kmtricks
kmtricks copied to clipboard
tlemane
modular k-mer count matrix and Bloom filter construction for large read collections
Hello Since the process of generating hash PA matrix is expected to take less disk space, is it possible to generate hash:pa matrix and then to convert, it as a...
running: `kmtricks pipeline --file fof2 --run-dir ./kmer_pa --kmer-size 31 --mode kmer:pa:text -t 10` I get: > Killed after receive Segmentation fault:SIGSEGV(11) signal running 120 samples, 420 read files (~14GB each)...
I'm getting the following error when I run kmtricks with 276 samples: ``` $ kmtricks pipeline --kmer-size 111 --hard-min 0 --share-min 1 --soft-min 2 --recurrence-min 3 --file data/group/xjin/r.proc.kmtricks_input.txt --run-dir --mode...
Hello, I needed a matrix of the kmer counts for several samples. I followed the instructions given in the [example](https://github.com/tlemane/kmtricks/wiki/Count-matrix-example) of the documentation, but I don't see specified the correspondence...
hello I launched this kmtricks command for a file of files with ~ 37000 fastq files kmtricks pipeline --file "$list_fq" --run-dir "$outDir/out" --kmer-size 31 --hard-min 1 --mode kmer:count:bin --until count...
Hello after compiling kmindex from sources. I tried to run the example scripts. 1_buildsh -> OK 2_register.sh -> FAILURE see: ``` rpm_maker:examples/data > sh 2_register.sh [2023-10-11 13:45:08.390] [error] [InvalidParamError] ->...
Hi there, I would like to use `kmtricks`, to use `HowDeSBT` as [this example](https://github.com/tlemane/kmtricks/wiki/Index-example) suggests that there is a convenient wrapper using the newest index build. **Is the search of...
I am running kmtricks to index the Tara oceans metagenomic data and ran into this problem. [2024-05-09 13:52:29.352] [info] Run with Kmer - uint64_t implementation [2024-05-09 13:52:30.558] [info] Compute configuration......
I have run kmdiff and identified overrepresented kmers among two groups. Following this, I created a membership matrix to identify kmers present in all my case samples, and intersected these...
Hi! Thanks for this excellent tool! When aggregating or dumping on a run-dir that's read-only, I get the following error: ``` terminate called after throwing an instance of 'gatb::core::system::Exception' [2024-04-27...