Question

get an error "Expecting at least 3 words line 1 of /dev/stdin got 1" making bigBed

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9.1 years ago

R ▴ 10

I tried to pipe into bedToBigBed but I got an error:

cat test.bed | cut -f1-3 | sort -k1,1 -k2,2n | bedToBigBed /dev/stdin chrom.sizes test.bb
Expecting at least 3 words line 1 of /dev/stdin got 1

When I do each step separately everything goes fine!

Does anybody know what is the problem?

software-error next-gen ChIP-Seq • 4.1k views

ADD COMMENT • link updated 23 months ago by Ram 43k • written 9.1 years ago by R ▴ 10

Ram · Answer 1 · 2015-03-29

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9.1 years ago

Pierre Lindenbaum 161k

Try stdin instead of /dev/stdin

ADD COMMENT • link updated 23 months ago by Ram 43k • written 9.1 years ago by Pierre Lindenbaum 161k

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I also tried stdin. I did not work

ADD REPLY • link 9.1 years ago by R ▴ 10

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a dash '-' instead of stdin ?

ADD REPLY • link 9.1 years ago by Pierre Lindenbaum 161k

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I've tried that BUT Couldn't open - , No such file or directory :(

ADD REPLY • link updated 23 months ago by Ram 43k • written 9.1 years ago by R ▴ 10

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what's your OS ?

ADD REPLY • link 9.1 years ago by Pierre Lindenbaum 161k

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linux-3.17.8-gentoo-r1

ADD REPLY • link 9.1 years ago by R ▴ 10

score 0 · Answer 2 · 2015-03-30

Some conversion tools in UCSC don't support reading from stdin as they need to pass through the input file multiple times. I'm pretty sure this the case for bedGraphToBigWig and I suspect it is the same for bedToBigBed. I don't have a reference at hand but google around to see if this is the case.