Hi,

I also execute STAR in a loop and use two differnt ways to get the file names. Either I submit the file names (with the respective paths) to STAR by a document which holds a filename per line:

# For every name in the file
while read SAMPLE; do

# Get single file name
FILEBASE=$(basename "${SAMPLE%.fq.rm_bl}")

# Make new directory for every sample
mkdir /path_to_later/gap_table/$FILEBASE.STAR

# Enter the new directory
cd /path_to_later/gap_table/$FILEBASE.STAR

# Align with STAR 
/path_to_STAR/STAR --outFilterType BySJout --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.04 --alignEndsType EndToEnd --runThreadN 8 --outSAMtype BAM SortedByCoordinate --alignSJDBoverhangMin 4 --alignIntronMax 300000 --alignSJoverhangMin 8 --alignIntronMin 20 --genomeDir /path_to/star_index_hg38_hiv_r100/ --sjdbOverhang 100 --quantMode GeneCounts --sjdbGTFfile/path_to/hg38_pnL43_fusion_annotation.gtf --outFileNamePrefix /path_to/gap_table/$FILEBASE.STAR/ --readFilesIn $SAMPLE > STARaligning.log 

done </path_to_filename_file/filename

Another way would be to search within a directory for certain filenames, to use them subsequently in STAR as input:

Here the first row of the code above is replaced with this 2 lines:

# For every file in the given directory (/path_to_file/), use the filenames showing a ".fq" at the end
find /path_to_files/ -name "*.fq" | while read SAMPLE

# Get single file name
FILEBASE=$(basename "${SAMPLE%.fq}")

I suppose, the extra space between individual2 individual3 is not in the real code? Otherwise, I don't know the reason for the error during your particular kind of loop.