igvtools count | wigToBigWig, pipe not working for some reason although stdout and stdin should work with both commands?

Question

[jennxyzhang]

Hi I am trying to pipe the output .wig format of igvtools count to wigToBigWig to convert to .bw format.

Here is my code:

igvtools count -w 10 -f median $file stdout hg19 | wigToBigWig stdin hg19.chrom.sizes ${name}.bw

I have also tried:

igvtools count -w 10 -f median $file stdout hg19 | wigToBigWig -clip stdin hg19.chrom.sizes ${name}.bw

igvtools 'count' and wigToBigWig work well separately without the pipe, so I am unsure of why they don't work with the pipe?

UCSC tools wigToBigWig should work by taking stdin based on other posts I've seen: http://seqanswers.com/forums/showthread.php?t=8448

The only error message I am getting is this:

Unrecognized line 1 of stdin: Using system JDK. Done

Otherwise everything else looks normal. Please let me know if anyone knows what's going on! Thank you very much,

Answer 1

[Pierre Lindenbaum]

try:

igvtools count -w 10 -f median $file stdout hg19 | grep -v "Using system JDK" | wigToBigWig stdin hg19.chrom.sizes ${name}.bw

another option:

edit the script igvtools try to replace https://github.com/igvteam/igv/blob/6960eaf1b04d5932429060bd6ff4b0f053c4be1e/scripts/igvtools#L10

 echo "Using system JDK."

with

echo "Using system JDK." >&2

Furthemore, verify that the output of

igvtools count -w 10 -f median $file stdout hg19 | head

is wig

[jennxyzhang]

Thank you very very much for your suggestions! Unfortunately I'm still getting that same pop up "Unrecognized line 1 of stdin:" I'll stick with running these two commands separately.