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STAR alignment loop segmentation fualt (core dumped)

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)
star

1 answer

How much memory do you have? Seg faults may indicate that the program is running out of memory.

I’m requesting 19 cores, submitting a job into the server. But still getting same error If am not mistaken I think —readFilesIn $CURRENT_FILE should be supported by tab separated according to STAR documentation but not sure how to add this to the command line

you could try requesting more memory than you would get by default w/ 19 cores though

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