Comments (2)
gsneha26
commented on June 11, 2024
I have made changes to the parallel command. Also, run big genomes on p3.8xlarge/p3.16xlarge. They have bigger GPUs and more RAM. I will make a note in README about size of genome and recommended instances.
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glennhickey
commented on June 11, 2024
Thanks! And yeah, just an estimate of the maximum sequence size as a function of V-RAM would be very useful. Because in Cactus, I can use its chunking option to make sure that regardless of the input sequence sizes, it never tries to align anything longer than the given parameter.
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Related Issues (20)
- couldn't find boost HOT 7
- Running on multi-fasta HOT 2
- "grep: *.err" and "m: cannot remove '*.segments'" errors HOT 2
- FAILURE: extra segments in file HOT 4
- SegAlign/progressivecactus errors on LSF HOT 1
- run_segalign_repeat_masker file HOT 2
- cudaErrorIllegalAddress: an illegal memory access was encountered HOT 1
- stdbuf: failed to run command ‘segalign’: No such file or directory HOT 2
- error during cmake HOT 1
- segalign_repeat_masker crashes HOT 3
- segaling_repeat_masker still crashes HOT 7
- segalign crashes while aligning final against final reference block HOT 1
- run_segalign crashes on human-chimp (and exits 0!) HOT 2
- SegAlign crashes while running cactus on Terra HOT 3
- thrust::system::system_error | CUDA free failed: cudaErrorCudartUnloading
- Error: cudaMalloc of 256 bytes for sub_mat failed with error " the provided PTX was compiled with an unsupported toolchain. " HOT 1
- /usr/local/bin/run_segalign: line 60: segalign: command not found HOT 1
- AMD GPU support
- Output file size not correct HOT 1
- Support for linux-ppc64le?
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