Matt MacManes

Scratch that. I've identified the bug: ``` /mnt/lustre/macmaneslab/macmanes/Scaff10X/src/scaff-bin/scaff10x /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/genome/Neotomodon_alstoni_10x_v6a.fasta /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/reads/NEAL_S1_L006_R1_001.fastq.gz /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/reads/NEAL_S1_L006_R2_001.fastq.gz Neotomodon_alstoni_10x_v234.fasta File not in the working directory! Input target assembly file1: /mnt/lustre/macmaneslab/shared/pero_genomes/Neotomodon_alstoni/genome/Neotomodon_alstoni_10x_v6a.fasta File not in the working directory! Input...

Thank you this is an excellent suggestion. I don't have time to work on in immediately, but would very much welcome a pull request.

but to keep is simple, for the running of the assembly itself, just stick with the default Euk database. Once you have an assembly agree that Tetrapoda will be good!

So just to confirm, the test dataset now runs properly, and gives an output something like ``` 6| # 5| ## 4| ### 3| ### 2| ### # 1| ###...

ok good.. the other issues aside, have you been able to successfully run a real dataset through the pipeline?

running the 1st command runs the entire pipeline, including TransRate and BUSCO (with Euk database). After that, you can annotate or do whatever else you want to. Does this make...

Concatenate them all together 1st, but remember the rec for including samples. In general, we strongly recommend that you assembly 1 individual per treatment or group. On Apr 29, 2019,...

How about this - try one assembly using my rec - concatenate 2 individuals together (1 normal and 1 not), and then do another experiment where you concatenate all the...

I've updated the repo with the Python changes. You should be able to `git update -> make` at this point. Let me know if starting from scratch works - I'm...

I think I’d try for choosing samples from within a family if possible, but not knowing how different families are, it’s hard to say. Matt On Apr 30, 2019, at...