$ parallel --plus --dry-run cp {} newfolder/{} :::: list.txt

Remove dry-run if you are okay with dry run (dummy) execution. Always post data to address the issue. In this context, partial tree (folder contents) and content of text files would have helped addressing the issue better.

Just use while loop.

$ tree 
.
├── 2/
├── 2.list
└── folder/
    ├── 100989.fasta
    ├── 43985.fasta
    ├── 84649.fasta
    └── 9606.fasta

$ cat 2.list | while read f; do cp folder/$f 2/; done

$ tree 
.
├── 2
│   ├── 100989.fasta
│   ├── 43985.fasta
│   └── 84649.fasta
├── 2.list
└── folder
    ├── 100989.fasta
    ├── 43985.fasta
    ├── 84649.fasta
    └── 9606.fasta