使用conda安装kofamscan之后,在运行时发现出了一些问题。
Traceback (most recent call last):
10: from /work/workspace/path/software/Anaconda3/envs/Kofamscan/bin/exec_annotation:7:in `<main>'
9: from /work/workspace/path/software/Anaconda3/envs/Kofamscan/bin/lib/kofam_scan/cli.rb:21:in `run'
8: from /work/workspace/path/software/Anaconda3/envs/Kofamscan/bin/lib/kofam_scan/executor.rb:8:in `execute'
7: from /work/workspace/path/software/Anaconda3/envs/Kofamscan/bin/lib/kofam_scan/executor.rb:35:in `execute'
6: from /work/workspace/path/software/Anaconda3/envs/Kofamscan/bin/lib/kofam_scan/executor.rb:107:in `run_hmmsearch'
5: from /work/workspace/path/software/Anaconda3/envs/Kofamscan/bin/lib/kofam_scan/parallel.rb:27:in `exec'
4: from /work/workspace/path/software/Anaconda3/envs/Kofamscan/lib/ruby/2.5.0/open3.rb:95:in `popen3'
3: from /work/workspace/path/software/Anaconda3/envs/Kofamscan/lib/ruby/2.5.0/open3.rb:205:in `popen_run'
2: from /work/workspace/path/software/Anaconda3/envs/Kofamscan/bin/lib/kofam_scan/parallel.rb:28:in `block in exec'
1: from /work/workspace/path/software/Anaconda3/envs/Kofamscan/bin/lib/kofam_scan/parallel.rb:28:in `puts'
在对应的kofamscan github 有提交的一个issues也有类似的问题,不过按照那个人的方法并没有解决。
应该是环境出了问题,后面检查了一些依赖的软件,ruby, hmmscan, parallel这些软件,发现又有新的问题了。
perl: error while loading shared libraries: libnsl.so.1: cannot open shared object file: No such file or directory
有新错误就好办,重新在当前的kofamscan环境中安装libnsl,安装完成后还是不行。根本找不到libnsl.so.1,不过找到了libnsl.so, libnsl.so.3和libnsl.so.3.0.0其实前两者都是连接,指向最后一个文件。同样也可以尝试使用软连接创建一个libnsl.so.1。完成后所有的就可以了。