index error

[JXAUDZF]

code:
cut -f 1 -d ' ' ./SQANTI3_1_output/muscle_corrected.fasta > ./SQANTI3_1_output/cdna.new.fa
grep '^>' ./SQANTI3_1_output/cdna.new.fa | cut -d ' ' -f 1 | sed 's/^>//g' > /home/Dingzifeng/SQANTI3_1_output/cdna.decoys.txt
cat ./SQANTI3_1_output/cdna.new.fa ~/data/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa > ./trans_genome.fa
singularity exec /home/Singusoft/miniconda3_bedtools_mashmap_salmon.simg salmon index -t /home/Dingzifeng/SQANTI3_1_output/trans_genome.fa -d /home/Dingzifeng/SQANTI3_1_output/cdna.decoys.txt -i ~/salmon_index

result:
[2024-03-18 23:23:14.069] [puff::index::jointLog] [critical] Observed a non-decoy sequence [1] after having already observed a decoy. However, it is required that any decoy target records appear, consecutively, at the end of the input fasta file. Please re-format your input file so that all decoy records appear contiguously at the end of the file, after all valid (non-decoy) records

[alexdhill]

Looks like you are using ./SQANTI3_1_output/cdna.new.fa as your decoy file. In the indexed file, decoy sequences must come after the txome sequences, so:
cat ./SQANTI3_1_output/cdna.new.fa ~/data/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa > ./trans_genome.fa

should instead be
cat ~/data/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa ./SQANTI3_1_output/cdna.new.fa > ./trans_genome.fa

such that the decoy sequences occur last.

[JXAUDZF]

The ~/data/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa is genome, the ./SQANTI3_1_output/cdna.new.fa is trans, therefore I don't know where is error.

[alexdhill]

You specify in the salmon index command that the cda.new.fa sequences are the decoys though.
-d /home/Dingzifeng/SQANTI3_1_output/cdna.decoys.txt
This line means "use the sequences with the titles in the text file as my decoy sequences."
If the cda.new.fa sequences are not supposed to be decoys, remove that flag. Otherwise, my above answer should resolve the error.