Error when run tophat2 (update: solved)

Question

[Chris]

Hi all,

I know this tool is quite out of date but I am trying to reproduce the result of this paper to learn to build an RNA-Seq pipeline.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6373869/

   tophat2 -r 200 -p 8 -o ~/protocol_1/data/MT1/Tophat_Out -G ~/Mus_musculus.GRCm39.107.gtf ~/ncbi-genomes-2022-09-07/index_name ~/protocol_1/data/Fastq/Trim_MT1_1.fastq ~/protocol_1/data/Fastq/Trim_MT1_2.fastq

I found a similar error in the link below but still could not apply to my case:

Warning: Could not find FASTA file /home/praveenkumarr/rice_default/bwt/genome/genome.fa
Tophat Error : Couldn't build bowtie index with err = 1

Would you please tell me how to fix this? I appreciate your help.

[2022-09-09 10:55:25] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2022-09-09 10:55:25] Checking for Bowtie  
          Bowtie version:    2.2.5.0  
[2022-09-09 10:55:25] Checking for Bowtie index files (genome)..  
[2022-09-09 10:55:25] Checking for reference FASTA file  
    Warning: Could not find FASTA file /vcu_gpfs2/home/doanc2/ncbi-genomes-2022-09-07/index_name.fa  
[2022-09-09 10:55:25] Reconstituting reference FASTA file from Bowtie index  
  Executing: /vcu_gpfs2/home/doanc2/miniconda3/bin/bowtie2-inspect /vcu_gpfs2/home/doanc2/ncbi-genomes-2022-09-07/index_name > /vcu_gpfs2/home/doanc2/protocol_1/data/MT1/Tophat_Out/tmp/index_name.fa  
[2022-09-09 10:57:10] Generating SAM header for /vcu_gpfs2/home/doanc2/ncbi-genomes-2022-09-07/index_name
[2022-09-09 10:57:12] Reading known junctions from GTF file  
[2022-09-09 10:57:29] Preparing reads  
     left reads: min. length=80, max. length=80, 1317922 kept reads (0 discarded)
    right reads: min. length=80, max. length=80, 1317922 kept reads (0 discarded)  
[2022-09-09 10:58:11] Building transcriptome data files /vcu_gpfs2/home/doanc2/protocol_1/data/MT1/Tophat_Out/tmp/Mus_musculus.GRCm39.107  
[2022-09-09 10:58:32] Building Bowtie index from Mus_musculus.GRCm39.107.fa  
    [FAILED]  
Error: Couldn't build bowtie index with err = 1

[Chris]

I don't know why the link to the errors are showed incorrectly.