Aborted (core dumped) error message from STAR

[Jack Yen]

Hi,

I have been struggled to figure this out. I have an error message when I try to run STAR aligner "Aborted (core dumped)" . I saw in another post it could be due to the chr header is different from fasta file and gtf file. However I checked mine, both file I have chr1, chr2 etc. Could someone point me to the right direction how to resolve this? My STAR_AlignLog.out looks fine and I can't tell what's the reason to cause it to error out. 

Thanks,

Here's my full command 

STAR --runThreadN 8 \

     --genomeDir /media/fs02/reference/hg19/starindex \

     --readFilesIn <(zcat G11M15_S10_R1_001.fastq.gz) <(zcat G11M15_S10_R2_001.fastq.gz) \

     --limitBAMsortRAM 12000000000 \

     --outFileNamePrefix /home/lee/workspace/STAR_aligner_validation/STAR_Align \

     --genomeLoad LoadAndKeep \

     --outSAMtype BAM   SortedByCoordinate \

     --outSAMattributes NH   NM   MD \

--outSAMunmapped Within \

--outSAMmapqUnique 50 \

--outSAMattrRGline ID:1   SM:CS399882 \

--outSJfilterCountUniqueMin -1   2   2   2 \  

--outSJfilterCountTotalMin -1   2   2   2 \

--outFilterType BySJout \

--outFilterIntronMotifs RemoveNoncanonical \

--sjdbGTFfile /media/fs02/reference/hg19/annotation/genes.gtf \

--twopassMode BasicSTAR --runThreadN 8 \

     --genomeDir /media/fs02/reference/hg19/starindex \

     --readFilesIn <(zcat G11M15_S10_R1_001.fastq.gz) <(zcat G11M15_S10_R2_001.fastq.gz) \

     --limitBAMsortRAM 12000000000 \

     --outFileNamePrefix /home/lee/workspace/STAR_aligner_validation/STAR_Align \

     --genomeLoad LoadAndKeep \

     --outSAMtype BAM   SortedByCoordinate \

     --outSAMattributes NH   NM   MD \

--outSAMunmapped Within \

--outSAMmapqUnique 50 \

--outSAMattrRGline ID:1   SM:CS399882 \

--outSJfilterCountUniqueMin -1   2   2   2 \  

--outSJfilterCountTotalMin -1   2   2   2 \

--outFilterType BySJout \

--outFilterIntronMotifs RemoveNoncanonical \

--sjdbGTFfile /media/fs02/reference/hg19/annotation/genes.gtf \

--twopassMode Basic

output error message

7fd05c6a3000-7fd05c6a4000 r--p 00025000 08:01 74331735                   /lib/x86_64-linux-gnu/ld-2.23.so

7fd05c6a4000-7fd05c6a5000 rw-p 00026000 08:01 74331735                   /lib/x86_64-linux-gnu/ld-2.23.so

7fd05c6a5000-7fd05c6a6000 rw-p 00000000 00:00 0

7ffd09e8a000-7ffd09ebd000 rw-p 00000000 00:00 0                          [stack]

7ffd09efe000-7ffd09f00000 r--p 00000000 00:00 0                          [vvar]

7ffd09f00000-7ffd09f02000 r-xp 00000000 00:00 0                          [vdso]

ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]

Aborted (core dumped)

[Alexander Dobin]

Hi Jack,

please try to run mapping with all the default parameters, except --runThreadN --genomeDir  --readFilesIn, and it if it still fails, send me the Log.out file again.

One other thing to try is to use pre-compiled executables from STAR distribution, both static and dynamic.

Cheers

Alex