Killed: 9 while mapping

Gehoon Chung

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Aug 21, 2015, 11:41:03 PM8/21/15

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Hi Dr. Dobin,

My STAR process gets killed with error 9 while mapping paired reads to mm10 genome. I ran it on iMac with 32 GB RAM on single core (although it has 8 cores). I scanned through the previous threads here but none seemed to be applicable. Could you please look into the log and help me out? The exact parameters with the same read files were successful on linux machine with 512 GB RAM. I'd much like to see it works on my iMac since I've added 16 GB to make 32 GB solely for STAR aligner today.

Details are in the Log.out file attached.

ulimit -v was set to unlimited.

Thanks in advance!

Gehoon

Log.out

Alexander Dobin

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Aug 24, 2015, 5:49:27 PM8/24/15

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Hi Gehoon,

according to Log.out, there was a problem with SA genome file.

Did you generate the genome with the latest version of STAR? If not, please re-generate and try to map again.

Cheers

Alex

Gehoon Chung

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Sep 11, 2015, 9:55:36 AM9/11/15

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Hi Alex,

I've created new SA genome file but mapping is still terminated with error 9. I tried with and without --limitIObufferSize 50000000 flag for precaution but it didn't help.

I am running it on iMac i7 with 32 GB RAM and only 1 core was used for STAR

Could you take a look at my Log.out file please?

Thanks in advance!

Log.out

Alexander Dobin

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Sep 15, 2015, 12:44:07 PM9/15/15

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Hi Gehoon,

Log.out file looks OK, the genome files sizes are reasonable and should fit in the 32GB

What is the output of the following Linux commands:

$ free

$ ipcs

$ ulimit -a

Cheers

Alex

Gehoon Chung

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Sep 15, 2015, 10:46:21 PM9/15/15

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Hi Alex,

Thanks for reply.

I ran vm_stat instead because my OSX version doesn't have 'free.'

The results are below

#### vm_stat #####

Mach Virtual Memory Statistics: (page size of 4096 bytes)

Pages free: 6671093. ## equivalent to 26,058 MB

Pages active: 1059660.

Pages inactive: 53228.

Pages speculative: 89881.

Pages throttled: 0.

Pages wired down: 510194.

Pages purgeable: 2772.

"Translation faults": 44909428.

Pages copy-on-write: 920353.

Pages zero filled: 26265355.

Pages reactivated: 31259.

Pages purged: 42261.

File-backed pages: 189020.

Anonymous pages: 1013749.

Pages stored in compressor: 7553.

Pages occupied by compressor: 2099.

Decompressions: 5791.

Compressions: 5881441.

Pageins: 8679526.

Pageouts: 68.

Swapins: 1363.

Swapouts: 190528.

#### ipcs ####

IPC status from <running system> as of Tue Sep 15 22:35:55 EDT 2015

T ID KEY MODE OWNER GROUP

Message Queues:

T ID KEY MODE OWNER GROUP

Shared Memory:

m 65536 0x0108779a --rw------- root wheel

m 65537 0x0108779d --rw------- root wheel

m 65538 0x0108779e --rw------- root wheel

m 65539 0x010877a0 --rw------- root wheel

m 65540 0x00000000 --rw------- _devicemgr _devicemgr

m 655365 0x00000000 --rw------- _teamsserver _teamsserver

T ID KEY MODE OWNER GROUP

Semaphores:

