jiarong
jiarong
Fixed in development version. Thanks for the feedback and helping figure out the issue :)
Hi, the reason is the scores prediction relies on some genomic features (gene density, strand switch frequency, etc), and they needs a few genes to be meaningful (I set the...
Hi, did you get this error on a new run or a repeated run on the output directory that failed attempt before? A new run means `/bettik/virclust/results/VirSorter/EXAMPLE/EAF_Gu_TropicPondC4a0115_c.fna` is empty or...
I can not tell from the output. Do you mind send me the result folder `20201218_VIRSorter2_RNA_viruses`? Is this the only sample you ran and failed?
Hi, can you provide an example of your sequence name pattern? It would be great if you can find the one has "4.179426" in it.
Hi, I still can not identify the issue from your description alone. Could you share this file: /home/sej/VirSorter2/all_unknown.out/iter-0/all.pdg.hmm.tax
I am not sure. CPU 100% means the process is running, not stuck. How many provirus.py processes are there in htop? Are most of contigs very long (> 100kbp)?
Right, these contigs are not that long. With 110 threads (-j), step 3 should finish within hours. Are you running other processes takes many CPUs threads?
The default setting has a good balance of sensitivity and specificity and should be good in general. If you want to be more conservative, then you can increase the --min-score...
Hi, I found emapper.py still have issue with `--pfam_realign denovo`. In my case, there is ~1000 AA seqs, and the eggnog annotation step w/ diamond works fine, but all the...