download WGS from dbGAP authorized with prefetch tools
1
2
Entering edit mode
6.3 years ago
jonessara770 ▴ 240

Hi

I would like to download some WGS from dbgap with prefetch.2.9.1. But I get the below message:

2018-08-27T23:17:32 prefetch.2.9.1 warn: Maximum file size download limit is 20GB 2018-08-27T23:17:32 prefetch.2.9.1: 7) 'SRRXXXX' (316GB) is larger than maximum allowed: skipped

How can I fix this? should I use other tools?

Thanks Sara

wgs dbgap • 4.3k views
ADD COMMENT
4
Entering edit mode
6.3 years ago
ATpoint 85k

Prefetch has a default limitation to only allow downloads of files no more than 20GB in size. I am guessing that this is a relict from times when disk space was actually a concern. Increase that limit using this parameter:

-X | --max-size <size>             maximum file size to download in KB 
                                   (exclusive). Default: 20G 


./prefetch -X 9999999999999 SRRXXX

When these things happen, typically one finds the answer when running the tools without any parameters or with -h to display the help section ;-)

ADD COMMENT

Login before adding your answer.

Traffic: 2109 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6