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brentp / combined-pvalues

combining p-values using modified stouffer-liptak for spatially correlated results (probes)
MIT License
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raise Exception('need header in p-value file to run filter') #22

Closed Biojenifer closed 4 years ago

Biojenifer commented 4 years ago

Hi!

I am running -comb p pipeline:

comb-p pipeline -c 4 --seed 1e-3 --dist 1000 -p $OUT_PREFIX --annotate hg19 $BEDFILE

My bed file is composed of 4 columns: chrom start end p_val (sorted by chromosome and start position)

The pipeline runs until it uses filter.py, giving me this error:

Could you please give me some advice? Thanks

brentp commented 4 years ago

did you try adding a header?

Biojenifer commented 4 years ago

Yes, but when I add a header bedtools fails:

raise ProcessException(cmd) toolshed.files.ProcessException: bedtools intersect -b /scratch/3627075/tmpqyx80li0 -a mybedfile.bed -wo

I tried adding this header:

chrom start end p-value (tab separated)

Thanks, Jenifer

De: Brent Pedersen notifications@github.com Enviado: martes, 4 de febrero de 2020 4:16 Para: brentp/combined-pvalues combined-pvalues@noreply.github.com Cc: brea iglesias jenifer jenifer.brea@rai.usc.es; Author author@noreply.github.com Asunto: Re: [brentp/combined-pvalues] raise Exception('need header in p-value file to run filter') (#22)

did you try adding a header?

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brentp commented 4 years ago

you'll probably have to do without --annotate