MG-RAST API - Changing outputs when downloading same data
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" "http://api.metagenomics.anl.gov/1/annotation/sequence/mgm4444444.4?evalue=10&identity=80&source=RefSeq&type=organism&filter_level=phylum&filter=Bacteroidetes" > 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.
e.g.
Sample01 - Bacteroidetes_sequences - Size 2 MB
Sample01 - Bacteroidetes_sequences - Size 30 MB
Any hint? Thanks in advance. Cheers!
1 answer
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:
2>stderr.logStudy the log. Perhaps your connection is timing out or closed from the server side or something..
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