Issue finding fastq file

[rLannes]

Hi,
I encountered the following issue while trying to use this pipeline:

My fastq files are in the directory Sim_fastq/
Both mates are already present in Sim_fastq/

ls Sim_fastq/
trimmed_sim_1_S1_L001_R1_001.fastq.gz
trimmed_sim_1_S1_L001_R2_001.fastq.gz
.....

but I got the following output and error; notice how mates files passed to Salmon are incorrect?
Somehow something added "_R1_001.fastq.gz " and "_R2_001.fastq.gz " to my fastq files!

[ mates1 ] => { Sim_fastq/trimmed_sim_1_S1_L001_R1_001.fastq.gz_R1_001.fastq.gz }

[ mates2 ] => { Sim_fastq/trimmed_sim_1_S1_L001_R1_001.fastq.gz_R2_001.fastq.gz }

[ threads ] => { 12 }

[ validateMappings ] => { }

[ output ] => { Sim_TE/quant_out/trimmed_sim_1_S1_L001_R1_001.fastq.gz }

Exception : [
The following errors were detected with the read files

ERROR: file [Sim_fastq/trimmed_sim_1_S1_L001_R1_001.fastq.gz_R1_001.fastq.gz] does not appear to exist!

]

Would you be able to help me fix this issue?

Best,
Romain