[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 [email protected] 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.

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-- Camille Scott

Graduate Group for Computer Science Lab for Data Intensive Biology University of California, Davis

[email protected]