STAR_ALIGN error

Pipelines CLIP
1

Hi, I got an error in the STAR_ALIGN module for one of the samples. I did some research on the error and it seems like people tried to increase the limit size for the --limitOutSJcollapsed parameter, but still couldn’t make it work. Also, not sure why all of the other samples ran successfully, apart from this one. Would appreciate some help!

×
	STAR --genomeDir star --readFilesIn input1/KO_R1.unmapped.fastq.gz --runThreadN 12 --outFileNamePrefix KO_R1_multi. --sjdbGTFfile Mus_musculus_filtered.gtf --outSAMattrRGline ID:KO_R1_multi SM:KO_R1_multi --readFilesCommand zcat --outSAMtype BAM Unsorted --quantMode TranscriptomeSAM --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMattributes All --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 1000000 --outFilterScoreMin 10 --alignEndsType Extend5pOfRead1 --twopassMode Basic   
	STAR version: 2.7.9a   compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source   
Apr 25 02:48:08 ..... started STAR run   
Apr 25 02:48:08 ..... loading genome   
Apr 25 02:48:36 ..... processing annotations GTF   
Apr 25 02:48:42 ..... inserting junctions into the genome indices   
Apr 25 02:50:17 ..... started 1st pass mapping   
   
EXITING because of fatal error: buffer size for SJ output is too small   
Solution: increase input parameter --limitOutSJcollapsed   
   
Apr 25 03:06:56 ...... FATAL ERROR, exiting
2

Hi,

We’ve never come up against this before - reading up on this it can be caused by many things, including having lots of splice junctions in the output, perhaps your KO is causing lots of splicing errors! Just also FYI if your protein binds over splice junctions you might consider using the transcriptome mapped output.

In any case! To change the --limitOutSJcollapsed parameter in the clipseq pipeline you will need to go to “Command Line Options” and provide “STAR parameters”.

Here you should enter the default parameters we recommend for clip PLUS the --limitOutSJcollapsed param that you want to change, so that would look like:

“–outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMattributes All --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 1000000 --outFilterScoreMin 10 --alignEndsType Extend5pOfRead1 --twopassMode Basic --limitOutSJcollapsed 4000000”

Hope this helps,
Charlotte