STAR alignment error: quantmod not found

Question

[prabin.dm]

Hi all,

I am using STAR for aligment and gettting an error. I can't figure out why?

star 2.5.3a is located under /share/pkg/star/2.5.3a
/home/.lsbatch/1544131842.9569914.shell: line 22: --quantMode: command not found

Here is my code

module load star/2.5.3a

STAR -- genomeDir star_genome_mm10 \
        --readFilesCommand zcat \
        --readFilesIn L001_R1_001.fastq.gz \
        --outSAMtype BAM SortedByCoordinate \
        --outSAMunmapped Within \
        --twopassMode Basic \
        --outFilterMultimapNmax 1 \ 
        --quantMode TranscriptomeSAM GeneCounts \
        --runThreadN 6 \
        --outFileNamePrefix /STAR_output/test

Another issue I am having is, the output files are not stored in the STAR_ouput directory. It is stored in the directory where the code is executed ?

[Ram]

Maybe change this

--outFileNamePrefix /STAR_output/test

to

--outFileNamePrefix $PWD/STAR_output/test

unless there's actually a dir named STAR_output with proper permissions in the root directory?

Answer 1

[Devon Ryan]

-- genomeDir has a space in it.

[prabin.dm]

correcting that resulted in the same output. Should I have the rsem-prepare-reference run before I use --quantMode TranscriptomeSAM ?

[Devon Ryan]

Your command has a random space or a missing \ somewhere that you're not showing us. Write it all on one line without any \.