No gene_trans_map file in CD-HIT-EST output

Question

[ofarinas621]

Hello,

I am running an RNAseq pipeline where the next step is to generate the updated sqlite database with a gene_trans_map file. However, I noticed that my CD-HIT-EST run did not give me this file at all. I have only the fasta and clstr files in the output. I am not sure if there is a way to generate this somehow? It seems that the gene_trans_map file is crucial for several steps down the road. Here is my code below:

module load python/2.7-conda5.2


cd_hit_est="/fs/ess/PAS1182/cd-hit-v4.8.1-2019-0228/cd-hit-est" 


  "${cd_hit_est}" -o /fs/ess/PAS1182/Olivia/NYCHA/cd_hit_est/CD_HIT_EST_NYCHA_1.fasta -c 0.80 -i /fs/ess/PAS1182/Olivia/NYCHA/trinity_output/Trinity_NYCHA_1.fasta -n 4 -T 0 -M 0 

Any help would be greatly appreciated.

Thanks! Olivia