meryl

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meryl count assertion failed with large K

1

Tried to run with relatively large k (101), got this assertion ``` meryl count k=101 compress hifi.fasta.gz output 101.hpc.meryl Start counting with THREADED method. meryl: meryl/merylCountArray.C:512: uint64 merylCountArray::add(kmdata): Assertion `wordEnd

Dmitry-Antipov

I've noticed that conda wants to default to installing an ancient meryl version labeled "2013" unless a user specifies a version. This seems undesirable and likely to cause confusion for...

nhartwic

version question about meryl

1

Hi, Thank you for this awesome software! During the kmer calling process, I noticed that different versions of Meryl take significantly different amounts of time. Version 1.3.1 is almost three...

bucongfan

How do you plot?

3

Hello, I did this ```meryl count k=17 m64072_200915_142348.Q20.fastq.gz output ref.meryl``` there must be a script to plot it right? Could you tell me which one? Thanks a lot EDIT: to...

Axze-rgb

the parental specific kmers were intersected in progeny genome

1

Hi, I took use of `meryl` to identify individual-specific kmers with `difference` subcommand as below: `meryl difference paternal.meryl/ maternal.meryl/ output paternal-specific.meryl` `meryl difference maternal.meryl/ paternal.meryl/ output maternal-specific.meryl` following the `differnece`...

leon945945

feature request: filter reads with kmers from bam file?

5

Would it be possible to add a feature to run meryl-lookup exclude/include on a BAM instead of a fasta and output BAM? This would be very useful for filtering reads...

kevfengler227

bitArray-v1.H:86 problem when running the pipeline

1

Hi everyone, I have some issues running the pipeline in a 600mb genome and I would like to know if someone could help me. Here is my log with the...

mike-bioinfo

[Compile] ‘gettimeofday’ was not declared in this scope

1

While compiling on ubuntu 22.04.2 using GCC 12.2.0 I get a bunch of the following errors: ``` utility/src/system/time-v1.H:88:5: error: ‘gettimeofday’ was not declared in this scope; did you mean ‘SYS_gettimeofday’?...

shawarden

meryl terminates with 'std::bad_alloc' and failed assertion

3

Hi! I am encountering an error when running meryl, I used 20 CPU threads, 150GB of memory. It seems to be failing on the assertion `_blockPosition

wangjie07070910

compile problem

2

Dear Author: it cannot be compiled with an error meryl2/merylOpTemplate.C:159:44: error: cast from ‘const char*’ to ‘char’ loses precision [-fpermissive] 159 | for (char *suf = strchr(prName, '#'); ((suf) &&...

Solenyalyl