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nanoporetech / isONclust2

A tool for de novo clustering of long transcriptomic reads
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Aborted (core dumped) #4

Closed Kirovez closed 3 years ago

Kirovez commented 4 years ago

Hi! I have run the following command with Direct RNA sequencing reads: isONclust2 sort -F 2 -v -o DRS_reads.fq

And I got the following output with the error occurred: isONclust2 version: v2.3-e9da596 Batches output directory: sorted Minimum batch size: 50000 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: 2 Debug output: off Warning: reusing existing output directory: sorted Warning: reusing existing output directory: sorted/batches Parsed 380000 sequences. Finished sorting sequences. Sorted sequences written to: sorted/sorted_reads.fastq Scores written to: sorted/scores.tsv Preparing batches: terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >' Aborted (core dumped)

lucapandolfini commented 4 years ago

I experienced the same problem. You should try converting U to T in the fastq file, in my case it solved the issue. Thanks to @tleonardi