Question: Segmentation fault STAR Mapping
0
gravatar for ahmedebit
3.2 years ago by
ahmedebit0
ahmedebit0 wrote:

Hi all,

I have generated the genome using STAR and it works fine. Now I try to map PE reads (size 100000 reads for each file) to the generated genome using the following command:

srun STAR --genomeDir $hg_ref_path --outFileNamePrefix $output_prefix \
--seedSearchStartLmax 30 --outFilterMultimapNmax 10 --outFilterMismatchNmax 12      --alignMatesGapMax 1000 --outSAMattrIHstart 0 \
--outSAMmapqUnique 255 --outFilterIntronMotifs RemoveNoncanonical --outFilterScoreMinOverLread 0.4    --outFilterMatchNminOverLread 0.4 \
--chimSegmentMin 20 --outSAMtype BAM Unsorted --runThreadN 4 --readFilesIn $file_R1 $file_R2

but I still get the segmentation fault error:

May 09 00:20:27 ..... Started STAR run

May 09 00:20:27 ..... Loading genome

May 09 00:21:37 ..... Started mapping

srun: error: compute-1-14: task 0: Segmentation fault

I tried also to include the GTF annotation file with the --sjdbGTFfile option but the same error was occured:

May 09 01:04:01 ..... Started STAR run

May 09 01:04:01 ..... Loading genome

May 09 01:05:10 ..... Processing annotations GTF

srun: error: compute-1-14: task 0: Segmentation fault

Any suggestions about these errors ?

ADD COMMENTlink written 3.2 years ago by ahmedebit0

How much RAM do you have and/or you are allocating to this job? STAR requires a significant amount of memory (~30+G for human sized genomes).

ADD REPLYlink written 3.2 years ago by genomax69k

I allocated 45G of RAM to this job

ADD REPLYlink written 3.2 years ago by ahmedebit0
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