IOError [errno 2] No such file or directory: ‘-o’

Hello everyone.

I’m now running tophat in our server. First, I just simply tried "tophat -p 8 -G <gtf_file> <ref_genome> <fa1><fa2>" and it worked. Then I wrote a for loop scripts but It reported error:

[2019-04-03 10:49:16] Beginning TopHat run (v2.1.0)

-----------------------------------------------

[2019-04-03 10:49:16] Checking for Bowtie

                  Bowtie version:        2.2.9.0

[2019-04-03 10:49:16] Checking for Bowtie index files (genome)..

[2019-04-03 10:49:16] Checking for reference FASTA file

Warning: Could not find FASTA file mouse/bowtie2_index_mouse/mouse_ref.fa

[2019-04-03 10:49:16] Reconstituting reference FASTA file from Bowtie index

Executing: /opt/sw/packages/gcc-4.8/bowtie2/2.2.9/bin/bowtie2-inspect 
mouse/bowtie2_index_mouse/mouse_ref > ./tophat_out/tmp/mouse_ref.fa

[2019-04-03 10:51:05] Generating SAM header for mouse/bowtie2_index_mouse/mouse_ref

Traceback (most recent call last):

File "/opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost-1.59.0/tophat2/2.1.0/bin/tophat", line 4095, in <module>

sys.exit(main())

File "/opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost-1.59.0/tophat2/2.1.0/bin/tophat", line 3949, in main
    params.read_params = check_reads_format(params, reads_list)

File "/opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost-1.59.0/tophat2/2.1.0/bin/tophat", line 1844, in check_reads_format
    zf = ZReader(f_name, params)

File "/opt/sw/packages/gcc-4.8.3/mvapich2-2.1/boost-1.59.0/tophat2/2.1.0/bin/tophat", line 1797, in __init__
    self.file=open(filename)

IOError: [Errno 2] No such file or directory: '-o'

My for loop code is shown as below:

for name1 in R1/*_R1_001.fastq.trimmed_val.fq; 
do 
name2="R2/$(basename "$name1" _R1_001.fastq.trimmed_val.fq)_R2_001.fastq.trimmed_val.fq"; 

if [ ! -f "$name2" ]; then printf 'Missing "%s"n' "$name2"; 
continue; 
fi;
tophat -p 8 mouse/bowtie2_index_mouse/mouse_ref -o tophat_out/ -G mouse/ensembl_gtf/Mus_musculus.GRCm38.95.chr_patch_hapl_scaff.gtf $name1 $name2; 
done

It looks like the directory path problem but I have changed the path several times it still report this error. I wonder if anyone could help me about this?

Thank you!