Does hisat2 –rg flag eat the “/” character in multiline definitions?

Does hisat2 –rg flag eat the “/” character in multiline definitions?

0

Hello, I am trying to use hisat2, but I noticed something weird.

When running it like so:

hisat2 
       -p 8 
       --rg-id=UHR_Rep2 
       --rg SM:UHR 
       --rg LB:UHR_Rep2_ERCC-Mix1 
       --rg PL:ILLUMINA 
       --rg PU:CXX1234-TGACAC.1 
       -x $RNA_REF_INDEX 
       --dta 
       --rna-strandness RF 
       -1 "$RNA_DATA_DIR/${SAMPLE}_1.fastq.gz" 
       -2 "$RNA_DATA_DIR/${SAMPLE}_2.fastq.gz" 
       -S ./sams/UHR_Rep1.sam

I would get this output on the commandline:

(ERR): hisat2-align exited with value 1
./align_command.sh: line 16: --rg: command not found
./align_command.sh: line 17: --rg: command not found
./align_command.sh: line 18: --rg: command not found
./align_command.sh: line 20: -x: command not found

I thought this was pretty strange, and after mucking about I tried this, and it worked!

hisat2 
        -x ./$RNA_REF_INDEX 
        --dta 
        --rna-strandness RF 
        -1 $RNA_DATA_DIR/${SAMPLE}_1.fastq.gz 
        -2 $RNA_DATA_DIR/${SAMPLE}_2.fastq.gz 
        -S ./sams/UHR_Rep1.sam 
        --rg-id=UHR_Rep2 --rg SM:UHR

My question is does –rg actually eat up the “” character? Is that why I was getting the command not found error? If so, how can I ask it to not act like this?


bash


hisat2


script

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