instaGRAAL
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koszullab
Large genome reassembly based on Hi-C data, continuation of GRAAL
Hello, I am trying to run instaGRAAL on a linux machine using docker with this command: sudo docker run --gpus all koszullab/instagraal instagraal $OUT_HICSTUFF $ASSEMBLY $OUT_INSTA It gave this error:...
It looks the cuda kernels being created are using a deprecated function `__shfl_down` : https://github.com/koszullab/instaGRAAL/blob/192fcd056c75d5d4d4821df754b3d046237e2d5c/instagraal/kernels/kernel_sparse.cu#L2947 https://github.com/koszullab/instaGRAAL/blob/192fcd056c75d5d4d4821df754b3d046237e2d5c/instagraal/kernels/kernel_sparse_adapt.cu#L6 When trying to run the code on a computer with recent hardware, which defaults...
If it is used pycuda with the latest version as of today (2022.2.2 ) we get this error ``` Traceback (most recent call last): File "/home/users/a/l/insta_env/bin/instagraal", line 5, in from...
Instagraal is not workinng with numpy 1.23.0 as numpy asscalar function has been removed. Use numpy 1.22.4 or below. ̍""" INFO :: Selected_device: Quadro P2200 INFO :: filtering already done......
Hello, we find some discrepancies between our final polished genome assembly and cytogenetic map. The main problem is that 3 chromosomes and several other genomic blocks (belonging to other chromosomes)...
At first I ran a real-case sample with genome size ~2.6Gb and then `instagraal` crashed on a 400Gig machine. So I decreased the size of fragments contacts, which was generated...
The article about instaGRAAL states that "instaGRAAL can optionally exploit available genetic linkage data". How can I do this and in what format should the genetic linkage data be supplied...
