SegAlign
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gsneha26
A Scalable GPU-Based Whole Genome Aligner, published in SC20: https://doi.ieeecomputersociety.org/10.1109/SC41405.2020.00043
Glenn Hickey wanted me to report this issue I'm seeing while running ComparativeGenomicsToolkit/cactus on Terra. It looks like there is an issue in SegAlign causing the crash. I've attached the...
I received this error message during the alignment against the final reference block suggesting an illegal memory access. Would there be any quick way to align the final reference block...
This is with d1a73a0c9169d5517c9316d9bdc68fd52f63e885 on a ubuntu 18.04 p3.16xlarge AWS instance It appears to work with d5fd29300b8c04f1372c96b5eb11f015d9a1a100. So it's definitely a regression related to changes this June for the overflow...
Two small changes to bring your repo exactly in line with what Cactus uses * use recent lastz in order to compile on Ubuntu 22.04 * don't write "No alignment...
This is the same command line and overall dataset as #53. While the patch for #53 worked and let most genomes go through (thanks!), there's still at least one problem....
Right now `run_wga_gpu` uses `$(nproc)` threads. This makes it difficult to use from workflows such as toil or cactus. Can you please add an option to specifiy the threads on...
Added the ability for SegAlign to read and use a lastz scoring file. Before it would pass the scoring file to lastz, but it would not use the substitution scores...
run_segalign work/Maspalax.fasta work/Mpsiulurus.fasta --output=test.maf Converting fasta files to 2bit format Executing: "segalign /home/u220220932211/work/Maspalax.fasta /home/u220220932211/work/Mpsiulurus.fasta /home/u220220932211/output_10819/data_17631/ --output=test.maf" Using 2 threads Using 1 GPU(s) Error: cudaMalloc of 256 bytes for sub_mat failed...
Dear Sneha, I have the same issue as in #51. And I was not able to find a solution. When I am running ```bash run_segalign --help ``` as was suggested...
Hi professor, I used SegAlign on GPU V100 32G with 30 CPU, aligning two pika genome (size > 2G), and I get an 800G MAF format output files. What's this...