s 65536 0x0052e2c1 --ra------- _devicemgr _devicemgr

s 65537 0x0052e2c2 --ra------- _devicemgr _devicemgr

s 65538 0x0052e2c3 --ra------- _devicemgr _devicemgr

s 65539 0x0052e2c4 --ra------- _devicemgr _devicemgr

s 65540 0x0052e2c5 --ra------- _devicemgr _devicemgr

s 65541 0x0052e2c6 --ra------- _devicemgr _devicemgr

s 65542 0x0052e2c7 --ra------- _devicemgr _devicemgr

s 65543 0x0052e2c8 --ra------- _devicemgr _devicemgr

s 65544 0x0052e2c9 --ra------- _devicemgr _devicemgr

s 65545 0x0052e2ca --ra------- _devicemgr _devicemgr

s 65546 0x0052e2cb --ra------- _devicemgr _devicemgr

s 65547 0x0052e2cc --ra------- _devicemgr _devicemgr

s 65548 0x0052e2cd --ra------- _devicemgr _devicemgr

s 655373 0x0052e2ce --ra------- _teamsserver _teamsserver

s 655374 0x0052e2cf --ra------- _teamsserver _teamsserver

s 655375 0x0052e2d0 --ra------- _teamsserver _teamsserver

s 655376 0x0052e2d1 --ra------- _teamsserver _teamsserver

s 655377 0x0052e2d2 --ra------- _teamsserver _teamsserver

s 655378 0x0052e2d3 --ra------- _teamsserver _teamsserver

s 655379 0x0052e2d4 --ra------- _teamsserver _teamsserver

s 655380 0x0052e2d5 --ra------- _teamsserver _teamsserver

s 655381 0x0052e2d6 --ra------- _teamsserver _teamsserver

s 655382 0x0052e2d7 --ra------- _teamsserver _teamsserver

s 655383 0x0052e2d8 --ra------- _teamsserver _teamsserver

s 655384 0x0052e2d9 --ra------- _teamsserver _teamsserver

s 655385 0x0052e2da --ra------- _teamsserver _teamsserver

s 655386 0x0052e2db --ra------- _teamsserver _teamsserver

s 655387 0x0052e2dc --ra------- _teamsserver _teamsserver

s 655388 0x0052e2dd --ra------- _teamsserver _teamsserver

s 655389 0x0052e2de --ra------- _teamsserver _teamsserver

s 655390 0x0052e2df --ra------- _teamsserver _teamsserver

s 655391 0x0052e2e0 --ra------- _teamsserver _teamsserver

s 655392 0x0052e2e1 --ra------- _teamsserver _teamsserver

s 655393 0x0052e2e2 --ra------- _teamsserver _teamsserver

s 655394 0x0052e2e3 --ra------- _teamsserver _teamsserver

s 655395 0x0052e2e4 --ra------- _teamsserver _teamsserver

s 655396 0x0052e2e5 --ra------- _teamsserver _teamsserver

s 655397 0x0052e2e6 --ra------- _teamsserver _teamsserver

s 655398 0x0052e2e7 --ra------- _teamsserver _teamsserver

s 655399 0x0052e2e8 --ra------- _teamsserver _teamsserver

s 655400 0x0052e2e9 --ra------- _teamsserver _teamsserver

s 655401 0x0052e2ea --ra------- _teamsserver _teamsserver

s 655402 0x0052e2eb --ra------- _teamsserver _teamsserver

s 655403 0x0052e2ec --ra------- _teamsserver _teamsserver

s 655404 0x0052e2ed --ra------- _teamsserver _teamsserver

s 65589 0x0b089bff --ra-ra-ra- gehoon staff

##### ulimit -a #######

core file size (blocks, -c) 0

data seg size (kbytes, -d) unlimited

file size (blocks, -f) unlimited

max locked memory (kbytes, -l) unlimited

max memory size (kbytes, -m) unlimited

open files (-n) 256

pipe size (512 bytes, -p) 1

stack size (kbytes, -s) 8192

cpu time (seconds, -t) unlimited

max user processes (-u) 709

virtual memory (kbytes, -v) unlimited

I ran STAR after a fresh reboot and killing all other applications including the cloud drive demons.

One thing I noticed is that the time required to be killed with Error 9 varies between trials. Does this mean something?

Cheers,

Gehoon

Alexander Dobin

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Sep 16, 2015, 11:59:37 PM9/16/15

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Hi Gehoon,

it looks like you have ~4GB of RAM occupied by some other processes (Pages active), could you check with top what those are?

26GB will not be enough to run STAR on this genome. If you cannot free up more RAM, one solution would be to use -genomeSAsparseD 2 at the genome generation step.