Nat Echols

Sorry @ananthrajb, we gave up and stuck with 2.0.0 for now and are investigating other platforms.

Please contact PacBio tech support for help with problems running Cromwell in SMRT Link. -Nat (PacBio software team) On Mon, Mar 6, 2023 at 6:27 PM muhyunkim12 ***@***.***> wrote: >...

I don't understand how this error can happen if you have actually installed the module. What happens when you run `python -c "import pyBigWig"`, using the bioconda python?

I think @rhallPB has the right idea, you may have installed kineticsTools into the wrong Python.

No, because it's a compatibility function for Python 2: https://github.com/PacificBiosciences/kineticsTools/blob/master/kineticsTools/ResultWriter.py#L1 The next release of kineticsTools *will* switch to Python 3, however. (No, I don't have an ETA for this.)

It's probably not critical - it was part of a fix for working with multiplexed data, and I was concerned about possible corner cases so I made it output an...

Do not use samtools to merge PacBio BAMs if you want the output to work in downstream PacBio applications. Instead, use the `pbmerge` utility that is included with SMRT Link,...

Yeah, I suspect it's ending up with an uninitialized variable because of insufficient coverage, but still a bug in any case. I'll take a look.

@nick-youngblut Looks like the `--methylFraction` option got broken in the process of the py3 porting. Sorry! I'll post a diff here once I have a fix.

@nick-youngblut Try this patch: ``` diff --git a/kineticsTools/MultiSiteCommon.py b/kineticsTools/MultiSiteCommon.py index 96d06e8..aed1350 100644 --- a/kineticsTools/MultiSiteCommon.py +++ b/kineticsTools/MultiSiteCommon.py @@ -143,7 +143,7 @@ class MultiSiteCommon(object): def getContextMeans(self, start, end, sequence): meanVector = []...