merge_peaks_by_bedtools.sh: ***** ERROR: Requested column 4, but database file - only has fields 1 - 0.

[c-lonergan]

Hi,

I am trying to recreate Fig 4 from Dominissi et al (https://www.nature.com/articles/nature11112) using meripseqpipe, and keep getting the same error in the PeakMerge process:

***** ERROR: Requested column 4, but database file - only has fields 1 - 0.
There is no peaks in one of the merged peaks files`
Merge Peaks by macs2 may not be suitable for your data.`

I have checked all of the .bed files used in this process, and all have 5 columns of data. By breaking up the mergebedByBedtools() function I've deduced this line results in an empty tmp._others_allPeaks.bed file.

ls *${prefix_id}*normalized.bed | grep -v ${peakCalling_tools_main} | xargs -i cat {} | sortBed -i - | mergeBed -i - -c 4,5 -o count,mean > tmp.${prefix_id}_others_allPeaks.bed

When, for example, macs2 is used, only macs2*normalized.bed are available so grep -v returns nothing and mergeBed terminates with the error ***** ERROR: Requested column 4, but database file - only has fields 1 - 0. (See screenshots).

You can see my temp3.bed file is producing the error from mergeBed, since its empty.

• What is the purpose of tmp._others_allPeaks.bed?
• Can I simply comment out the offending line?