Catarina Loureiro comments

Results 8 comments of


                                            Catarina Loureiro

MIBiG t2pks BGCs not grouping into families

Hi! It appears you are giving BiG-SCAPE MIBiG gbks that are not an output of antiSMASH -> BiG-SCAPE requires antiSMASH processed gbks as input. To get these you can open...

accessing noabund param in sourmash python API

Hi Tessa! Thank you for the info and quick reply here! I will be building sketches from protein sequences directly. Could you elaborate on what are the differences between making...

accessing noabund param in sourmash python API

Hi Tessa, Thanks again for your input! So, this is all outside my skill comfort zone ahah, so I have to admit I am a bit lost. So for context:...

accessing noabund param in sourmash python API

Hi all! I was wondering if you had any thoughts wrt my comments above? I have been trying the sourmash branchwater plugin, but the output files it generates are prohibitively...

add option to switch subprocess spawn method

Lets put this in the config instead of CLI

add option to switch subprocess spawn method

Currently there is something going on with the config hash checking in macbooks. If i run a few bigscape cluster runs, and then a bigscape query run all in the...

BiG-SCAPE v2 card Found connected components step for more than 48 hours

Hi! You are correct that the --clan_cutoff parameter has been deprecated, and therefore there is no direct way to get GCC-like results with BiG-SCAPE 2. Giving a higher cutoff to...

BiG-SCAPE v2 card Found connected components step for more than 48 hours

Hi Gavin! This is a good point! I'm afraid there isn't a great reason for the 'gcf-cutoffs' param name other than it being left as a legacy thing :) We'll...