Devon Ryan

You could in theory do that, by making a BED file with 1 entry for each chromosome. However the boxes won't be scaled to the length of the chromosome, since...

Is the BAM file empty? The error suggests that some sections were processed in 0 seconds (even with an empty BAM file I'm amazed that it could be processed faster...

Oh, that's incredibly strange. Can you post your bigWig files somewhere so we can debug this?

Can you post the command you used? There are a variety of possible reasons for this and having the command will narrow them down.

@ANDdna1991 Can you try using the `--averageTypeSummaryPlot median` with plotProfile? I recall that there's some clipping that happens in the heatmap so outliers don't make the plots uninterpretable and I...

Can you upload the matrix somewhere? It'll be easier to check into this with it.

Can you post the entire error back-trace?

I'm not sure if pysam returns a useful error indicator in this case. Can you check what happens with the following? ``` python -c "import pysam; bam = pysam.AlignmentFile('SRR3705515-abra2.bam'); print(bam);"...

This would make the most sense in computeMatrixOperations, since there should be a matrix file produced. I'm not sure how well it would work though since inevitably people will try...

computeGCBias is deprecated and rarely needed anymore, are you sure you actually even need to run it?