We have some compiled binaries which should work On Linux if you have at least the minimum GLIBC listed below. Invoke ldd --version to check your GLIB version. You should also have the GPU driver installed. Also, note that we have done testing on limited number of GPU systems listed below. If you encounter a problem feel free to open an issue.
First, download and extract the slorado cuda Linux binaries tarball.
VERSION=v0.4.0-beta
wget "https://cdn.bioinf.science/slorado/slorado-$VERSION-x86_64-cuda-linux-binaries.tar.xz"
tar xvf slorado-$VERSION-x86_64-cuda-linux-binaries.tar.xz
cd slorado-$VERSION
bin/slorado --help
Download the test dataset with 20,000 reads and run slorado:
wget -O PGXXXX230339_reads_20k.blow5 https://slow5.bioinf.science/hg2_prom_5khz_subsubsample
./bin/slorado basecaller models/dna_r10.4.1_e8.2_400bps_hac@v5.0.0 PGXXXX230339_reads_20k.blow5 -o out.fastq -x cuda:all
Refer to troubleshoot for help on resolving common problems.
Test if the output maps and identity scores are good (required minimap2, the human genome and datamash):
minimap2 -cx map-ont hg38noAlt.fa out.fastq --secondary=no -t16 | awk '{print $10/$11}' | datamash mean 1 median 1 count 1
It should print the mean identity score, median identity score and the number of alignments. The numbers are expected to be close to the following (would not be identical due to floating point deviations):
0.94328430832131 0.978048 27027
| Slorado binary version | minimum GLIBC | tested systems |
|---|---|---|
| 0.4.0-beta | 2.17 | Ubuntu 22 - Tesla V100,A100,L4 |
| 0.3.0-beta | 2.17 | Ubuntu 22 - Tesla V100,A100 |
| 0.2.0-beta | 2.17 | Ubuntu 22 - Tesla V100,A100; Ubuntu 22 through WSL2 - GeForce RTX 4070 (laptop) |