Question: STAR alignment killed
0
gravatar for junsionglow
10 weeks ago by
junsionglow20
junsionglow20 wrote:

Hi, I am trying to run STAR alignment using the command below:

STAR --runThreadN 10 --runMode genomeGenerate --genomeDir /home/user/scratch60/beargenomes –genomeFastaFile /home/user/scratch60/hg38.fa --readFilesIn /home/user/scratch60/SRR7059137.fastq --sjdbGTFfile /home/user/scratch60/gencode.v28.annotation.gtf  --sjdbOverhang 99 --outFileNamePrefix /home/user/scratch60/SRR7059137 --outSAMtype BAM

and this came up

Aug 09 11:40:01 ..... started STAR run
Aug 09 11:40:01 ... starting to generate Genome files
Killed

I would like to understand why... if anyone can shed some light to this that'd be much appreciated. Thanks!

rna-seq alignment • 269 views
ADD COMMENTlink written 10 weeks ago by junsionglow20
0
gravatar for genomax
10 weeks ago by
genomax57k
United States
genomax57k wrote:

How much memory is being assigned? STAR requires 30+G of RAM for human genome generation/alignments.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by genomax57k

And maybe that --runThreadN=10 is multiplying the requirements. Try 1 thread, and monitor memory usage, then try two threads and monitor memory usage.

ADD REPLYlink written 10 weeks ago by karl.stamm3.3k

I tried 1 thread but it still didnt work :(

ADD REPLYlink written 10 weeks ago by junsionglow20

I'm running on a cluster on interactive bash... how can i determine the memory?

i ran /usr/bin/time in front of the STAR command. 11.76user 4.19system 0:16.34elapsed 97%CPU (0avgtext+0avgdata 5243688maxresident)

does this help?

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by junsionglow20

Can you run top and show us the 4-5 lines at top of the window?

ADD REPLYlink written 10 weeks ago by genomax57k

I cant copy it, so here's an image of the top 4-5lines at the top of the window! https://s22.postimg.cc/mxqg8764x/top.png

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by junsionglow20

Find the log file generated from the run and see why it got killed. Alternatively, upload it somwhere (like pastebin) for us to see.

ADD REPLYlink written 10 weeks ago by Marks40

Hi Marks,

I've uploaded the log.out file onto pastebin like your suggested

https://pastebin.com/WUhxYpix

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by junsionglow20

nothing there unfortunately, can you paste Log.progress.out and Log.final.out just to make sure

ADD REPLYlink written 10 weeks ago by Marks40

Do you know how much ram the cluster has available? This is probably an issue with STAR reaching the RAM limit. You could try changing genomeChrBinNbits to 12 to limit the ram usage.

ADD REPLYlink written 10 weeks ago by Marks40

Thanks Marks. there isnt a log.progress.out or log.final.out associated with that run. But i did try the genomeChrBinNbits and the run was aborted with the follow:

Aug 10 07:16:06 ..... started STAR run
Aug 10 07:16:06 ... starting to generate Genome files
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted
ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by junsionglow20

junsionglow : I would like to see something right at top that shows the amount of memory available on your node.

%Cpu(s):  0.5 us,  0.4 sy,  0.0 ni, 99.1 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem : 32781404 total,   483144 free, 17888072 used, 14410188 buff/cache
KiB Swap:  2097148 total,  2080764 free,    16384 used. 14402508 avail Mem
ADD REPLYlink written 9 weeks ago by genomax57k

ah, this is it.

Tasks: 699 total,   1 running, 696 sleeping,   2 stopped,   0 zombie
%Cpu(s):  0.0 us,  0.4 sy,  0.3 ni, 99.2 id,  0.0 wa,  0.0 hi,  0.0 si,  0.0 st
KiB Mem : 13131726+total,   352784 free,  6140812 used, 12482367+buff/cache
KiB Swap: 16777212 total, 16484712 free,   292500 used. 12422304+avail Mem
ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by junsionglow20
1

If I am reading it right, it looks like you only have 16GB of RAM on this machine. That is not going to be enough to run STAR.

ADD REPLYlink written 9 weeks ago by genomax57k

How much is recommended for STAR?

ADD REPLYlink written 9 weeks ago by Marks40
1

A minimum of 30G free for human genome.

ADD REPLYlink written 9 weeks ago by genomax57k
1

Thanks genomax and Marks. I will see what work around and get back to you guys.

ADD REPLYlink written 9 weeks ago by junsionglow20
1

Dear Marks and Genomax,

Finally gotten it to work. There was 2 part problem, one was my indexing, the other was memory (I believe). So when I submitted a Slurm job requesting for memory, that worked! Thanks guys!

ADD REPLYlink written 9 weeks ago by junsionglow20

Nice, glad we could help. Good luck and have fun

ADD REPLYlink written 9 weeks ago by Marks40
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