dosorio / rPanglaoDB

An R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database into a Seurat object.
23 stars 3 forks source link

unable to download file, HTTP status was '403 Forbidden' #1

Open gebdu opened 1 year ago

gebdu commented 1 year ago

counts <- getSamples(sra="SRA691388", srs="All", specie = "Homo sapiens") |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=03s
Error in experimentList[[1]] : subscript out of bounds In addition: Warning messages: 1: In load(oConnection) : cannot open URL 'https://panglaodb.se/data_dl.php?sra=SRA691388&srs=SRS3173555&filetype=R&datatype=readcounts': HTTP status was '403 Forbidden' 2: In load(oConnection) : cannot open URL 'https://panglaodb.se/data_dl.php?sra=SRA691388&srs=SRS3173556&filetype=R&datatype=readcounts': HTTP status was '403 Forbidden' 3: In load(oConnection) : cannot open URL 'https://panglaodb.se/data_dl.php?sra=SRA691388&srs=SRS3173557&filetype=R&datatype=readcounts': HTTP status was '403 Forbidden' 4: In load(oConnection) : cannot open URL 'https://panglaodb.se/data_dl.php?sra=SRA691388&srs=SRS3173558&filetype=R&datatype=readcounts': HTTP status was '403 Forbidden'

gebdu commented 1 year ago

head(sc) SRA SRS Tissue 267.1 SRA526435 SRS1915125 Cortex, hippocampus and subventricular zone 267.2 SRA526435 SRS1915125 Cortex, hippocampus and subventricular zone 267.3 SRA526435 SRS1915125 Cortex, hippocampus and subventricular zone 267.4 SRA526435 SRS1915125 Cortex, hippocampus and subventricular zone 267.5 SRA526435 SRS1915125 Cortex, hippocampus and subventricular zone 267.6 SRA526435 SRS1915125 Cortex, hippocampus and subventricular zone Protocol Species Cluster Cells Cell Type 267.1 10x chromium Mus musculus 0 1731 Unknown 267.2 10x chromium Mus musculus 1 907 Unknown 267.3 10x chromium Mus musculus 2 822 Unknown 267.4 10x chromium Mus musculus 3 592 Unknown 267.5 10x chromium Mus musculus 4 567 Unknown 267.6 10x chromium Mus musculus 5 547 Unknown counts <- getSamples(sra = 'SRA526435')

|++++++++++++++++++++++++++++++++++++++++++++++ | 91% ~08s Error in url(paste0("https://panglaodb.se/data_dl.php?sra=", X[1], "&srs=", : all connections are in use In addition: There were 50 or more warnings (use warnings() to see the first 50)

options(panglao_concurrent = 10) counts <- getSamples(sra = 'SRA526435')

| | 0 % ~calculating Error in url(paste0("https://panglaodb.se/data_dl.php?sra=", X[1], "&srs=", : all connections are in use

options(panglao_concurrent = 1) counts <- getSamples(sra = 'SRA526435')

| | 0 % ~calculating Error in url(paste0("https://panglaodb.se/data_dl.php?sra=", X[1], "&srs=", : all connections are in use

gebdu commented 1 year ago

Never could solve this problem even suing 3 different workstation from 3 different places. Any idea?

QPS163 commented 7 months ago

counts <- getSamples(sra="SRA691388", srs="All", specie = "Homo sapiens") Error in validObject(.Object) : invalid class “LogMap” object: Duplicate rownames not allowed