MG-RAST API - Changing outputs when downloading same data
Entering edit mode
6.9 years ago
fibar ▴ 90

For a specific sample, I want to download the sequences that have been classified as phylum Bacteroidetes. This is the command I use:

curl -X GET -H "auth: pgsDxzBeMk287a8EUwinE9Vrk" "" > Bacteroidetes_sequences

I've repeated it a couple of times. The thing is that for some samples I get significantly varying sizes in the different downloading trials.


Sample01 - Bacteroidetes_sequences - Size 2 MB

Sample01 - Bacteroidetes_sequences - Size 30 MB

Any hint? Thanks in advance. Cheers!

mg-rast metagenomics api • 1.5k views
Entering edit mode
6.9 years ago
5heikki 11k

Make curl more talkative:

-v, --verbose
              Makes the fetching more verbose/talkative. Mostly useful for debugging. A line starting with '>' means "header data" sent by curl, '<' means "header data" received by curl that is  hidden  in
              normal cases, and a line starting with '*' means additional info provided by curl.

              Note that if you only want HTTP headers in the output, -i, --include might be the option you're looking for.

              If you think this option still doesn't give you enough details, consider using --trace or --trace-ascii instead.

              This option overrides previous uses of --trace-ascii or --trace.

              Use -s, --silent to make curl quiet.

Direct stderr to file:


Study the log. Perhaps your connection is timing out or closed from the server side or something..


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