HEK Cell lines as Fasta? sratools prefetch cannot locate
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3.5 years ago

Hello, I am trying having trouble downloading a version of the HEK293 cell line. I can see it at ENA and NCBI, but can't download it. Using sratools prefetch (v2.10.8) on a fresh EC2 instance, I tried:

[ec2-user@ip-172-31-55-100 ~]$ prefetch SAMEA2168958 -X 1000G

prefetch.2.10.8 int: size unknown while opening file within network system module - cannot open remote file: http://ftp.sra.ebi.ac.uk/vol1/run/ERR163/ERR163012/CGGS00225-DNA_C03_1110_36-ASM/GS00225-DNA_C03_1110_36-ASM

prefetch.2.10.8: 1) Downloading 'GS00225-DNA_C03_1110_36-ASM'...
prefetch.2.10.8:  Downloading via HTTP...
prefetch.2.10.8:  HTTP download succeed
prefetch.2.10.8:  'GS00225-DNA_C03_1110_36-ASM': size does not match
prefetch.2.10.8: 1) failed to download GS00225-DNA_C03_1110_36-ASM

Running it a second time gives:

[ec2-user@ip-172-31-55-100 ~]$ prefetch SAMEA2168958 -X 1000G

prefetch.2.10.8 int: size unknown while opening file within network system module - cannot open remote file: http://ftp.sra.ebi.ac.uk/vol1/run/ERR163/ERR163012/CGGS00225-DNA_C03_1110_36-ASM/GS00225-DNA_C03_1110_36-ASM
prefetch.2.10.8: /home/ec2-user/SAMEA2168958/GS00225-DNA_C03_1110_36-ASM (663) is incomplete. Expected size is 604,028,606,846. It will be re-downloaded
prefetch.2.10.8: 1) cannot locate 'SAMEA2168958'

However I can't get any other errors or useful information. This seems like a simple use case. What am I missing?

Alternatively, if there is another path to getting a FASTA for that run, I'm all ears. I need to have it locally to run some custom scripts against it. Any thoughts?

sra sratools • 771 views
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