core dumped

[ikalatskaya]

core dumped

[ZhiliChang]

Which ulimit parameter should I set? max user processes or open files?

# ulimit -n 65536
# ulimit -u 65536
# ulimit -a

core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 1029400
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 65536
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 65536
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited

None of these operations solve the problem

Which ulimit parameter should I set? max user processes or open files?

# ulimit -n 65536
# ulimit -u 65536
# ulimit -a

core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 1029400
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 65536
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 65536
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited
None of these operations solve the problem

Hi Shuling,

Did you get the problem solved? I encountered exactly the same problem and changing the ulimit did not seem to work...

Try "ulimit -s 65536"

[qtrinh]

can you set your ulimit to 65536 and try again ?
Thanks

[youshuling]

Which ulimit parameter should I set? max user processes or open files?

# ulimit -n 65536
# ulimit -u 65536
# ulimit -a

core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 1029400
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 65536
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 65536
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited

None of these operations solve the problem

[ZhiliChang]

i got the same error(Segmentation fault (core dumped)), how to fix this ?

run on RHEL 7.2 system, glibc version 2.17.
this is my ulimit settings:

core file size (blocks, -c) 1048576
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 4127001
max locked memory (kbytes, -l) unlimited
max memory size (kbytes, -m) unlimited
open files (-n) 1048576
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 4096
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited

[LuoPangpang]

Which ulimit parameter should I set? max user processes or open files?

# ulimit -n 65536
# ulimit -u 65536
# ulimit -a

core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 1029400
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 65536
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 8192
cpu time (seconds, -t) unlimited
max user processes (-u) 65536
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited

None of these operations solve the problem

Hi Shuling,

Did you get the problem solved? I encountered exactly the same problem and changing the ulimit did not seem to work...

[amit21AIT]

Did anyone successfully ran ISOWN ? Can anyone provide the Polyphen and dbsnp indexed databases link?

[sergeyvilov]

I had this error while annotating with dbSNP because the chromosome names didn't match (e.g. 'chr1' in the dbSNP file and just '1' in the input vcf). So, the chromosome notation should be the same in the input vcf files and all databases.