Entering edit mode
15 months ago
mobasherbarsi
•
0
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)
thanks it was memory issue.