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.