Closed MadeleineCarruthers closed 4 years ago
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).
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
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