STAR alignment loop segmentation fualt (core dumped)

Question

[mobasherbarsi]

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)

[mobasherbarsi]

thanks it was memory issue.

Answer 1

[GenoMax]

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

[mobasherbarsi]

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

[curious]

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