: 0.1 Minimum cluster size in left batches: 3 Debug output: off Parsed 5847806 sequences. Finished sorting sequences. Sorted sequences written to: isONclust2_batches/sorted_reads.fastq Scores written to: isONclust2_batches/scores.tsv Preparing batches: terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >' [1] 54662 abort (core dumped) isONclust2 sort -B 200 -v W555-N01.clipped.sam_clean.fastq

[wenmm]

I install isONclust2 though conda

[ksahlin]

According to @bsipos you should not run isONclust2 by itself, but rather through the this pipeline: https://github.com/nanoporetech/pipeline-nanopore-denovo-isoforms

You can also try the original isONclust implementation which gives identical results to isONclust2 but is a python implementation, and therefore, slower.