Something wrong when I use pangene‘s code
Closed this issue · 4 comments
Hello Professor Li, I have some problems when running with the code you presented. The problems are as follows:
$k8 ~/software/pangene-1.1/pangene.js getaa 00.data/genomic.gtf 00.data/protein.faa > 01.pro_align/proteins.faa
/storage/public/home/2022060223/software/pangene-1.1/pangene.js:9: SyntaxError: Unexpected identifier
for (let j = i; j < this.length - 1; ++j)
^
SyntaxError: Unexpected identifier
I checked what seems to be the problem with this file pangen.js? In order to check whether there is a problem with the k8 version, I used node to run, and the results are as follows:
$node ~/software/pangene-1.1/pangene.js getaa 00.data/genomic.gtf 00.data/protein.faa > 01.pro_align/proteins.faa
/storage/public/home/2022060223/software/pangene-1.1/pangene.js:1349
var cmd = args.shift();
^
TypeError: args.shift is not a function
at main (/storage/public/home/2022060223/software/pangene-1.1/pangene.js:1349:17)
at Object. (/storage/public/home/2022060223/software/pangene-1.1/pangene.js:1363:1)
at Module._compile (node:internal/modules/cjs/loader:1369:14)
at Module._extensions..js (node:internal/modules/cjs/loader:1427:10)
at Module.load (node:internal/modules/cjs/loader:1206:32)
at Module._load (node:internal/modules/cjs/loader:1022:12)
at Function.executeUserEntryPoint [as runMain] (node:internal/modules/run_main:135:12)
at node:internal/main/run_main_module:28:49
Node.js v20.12.2
I'm not sure why, but it looks like there's something wrong with the pangene-1.1 script, but I'm not sure.
Hope to get your reply, thank you!
You need to use k8 v1.0. Node or older k8 wouldn't work.
Your 1.0 version of k8 requires v8 to be installed, but requires that the location of v8 be fixed to... /, manual installation of v8 requires google's depot_tools, which is difficult to verify file integrity when not connected to the Internet (not easy to install, always missing files), so I hope you can share the latest version of k8 files to conda?
As a novice thank you for your contribution to scientific research and care for the novice!