Margaret Ho

I have exactly the same issue, what do you advise? thanks!

Thanks this did work! In the correct conda environment, check that 0.36.0 is actually installed: conda list or conda list doit remove it: conda remove doit check that it's gone:...

No, I ended up using tools for long read gap filling like samba and TGS-gapcloser and then just polishing with short reads and pilon

@DRL I have also noticed the same thing, as well as other mysterious behavior from blobtools bamfilter. See these arguments provided by blobtools bamfilter don't match the documentation (https://blobtools.readme.io/docs/bamfilter) The...

It's not in the web documentation on the site (https://blobtools.readme.io/docs/bamfilter), but you can output fastq using the `-f fq` flag of blobtools bamfilter. Just tested and it works. Fasta is...

I ran into this same error and keeping the conda install of Augustus 3.5.5 was fine as long as I updated funannotate to the latest master `python -m pip install...

Is there any plan to fix the `excessive gaps when scaffolding pacbio reads`? I couldn't get redundans to gap close with the long reads, and ended up running MASURCA's samba...

I have the same question! I am following these instructions https://immunarch.com/articles/web_only/load_10x.html#prepare-10x-data and trying to read in the data downloaded from this 10X genomics dataset (seems like a very standard dataset)...

It seems like this is a common issue that many others are having when trying to load in 10X Genomics data https://github.com/immunomind/immunarch/issues/363 https://github.com/immunomind/immunarch/issues/358 We are all seeming to get this...

Hi @adigenova I also have Error 1 and I can't seem to find in the issues what this means The base command is perl /sysapps/cluster/software/wengan/0.2/wengan.pl -x ontraw -a M -s...