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This is due to the fact that TransDecoder does _not_ create the BED file during LongOrf, but only a GFF3 file. This will require a separate parsing.
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There seems to be a problem with invalid options for lastal. I have installed last-658 and last-731. Maybe some options have changed. Will dammit take up after this step if i do this by hand?
```
---…
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Hi,
we added recently [https://github.com/gentoo-science/sci/tree/e894fffa75d809914ef009a06bfe3ce4052a91c3/dev-java/htsjdk](a package for cramtools to Gentoo Linux) and I am unhappy you decided to m…
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[originally from @abshah]
Hi Camille,
I just tried running the example datasets and ended up with a slightly different error!
`--- Running annotate!
```
Transcriptome file: cdna_nointrons_u…
-
getting an error with dammit at the very end of the annotation process:
```
$ dammit annotate Rimi.v1.02.fasta --busco-group vertebrata --n_threads 60 --database-dir /mnt/data3/macmanes/dammit_databa…
-
using 0.2.8
```
dammit databases --install --database-dir /data/dammit_databases/
========================================
dammit! a tool for easy de novo transcriptome annotation
Camille Scott 2015
…
-
using dammit 0.2.0
```
$ dammit databases --install --full --database-dir /mnt/harmonia/
========================================
dammit! a tool for easy de novo transcriptome annotation
Camille Scot…
-
using dammit v. 0.2.0
```
dammit annotate Harmonia.v1.0.0.fasta --busco-group arthropoda --full -o harm2 --n_threads 32 --database-dir /mnt/dammit/
```
```
transdecoder is finished. See output file…
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I am trying to run dammit on a clean Ubuntu install within VirtualBox on Mac OS 10.11. I am afraid that one of the tools didn't install properly -- I remember a lot of error codes being thrown. But un…
-
```
What steps will reproduce the problem?
1. download the cd-hit-v4.5.4-2011-03-07.tgz file from website
2. tar xvf cd-hit-v4.5.4-2011-03-07.tgz --gunzip
3. make openmp=yes
What is the expected outp…