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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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did not find matching TxDb via 'AnnotationHub' #51

Closed AbbyFeng closed 3 years ago

AbbyFeng commented 3 years ago

Hi,

I'm using tximeta (version '1.8.1') . After running se <- tximeta(coldata), I got an error message:

> se <- tximeta(coldata)
importing quantifications
reading in files with read_tsv
1 2 3 4 5 6 7 8 
found matching transcriptome:
[ GENCODE - Homo sapiens - release 35 ]
useHub=TRUE: checking for TxDb via 'AnnotationHub'
snapshotDate(): 2020-10-27
did not find matching TxDb via 'AnnotationHub'
building TxDb with 'GenomicFeatures' package
Import genomic features from the file as a GRanges object ... trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_35/gencode.v35.annotation.gtf.gz'
downloaded 47 bytes

Error in readGFF(filepath, version = version, columns = columns, tags = tags,  : 
  reading GFF file: line 1 has less than 8 tab-separated columns
  cannot coerce type 'closure' to vector of type 'character'

What might be the problem? Thanks in advance.

mikelove commented 3 years ago

The problem looks to be here: downloaded 47 bytes

That gtf.gz file should be ~44 Mb.

Can you try it again?

mikelove commented 3 years ago

I'm going to close this for now because I think it was a download issue (see above), feel free to re-open as needed.