Francoise Thibaud-Nissen

> 1_length=4998493_depth=1.00x_circular=true_[location=chromosome] Please review https://github.com/ncbi/pgap/wiki/Input-Files#Genome-assembly-sequence-file. There are several characters that are not allowed in this SeqID (the SeqID is everything before the first space). You can try SeqID of 1...

Hi Arun - thank you for providing this report. > Also, auto-correct-tax did not override the Alteromonas to Matelella in the final output. The ANI report you provided is truncated....

Based on the data you report here, there is more evidence that the genome belongs to Martelella lutilitoris (a Rhizobiales) rather than Alteromonas, but ANI is not able to provide...

Hi - Thank you for your question. Please see: https://github.com/ncbi/pgap/wiki/Taxonomy-Check#description-of-the-reports (There is a link to this page in https://github.com/ncbi/rapt/wiki/Standalone_RAPT_doc#rapt-output). The numbers in parenthesis are query coverage and subject coverage. The...

Hi! Unfortunately, RAPT is not suitable for fungi. The assembler was developed for (small) prokaryotic genomes and the annotation pipeline that RAP uses is very much tailored for proks and...

Thank you for trying RAPT! SRS10489852 is the identifier for a _sample_, which corresponds to multiple SRA experiements and runs. RAPT takes _runs_ as input, with identifiers starting with the...

I tried running RAPT on [SRR16250963](https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR16250963). Unfortunately, the run failed in the assembly step. I suspect this is because this sample is a mixture. If you look in the analysis...

Sorry for the inconvenience! v0.3.0 is not available anymore. Please download RAPT again using the directions on [our wiki](https://github.com/ncbi/rapt/wiki/Standalone%20RAPT%20In-depth%20Documentation%20and%20Recommendations): `curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.1/rapt-v0.5.1.tar.gz` Thanks!

Hi, thanks for your question. Can you please running `run_rapt.py` with `--no-usage-reporting`? I think it will address the issue you see.

There is currently no environment variable that can be used as an alternative, but yes, this is something we should think about... As for downloads, I don't see a way...