Ryley Dorney

Results 6 comments of Ryley Dorney

Java and Groovy error while first time using JAFFA version 2.3

Hello, I have run into a similar issue with JAFFAL. And found the above solutions work also solve this issue :) ``` /opt/JAFFA-version-2.3/tools/bin/bpipe run -n 1 -p exclude="NoSupport,PotentialReadThrough" -p jaffa_output="jaf...

Pipeline fails at multiple stages on simulated nanopore dataset: mismatch between length of bases and qualities for reads

### More information on the error messages I receive while the pipeline is running and files are progressing through stages For several (but not all) files I will run into...

Pipeline fails at multiple stages on simulated nanopore dataset: mismatch between length of bases and qualities for reads

### Running JAFFAL on only the spiked fusions, and only the background simulated reads In an attempt to narrow down what may be cause the errors, I tried run JAFFAL...

Pipeline fails at multiple stages on simulated nanopore dataset: mismatch between length of bases and qualities for reads

Thank you for getting back to me so quickly 😊 I ran JAFFAL on the simulated LongReadFusionSimulation Dataset and had some errors appear ```` ======================== Stage extract_fusion_sequences (ONT_fus_sim_75err) ======================== bash:...

Pipeline fails at multiple stages on simulated nanopore dataset: mismatch between length of bases and qualities for reads

I'll respond later via email with a sample of my dataset that often has problems. I'll also make sure to check if the bases and quality lengths being different for...

Pipeline fails at multiple stages on simulated nanopore dataset: mismatch between length of bases and qualities for reads

with regards to the error about the bases and quality lengths being different for some reads, this actually was the case. Some of the reads simulated by BadRead did not...