Lisa K. Johnson

yes, than you - it downloaded after trying again. any way to prevent this from happening?

I experienced the same issue when finished. A little confusing: ``` [ljcohen@dev-intel14 CedarSwamp]$ osf -p y2n4z clone 5files [04:30, 48.72s/files] [ljcohen@dev-intel14 CedarSwamp]$ ███████████████████████████████████████████████████████| 1.55G/1.55G [00:53

I'm also experiencing a problem with not being able to connect:  @alexmorley Is there any progress with this issue? btw, thank you for this resource. It remains a very...

A work-around is setting up and using a conda env. See #118.

Any idea what this means? The `conda` version used to work just fine! Problem is, this was run on a different node then the dir was copied over. If I...

``` (py3.dammit) ljcohen@farm:~$ conda list # packages in environment at /home/ljcohen/anaconda2/envs/py3.dammit: # alabaster 0.7.9 Babel 2.3.4 click 6.7 cycler 0.10.0 py35_0 dammit 1.0.dev0 dbus 1.10.10 0 decorator 4.0.10 py35_0 decorator...

No, hpc - PSC Bridges. I have to write to temp $LOCAL node disk space then copy output at the end to avoid hammering storage disk. I ran it again...

Ah. It's a problem with the gff3 file itself generated with the master version of dammit. An old gff3 file does just fine. Command: ``` annotations = GFF3Parser(filename="A_xenica.trinity_out.Trinity.fasta.dammit.gff3").read() ``` No...

Any ideas how to fix the gff3 file after running dammit? Would prefer not to run dammit again on 17 of these. Here's an example: ``` curl -L https://osf.io/bz5de/download -o...

Has something changed with the way transcripts are sorted? Could this be the issue? Old version of dammit with `Transcript_100000` appearing first: ``` ljcohen@js-168-95:/kfish_annotations$ head A_xenica.trinity_out.Trinity.fasta.dammit.gff3 ##gff-version 3.2.1 Transcript_100000 LAST...