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