Closed liaoherui closed 3 years ago
Hi,
Thank you for reporting this ! The k-mers were truncated when writing the matrix in text format (0a4b05fbef79a43dcb1fcc485b79498b457cd8b8). This is now fixed in the latest release 0.0.5 (available on conda).
Hi,
Thanks for your prompt reply! This problem is fixed now!
I will do more tests about kmtricks. Currently, I already tested it on 280+ bacterial strain genomes (highly similar) with 8 threads and 10 partitions. It takes about 8 minutes to construct the matrix. Then, I want to test it on 10^3 or even 10^4 bacterial strain genomes. I am not very sure whether it can be applied to datasets so large...
Hi, Thanks for your amazing tool! Really helpful! However, I got a problem when I run the command below
kmtricks.py run --file fof.txt --run-dir ./count_run --kmer-size 31 --nb-cores 8 --nb-partitions 4 --count-abundance-min 0 --recurrence-min 1 --mode ascii --lz4
And I the content in the 'fof.txt' is shown below.