With the command:
nohup python get_seq.py TPH_hits all_genomes_eukaryotes_20200303.fas > TPH_seq2.fasta &
nohup: ignoring input and redirecting stderr to stdout
Will there be any effect on my output data?
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Nohup is telling you that the background process it is running has had those streams disconnected. That's because it can't guarantee they won't be used to kill the process (e.g. SIGINT on stdin, or SIGPIPE if stderr is connected to a pipe).
One side effect is that if python writes error messages, they will be inserted into your normal output (in random places due to buffering) which may disrupt any further processing on that data.
The safe procedure is to do those redirections yourself. stdin < /dev/null, stderr 2>&1 or 2>/dev/null or 2>some.log.