Skipping regions due to being absent in the computeMatrix output

[bleepbl...@gmail.com]

I've been getting this error message suddenly, potentially due to the bigwig file input:
"Skipping sex-indep_(robust)_r1422, due to being absent in the computeMatrix output"

At first blush, this seems similar to the issue described here: https://github.com/fidelram/deepTools/issues/447

However there are no overlapping (much less duplicate) regions in any of the bed files. I ran computeMatrix and plotHeatmap probably dozens of times using these same input regions in the past with no issues. Upon adding a few additional bigwig files to a new run I began to get the error above. The output looks as expected, just missing thousands of regions.

Things I've tried:
1) Changing the bed input to a single file or a merged file
2) Changing the version to 2.3.3 or 2.5.0.1

I'm in the process of slowly removing the bigwig files one at a time to see where the issue is coming from, but haven't found it yet. I've used all of the bigwigs sucessfully as input for Deeptools in the past but not in this particular combination. There is no additional error message indicating an issue with any bigwig file.

[Devon Ryan]

My only guess is that that contig is missing from one of the bigWigs, so
it'll get skipped. Otherwise, if you can reproduce this with a small
number of bigWigs then send them to me and I can try to diagnose this on
Monday.

Devon

--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dpry...@gmail.com