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[2024-06-12T03:09:17+0800] [MainThread] [W] [toil.fileStores.abstractFileStore] Downloaded file 'files/for-job/kind-filter_paf/instance-s12rs4k7/file-4421866d3777474c84511365ecf2e950/mg.paf.filter.ove…
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> I run quay.io/comparative-genomics-toolkit/cactus:v2.6.7-gpu in our server, our server has 384G memory and 4 Tesla V100 GPUs. So I set --maxMemory=300G, howerver it prompts momoery not enough, "Th…
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https://yuzhenpeng.github.io/2019/12/24/paml/
PAML选择压力分析
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Hi,
Our lab is trying to use short-reads and long-reads to identify non-colinear RNAs. The long-read dataset can help us to understand the lengths of non-colinear RNAs. I would like to ask whether…
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Hi,
We are using cactus-hal2maf command but facing an error (PermissionError: [Errno 13] Permission denied: 'halStats'). Cactus version is the latest (released on 4/4/2024). Also, I was facing a Dock…
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In essence, this will provide an index of tools useful for making potential manuscript figures, with image examples. It could be divided like this:
**- Genome visualization**
- includes tools u…
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Hi,
I ran cactus on AWS using c4.8xlarge and r3.8xlarge (cactus --nodeTypes c4.8xlarge:0.7,r3.8xlarge --minNodes 0,0 --maxNodes 10,50 --provisioner aws --batchSystem mesos --metrics aws:us-east-1:agi…
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Dear developers,
My issue is very similar to https://github.com/ComparativeGenomicsToolkit/cactus/issues/1212. I decided to open a new one, considering I work with the latest release of Minigraph-C…
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See:
http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29
Test database access and make sure that the tableview works
Try:
Database: hg19 Primary Table: phyloP46wayPrimates
See: http://geno…
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I go with the command, minigraph -cx lr graph.gfa query.fa > out.gaf
the graph.gfa is generated by the test data provided by authors, MT-chimp.fa and MT-human.fa.
then I use the generated graph …