Jake Lehle, Ph.D.

Hmmm good question. I'm guessing have already looked at the config file that is fed into the ``` gemBS prepare ``` step correct? You could mess with the threads and...

Hey Paul. That is super weird. So you mentioned that it isn't an issue with the fastq. So you used like vi to check the fastq and make sure that...

Yeah, I really like the containerized approach and there shouldn't be an issue with the software that lives in the container. I get you about not wanting to get too...

Yeah if you can process it with bowtie then something is going on. Well there a ton of options you can modify for GEM. Maybe heath can give you some...

Hello @ottojolanki. Hmm well with paired FASTQ files you probably already know that each read starts with an @ symbol with info about the read and then a new line...

@ottojolanki ah okay I found it. That number isn't a line in the input file. I don't know what it is, but it isn't a line. This issue has to...

Circling back to this issue as I hit it too today. I was able to get around it but in a rather dumb way. So the curl command don't respect...

Looks like this is the issue from the cello.py file ``` def _download_resources(rsrc_loc): if not os.path.isdir(join(rsrc_loc, "resources")): msg = """ Could not find the CellO resources directory called 'resources' in...

@cstubben Thank you! Here was the code I ran to fix this issue. ``` library(enrichplot) library(ggtangle) (other code ...) p

Just for some clarity for anyone hitting this issue. I just followed @papanikos response and changed my version of bracken-build with the changes suggested and it worked. Thank you @papanikos...