[dammit.annotate:ERROR] TaskError - taskid:TransDecoder.Predict

[mddawson77]

Hi Camille,

I have an error with the TransDecoder.Predict command from Transdecoder v3.0.0 w/ dammit v0.3.2. I tried resolving this with Transdecoder v2.0.1 (different error) and also updating to v3.0.1, but I can't find a fix.

          Transcriptome file: good.transfuse_imitator_cons.fa

          Output directory:
          /home/molly/imitator/dammit_v0.3.2/good.transfuse_imitator_cons.fa.dammit

          [x] good.transfuse_imitator_cons.fa

          [x] transcriptome_stats:good.transfuse_imitator_cons.fa

          [x] busco:good.transfuse_imitator_cons.fa-vertebrata

          [x] TransDecoder.LongOrfs:good.transfuse_imitator_cons.fa

          [x] hmmscan:longest_orfs.pep.x.Pfam-A.hmm

          [x] remap_hmmer:longest_orfs.pep.pfam.tbl

          [ ] TransDecoder.Predict:good.transfuse_imitator_cons.fa

Some tasks failed![dammit.annotate:ERROR]
TaskError - taskid:TransDecoder.Predict:good.transfuse_imitator_cons.fa[dammit.annotate:ERROR]
Command error: '/opt/TransDecoder-3.0.0/TransDecoder.Predict -t good.transfuse_imitator_cons.fa --retain_pfam_hits good.transfuse_imitator_cons.fa.transdecoder_dir/longest_orfs.pep.pfam.tbl             --retain_long_orfs 600' returned 127
[dammit.annotate:ERROR]

[lassancejm]

Just encountered the same error.

I think this is caused by a change in the Transdecoder options
In more recent versions of Transdecoder, Transdecoder.Predict expects --retain_long_orfs_length instead of retain_long_orfs.

If I am not mistaking, @camillescott fixed this 2 days ago, so updating would do the trick.

[camillescott]

Thanks for the confirmation! I'm actually in the process of building a bioconda recipe for dammit 1.0 right now, and this is one of the things that gets fixed in that release. I'm hoping it will be up and released by tomorrow.

…

On Thu, Mar 8, 2018 at 5:47 PM, lassancejm ***@***.***> wrote: Just encountered the same error. I think this is caused by a change in the Transdecoder options In more recent versions of Transdecoder, Transdecoder.Predict expects --retain_long_orfs_length instead of retain_long_orfs. If I am not mistaking, @camillescott <https://github.com/camillescott> fixed this 2 days ago, so updating would do the trick. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#90 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACwxrWZ41Iir3RynE6EBz_FvQG50xAkaks5tcd8egaJpZM4MRLEm> .

-- Camille Scott Graduate Group for Computer Science Lab for Data Intensive Biology University of California, Davis [email protected]