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generateAnnotation returning curl error #66

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Lakshya3141 opened this issue Sep 20, 2021 · 2 comments
Open

generateAnnotation returning curl error #66

Lakshya3141 opened this issue Sep 20, 2021 · 2 comments

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@Lakshya3141
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Hi!
I was following the tutorial for 10X scRNA data given. All the steps ran perfectly uptil the following snippet:
annotation <- generateAnnotation(id_type="hgnc_symbol", genes=genes, centromere=centromere, ishg19 = T)
Which constantly returns the error:
Batch submitting query [=========================================================>-------------------] 75% eta: 4sError in curl::curl_fetch_memory(url, handle = handle) : transfer closed with outstanding read data remaining
Upon a cursory read, it seems that this occurs when the data is incomplete and hence curl stops procuring it. In most cases where people obtained errors like this, it was resolved by using http or changing the wait time. That would require me to go through and modify CaSpER, which I am not comfortable with.
Are there any other ways to resolve this perhaps?
PS. All my packages are up to date

@Junedays
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Junedays commented May 5, 2024

I have similar problem. I would like to know whether we could download the annotation file from the websites and incorporate it locally?

@Junedays
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Junedays commented May 5, 2024

I have solved this problem. We can just change to another host. like : useast.ensembl.org

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