Question: Annoying STAR aligner problem
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gravatar for Biogeek
15 months ago by
Biogeek240
Biogeek240 wrote:

Can anyone help?

My commands for star alignment:

./STAR --genomeDir genomedir --readFilesIn all_left_fwd_reads.fastq all_right_rev_reads.fastq --alignIntronMax 25000 --outSAMtype BAM SortedByCoordinate --runThreadN 60 --outBAMsortingThreadN 6 --outFileNamePrefix ALIGNEDREADS_

I keep getting a FATAL ERROR. I am running 250GB with 60 threads. 6 threads for BAM sorting, as i read sorting doesn't work above 6 threads.

Max memory needed for sorting = 9781928623 EXITING because of fatal ERROR: not enough memory for BAM sorting: \ SOLUTION: re-run STAR with at least --limitBAMsortRAM 10781928623 Aug 14 23:18:21 ...... FATAL ERROR, exiting

I've been through this process a few times now. Can anyone provide me with settings that won't make the program crash consistently or point to what's going wrong? My concatenated forward and reverse reads are pretty large files, but it only seems to be when I ask for a bam COORDINATED SORTED FILE.

Any help appreciated.

star aligner • 892 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by Biogeek240

I'm now proceeding with unsorted BAM output, then using SAM tools. Probably quicker anyway?

ADD REPLYlink written 15 months ago by Biogeek240
3

I'm guessing that STAR holds everything in memory, as opposed to samtools, which writes temp files. STAR will be faster, but man would it blow up memory requirements.

ADD REPLYlink written 15 months ago by Devon Ryan73k

Thanks for the insight! Seems to be running sweet now.

ADD REPLYlink written 15 months ago by Biogeek240
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