drhoads

Command "python setup.py egg_info" failed with error code 1

1

Win10 Python2.7 or 3.7 get this error on pip install imagepy updated everything possible but can't figure out why getting this error. Been all over GitHub and every message board...

Trying to setup the command line in Win10 using fgbio-0.8.1.jar and have everything working for calling DeMuxFastqs but am running in Win10 and no matter how I try to specify...

snippy-multi ERROR: Could not find .aligned.fa/.vcf in 100AEA1

5

Running in WSL2Ubuntu. Have 227 assemblies in contigs in .fna. commands: snippy-multi files.txt --ref ../prokka227/SA1.gbk --cpus 16 > runme.sh sh ./runme.sh symptoms: completes all the calls to snippy but then...

Have run roary-scoary pipelines and now experimenting with pirate. I like the output with the percentages for each of the genes and how pirate provides more complete analysis of when...

Question on ordering of analyses in the pipeline

2

We have noted that the pipeline runs nanoq on the long reads and then porechop. WE are wondering if the order can be reversed, since if we set minlength at...

Where is the polished genome

8

Using DragonFlye on a linux server. Have run the assembly successfully with just the ONT data but now adding the shortreads for polishing. Tried polypolish 2 with forward and reverse...

Subscript out of bounds

1

Trying to run pafr in R4.3.2 in RStudio2024.12.1 on Win11 64 bit Have .paf aligning a 2.5Gb genome with a 4.4 Gb genome. Using your code from https://cran.r-project.org/web/packages/pafr/vignettes/Introduction_to_pafr.html Testing as...

Has anyone installed in Ubuntu-WSL2?

2

Hoping to run JellyFish so I can feed into GenomeScope for 5 large genomes I am working on. Only JellyFish in Conda is a very old one. Followed the instructions:...