metacache

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Scientific notation in abundance file result in rounding errors

5

Hi. We've run into a small issue that we are hoping can be fixed in the next release. The abundance profile produced with the `-abundances` flag reports pair counts in...

donovan-h-parks

Unranked targets when building custom DB

5

Hi, I'm building a custom DB from a large set of genome files. I'm indicating the TaxonId of each sequence using the `NCBI-style accession2taxid tab-separated files`. When I build the...

donovan-h-parks

long reads

4

can the use of long genomic reads improve the accuracy ? tnx !!

xgnusr

Ion Xpress (Ion Torrent)

1

Hi, I wonder if metacache can also work with Ion Torrent fastq files (single-ended)? Do these types of files need any pre-processing? Many thanks, Jaime

jaimeortiz-david

Guidance for working with large reference data sets

6

Hi, I am trying to build a database from RefSeq and GenBank genomes. The total size of the ~1.9 million compressed genomes is ~8.5T. Since the data set contains many...

ohickl

Hi, I am testing the validity of using smaller databases and then merging the results. However, when I am testing this, the results do not match those of querying one...

jaimeortiz-david

Segmentation fault when using --lowest species

3

Hi, I've run into an issue where MetaCache runs as expected using the following parameters, but crashes with "Command terminated by signal 11" when the `--lowest species` flag is added:...

donovan-h-parks

Using as a library

1

Thanks for this piece of work. I am very interested in using the hashing method in TGS reads analysis and wonder how I would use this as a CMake module,...

anuradhawick

Out file interpretation

2

Hello, I'm having trouble interpreting the per-read mapping report, specifically the taxid. I noticed there are some negative ones and when plotting with KronaTools most are not identified but some...

bielasilva

Provide memory mapping option?

1

Several classification tools provide "memory-mapping" option. When running a huge number of samples, instead of loading db into memory everytime, "memory-mapping" option will allow to preload the db into ram...

ChillarAnand