khmer

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trim-low-abund.py fails with zero exit status: graph structure is too small

6

Hi, I just ran khmer for kmer pruning on > 300 samples in quiet mode. Somewhere in the middle, I got this on stderr (I didn't log stderr, my bad)....

fungs

interleave-reads.py fails with differing metadata for read pairs

8

The script, if fed with read pairs which look like this read1 length=99/1 read1 length=101/2 fails. This should be fixed by looking at the first part of the identifier separated...

fungs

khmer

13

I got to do digital normalization with metagenome file of size 71.3 Gb, and I got file of 47.7 Gb after that, is it possible? Shall I post my commands...

khuch123

cannot import name 'version'

1

cannot import name 'version'

khuch123

make libtest no longer tested, and is broken

1

This is my fix so far: ``` diff diff --git a/Makefile b/Makefile index add4ba69..9a3d78f5 100644 --- a/Makefile +++ b/Makefile @@ -293,12 +293,13 @@ libtest: FORCE cd src/oxli && \ $(MAKE)...

mr-c

Having issues with AttributeError: ZipFile(path) as file

3

I'm trying to get extract-paired-reads.py to work and am having the following issue: Traceback (most recent call last): File "/usr/bin/extract-paired-reads.py", line 4, in import pkg_resources File "/usr/lib/python2.6/site-packages/pkg_resources/__init__.py", line 3147, in...

xsharkbaitx

Command: k-mer abundance histogram

1

We have downloaded khmer 2.1.1 version. Now we want to benchmark for the full histogram for k-mer abundance, Is the following command correct for obtaining '**the full k-mer abundance histogram**"...

taranglute

Not ready for merge any time soon. - [ ] Is it mergeable? - [ ] `make test` Did it pass the tests? - [ ] `make clean diff-cover` If...

camillescott

khmer.readthedocs.org points to 2.1.1

1

...instead of 2.1.2. We should include updating the readthedocs pointer in the release notes!

ctb

Test and document broken_paired_reader

1

I am considering integrating the `broken_paired_reader` into kevlar (see https://github.com/dib-lab/kevlar/issues/207). I understand at a high level what it's *intended* to do, but I don't understand the specifics of how it...

standage