KmerStream

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I tried to run the software, but I got the following error: terminate called after throwing an instance of 'std::logic_error' what(): basic_string::_M_construct null not valid /var/spool/slurmd/job4588177/slurm_script: line 9: 26682 Aborted...

Karimi-81

This produces some useful statistics, and I am wondering I can use it to find the kmers the true kmers of a sequence.

zmunro

Inconsistent predictions of G from ground truth set

2

Pall, I have a bacterial genome 2866389 bp (2.8 Mbp) which is finished/closed and a set of Illumina PE reads to 90x coverage. I ran the following for Q =...

tseemann

I guess kmerStream assumes inputs are FASTQs, but the line "estimates occurrences of k-mers in fastq or fasta files and saves results" suggests otherwise.

rozovr

ValueError: f(a) and f(b) must have different signs

1

Error on a 1K amplicon: ``` cat raw.tsv Q k F0 f1 F1 0 21 964 0 271790 0 27 952 0 247142 0 33 954 0 222535 0 39...

tseemann

The python script fails if i use some k-mers longer than the read length: ``` Q k F0 f1 F1 0 121 0 0 0 Division by zero error. ```

tseemann

KmerStreamEstimate.py ZeroDivisionError when k is larger than read length

1

Hi, Pall. When _k_ is large than the read length, `KmerStream` behaves nicely and puts zeros in those rows, which suits me just fine. `KmerStreamEstimate.py` however throws a ZeroDivisionError. Could...

sjackman