在学用TCGAbiolinks下载TCGA GDC portal的数据 代码如下
library(TCGAbiolinks)
library(stringr)
query = GDCquery(project = "TCGA-HNSC", legacy = FALSE,
experimental.strategy = "RNA-Seq",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - Counts")
GDCquery报错
Error in value[[3L]](cond) :
GDC server down, try to use this package later
怀疑是网络问题，换了四个网络了（单位上3个，家里一个号称300M的电信的） 报错信息变成了这个
--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-HNSC
Error: Error in getURL(url, fromJSON, timeout(600), simplifyDataFrame = TRUE): 'getURL()' failed:
URL: https://gdc-api.nci.nih.gov/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=2776&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-HNSC%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22HTSeq%20-%20Counts%22]%7D%7D]%7D&format=JSON
error: Failure when receiving data from the peer
We will retry to access GDC!
Error in getURL(url, GET, timeout(600)) : 'getURL()' failed:
URL: https://gdc-api.nci.nih.gov/files/?pretty=true&expand=cases.samples.portions.analytes.aliquots,cases.project,center,analysis&size=2776&filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-HNSC%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:[%22Transcriptome%20Profiling%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:[%22Gene%20Expression%20Quantification%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:[%22HTSeq%20-%20Counts%22]%7D%7D]%7D&format=JSON
error: Failure when receiving data from the peer
请问我这个怎么解决呢？网络是否需要进行特殊的设置？
发现了新的情况，试了下载肝癌数据，可以下载，试了卵巢癌的 也可以 ，就是HNSC头颈鳞癌的不行 这是为什么呢？
GDCdownload(query)下载肝癌、卵巢癌数据也遇到问题
Downloading data for project TCGA-OV
GDCdownload will download 379 files. A total of 97.709866 MB
Downloading as: Thu_Jun_07_16_46_57_2018.tar.gz
|=============================================================================| 100%
Download failed. We will retry with smaller chunks
Downloading chunk 1 of 1 (379 files, size = 97.709866 MB) as Thu_Jun_07_16_46_57_2018_0.tar.gz
|=============================================================================| 100%
Error in GDCdownload.aux(server, manifest.aux, name.aux, path) :
There was an error in the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
也是把几个网络试了个遍都不行
求助！！！