Problem with file location address in HISAT2

Question

[Yoosef]

Hello dear Biostars community I was trying to align my sequence with hg-19 genome reference using HISAT2. My system is dual boot with windows 10 and Ubuntu. so, when i want to give my file address i get the following error:

./hisat2 -q -t -p 8 --add-chrname -x /media/yousef/EEFC0BDBFC0B9CC9/2.Medical labratory scineces/Genetice/bioanformatics/NGS/hg19_genome/genome /home/yousef/ncbi/public/sra/SRR6040558_Trimmed.fastq -s /home/yousef/ncbi/public/trimmed.sam
(ERR): "/media/yousef/EEFC0BDBFC0B9CC9/2.Medical" does not exist
Exiting now ...

And my file location is:

/media/yousef/EEFC0BDBFC0B9CC9/2.Medical labratory scineces/Genetice/bioanformatics/NGS/hg19_genome/genome

I also need to address that i have no folder named "EEFC0BDBFC0B9CC9" in my drive. Also,The trimmed FASTQ file that i'm trying to use is not in the same drive that my Ubuntu is installed. How can i solve this problem?

Answer 1

[ATpoint]

Whitespaces have to be escaped in bash. Best is to either remove them from the folder name or if this is not possible type

realpath path/to/genome

and copy the output.

[Yoosef]

Thanks a lot. It solved my problem.