gravatar for mobasherbarsi

2 hours ago by

Hi,
I wonder if I can get help fix my loop for alignment with star

# Create a list of each directory:
DIRS=$(lfs find /crex/proj/uppstore2019072/ESCG_data/plates/SS2_17_531/rawdata/ -name "*.fastq")

#DIRS=($(lfs find /crex/proj/uppstore2019072/ESCG_data/plates/SS2_17_531/rawdata/A1/A1_R1.fastq))         #for testing
echo $DIRS

# for testing: DIRS=(At Bi Ce)
# Fetch one directory from the array based on the task ID (index starts from 0)
CURRENT_FILE=${DIRS[$SLURM_ARRAY_TASK_ID]}

echo "Doing file $CURRENT_FILE"


STAR --genomeDir /crex/proj/uppstore2019072/ESCG_data/dro-genome/dmel-genome 
--runThreadN 2 
--readFilesIn  $CURRENT_FILE 
--outSAMtype BAM SortedByCoordinate 
--outSAMunmapped Within 
--outSAMattributes Standard 
--outFileNamePrefix $CURRENT_FILE

 ERROR : line 37:  5097 Segmentation fault      (core dumped)



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