pianpianyouche / plascad Goto Github PK

Hi, @pianpianyouche
I found this software and I couldn't help trying it. I installed this software using conda. However, when I ran with the example fasta file, it reported that something was wrong:

 Error: Sequence file /mnt/d/test2/example_MOB_temp_mob.faa is empty or misformatted

cat: '*ATPase.hmm_domtblout_parsed_out': No such file or directory
cat: '*T4CP*_domtblout_parsed_out': No such file or directory
cat: '/mnt/d/test2/example*MPFF*_result_out': No such file or directory
cat: '/mnt/d/test2/example*MPFG*_result_out': No such file or directory
cat: '/mnt/d/test2/example*MPFI*_result_out': No such file or directory
cat: '/mnt/d/test2/example*MPFT*_result_out': No such file or directory
Warning: [blastp] Number of threads was reduced to 8 to match the number of available CPUs

I updated the software with conda but the issue was still there. Could you help me? Thanks.

Hi, @pianpianyouche,
When plascad judges the mobility of a plasmid, does it search the oriT? As far as I know, a plasmid lack of oriT should be concerned as unmobilizable even if having complete T4SS and relaxase.

e.g. if I want particular virulence genes annotated as well as the standard plascad output?

Hi, @pianpianyouche
I found database of plascad did't updated last several years. I tried replaceing it directly but failed, probably because I installed it with conda?
There are some ways that I can update the database to the newest by myself?

Hi!
I tried to run Plascad on plasmid assemblies and also on the example file here in the repo, both returned
Warning: [blastp] Number of threads was reduced to 8 to match the number of available CPUs sort: Broken pipe
Any advice?

Hi, @pianpianyouche
I installed Plascad as you mentioned in the tutorial with conda environment. However, it will report an error when I ran Plascad with example.fasta or my own plasmids files.

Error: Sequence file example_MOB_temp_mob.faa is empty or misformatted


Error: Sequence file example_MOB_temp_mob.faa is empty or misformatted

cat: *ATPase.hmm_domtblout_parsed_out: No such file or directory
cat: *T4CP*_domtblout_parsed_out: No such file or directory
cat: example*MPFF*_result_out: No such file or directory
cat: example*MPFG*_result_out: No such file or directory
cat: example*MPFI*_result_out: No such file or directory
cat: example*MPFT*_result_out: No such file or directory

Hello,

So I have no idea how to visualize your .js file. Can you please provide some sort of tutorial on this? So far, your software is working better than anything I've used yet and I'd love to see your visualizations.