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FASTA file contains an unknown character error by rsem

RSEM produces "FASTA file contains an unknown character contains an unknown character, (ASCII code 13), at line XXX, position XXX" but not STAR during the indexing step. The problem has been mentioned elsewhere like https://groups.google.com/g/trinityrnaseq-users/c/BBvbInEQmLU/m/RqAM6k3MCgAJ?pli=1]

I solved my problem by:

  1. sed -n "l" XX.fa to check the fa file
  2. if you see \r in the file, you can use notepad++ to replace the \r with blank
fasta
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updated by Ram Ram • written by LC • LC

f you see \r in the file, you can use notepad++ to replace the \r with blank

tr -d '\r' < xx.fa
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written by Pierre Lindenbaum Pierre Lindenbaum

dos2unix will edit in place such files

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written by Malcolm.Cook Malcolm.Cook

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