Christopher Hughes

That was the entire output for refgenie pull. It just ends after the 'downloading URL' statement. Here is the debug log: ``` refgenie --verbosity 5 pull rCRSd/fasta DEBU 10:57:11 |...

Not sure I did this correctly, but for the second command, I assume you meant within python: ``` >>> from urllib.request import urlretrieve >>> urlretrieve("http://refgenomes.databio.org/v3/assets/archive/94e0d21feb576e6af61cd2a798ad30682ef2428bb7eabbb4/fasta", filename="rCRSd.fa.gz") ('rCRSd.fa.gz', ) >>> ```...

Hi Harald, I moved to Java 14 and don't see the issue anymore. Cheers, Chris

Hi Ding, I will need to look into this in more detail, but I do not think these data are stored in the raw file and are thus not accessible...

Hi @romanzenka, Sorry you had these issues, but I am glad you were able to sort it out. I haven't had a chance to work on RawTools in some time....

Hi, Can you give me some more details? Are you using the command line version of RawTools? If so, what is the command you are feeding it? If you are...

Hi, Thank you for this additional information. It appears the GUI and command line errors are different. I think we should just focus on the command line one for now....

If you check the QC directory, does it actually write the target decoy database?

It is a bit odd that your 'RawTools_custom_config.xml' file is in that directory and not in your xtandem/bin directory (or is this one just a copy?). Can you show me...

Hmm. I will have to try and track down what was happening in 2.0.7 at some point. It is odd though as nothing really changed in the QC pipeline between...