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Old 05-20-2014, 03:01 AM   #1
Location: Urbana Illinois

Join Date: Jan 2013
Posts: 28
Default STAR aligner issue

I am trying to align some paired end RNAseq data using STAR (version 2.3.0e), but I'm having an issue with the alignment. My code is:

$HOME/bin/STAR_2.3.0e/STAR --genomeDir /srv/mds01/shared/Epigenetics/Rnaseq/transcripts/STAR --readFilesIn Colon_R1_S6_L20_final.fq.gz.val_paired_1.fq.gz Colon_R2_S6_L20_final.fq.gz.val_paired_2.fq.gz --readFilesCommand zcat --runThreadN 4 --genomeLoad NoSharedMemory --outFileNamePrefix ../STAR/colon.paired --outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0

I receive the following output in the command line:

May 20 11:01:39 ..... Started STAR run
May 20 11:02:23 ..... Started mapping

The run only lasts about 5 minutes. When I check the end of the pairedLog.out file, I see the following message:

alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
EXITING because of a BUG: nTr=0 in outputAlignments.cpp

Does anyone have any experience with this sort of issue? Thanks.
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Old 05-20-2014, 03:40 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,077

Alex Dobin (author of STAR) participates on this forum but you may want to send him a PM (SeqAnswers user name: alexdobin) alerting him about this thread.
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Old 05-20-2014, 12:47 PM   #3
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Location: NY

Join Date: Feb 2009
Posts: 161

Hi @shocker8786,

please try the latest STAR patch:

If it does not work, please try running it without
"--outFilterScoreMin 0 --outFilterScoreMinOverLread 0 --outFilterMatchNmin 0 --outFilterMatchNminOverLread 0".

If it still does not work, please send me the Log.out file.

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Old 05-21-2014, 01:59 AM   #4
Location: Urbana Illinois

Join Date: Jan 2013
Posts: 28

I downloaded the patch and everything seems to be running properly now. Thank you very much!
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