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Hi, I am trying to run the sequences section of Trinotate but run into an error with the tmhmmv2 command:
```
[Wed Sep 11 15:47:29 2024] Running CMD: tmhmm --short /data/putnamlab/dbecks/Heatwave_…
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Hi there!
I am using EvidenceModeler to produce an annotation.
I am using this data to produce the final annotation:
- Augustus prediction
- Transdecoder annotation
- Alignment of PacBio …
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hey,
I first ran TransDecoder.LongOrfs and then Predict and I got that error message:
Selecting best orfsError, cannot find file blastp.outfmt6 at /usr/local/packages/transdecoder-5.7.1/util/se…
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Hello,
I have created a conda environment with (what I think) all the requisite programs with:
```
conda activate trans2express
mamba install -y diamond beautifulsoup4 biopython biothings_clie…
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您好,我在运行TransDecoder.Predict时出现了一些报错:
TransDecoder.Predict -t MMETSP.unigenes.fa
-T 8
* Running CMD: /usr/lib/transdecoder/util/get_top_longest_fasta_entries.pl MMETSP.unigenes.fa.transdecoder_diSe…
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if I remove the assembly, and then `run_eelpond trinity default`, the dammit step fails. output below.
I can get it to work properly by removing the annotation directory. I suspect that there is a …
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Hi!
I'm working in the annotation of a red algae which have "transl_table=4" genetic code. Can Transdecoder use this type of genetic code?
I was looking in the manual but I can't find nothing.
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I ran the pipeline on my laptop like this:
``` sh
time sh lincRNA_pipeline.sh -c sample.data/cuffcompare_out_annot_no_annot.combined.gtf -g sample.data/Brapa_sequence_v1.2.fa -r sample.data/Brassica_…
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Step 3: Transcript
PWD: ~/3_geta/3/p/out.tmp/3.transcript
CMD(Skipped): ~/software/geta-geta-2.4.12//bin/split_sam_from_non_aligned_region ../2.hisat2/hisat2.sorted.sam splited_sam_out 10 > splited…
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Hi,
I'm trying to use trinotate using data from gene prediction produced by Braker2.0 (augustus).
Thank to your help I managed to go through the first step of Transdecoder (https://github.com/Tra…