Error at 'begin coverage matrix processing'

[MadeleineCarruthers]

Hi Frank,

So I did still end up with an error but much further on in the pipeline now. The following information is from a degNorm run performed on a subset of 6 samples. Samples are RNAseq data generated from lizard ovary tissue which was highly degraded. I used STAR for genome indexing (indexed with GTF file) and mapping.

Now the GTF file reads in successfully and all reads for all 6 samples loaded successfully but I am getting an error right after the 'begin coverage matrix processing' part of the pipeline.

I have attached a copy of the log file, the traceback message from the command terminal. degnorm.log degNorm_traceback_error.txt

And here is a Dropbox link to bam file for sample Lib-099, my GTF file and the script I am using to run the pipeline: https://www.dropbox.com/s/62hpxck9t6202h2/Lib-099_sorted.bam?dl=0

Thanks very much in advance for your help.

All the best,

Madeleine

[ffineis]

Hi Madeleine,

I've attempted to fix this bug from the hotfix/indexing branch. Can you please install degnorm from there and attempt your run again?

Re-install commands:

git checkout hotfix/indexing
git pull origin hotfix/indexing
pip uninstall degnorm
rm -rf DegNorm.egg-info build dist
./install

And then run degnorm again.

If this does not work, please post two .bam files so I can test the pipeline end-to-end (as degnorm requires at a minimum 2 rna-seq files to run).

[MadeleineCarruthers]

Hi Frank,

Success!! Full pipeline has just finished without ant issues on a subset of the samples. All the results look how they should.

Thank you so much for your time and help with this!

All the best,

Madeleine