mothur

sub.sample - segmentation fault


#1

Hello,

I recently ran:
sub.sample(shared=BA_undil_data_silva128.0.01.shared, size=60000)

and received the following just before mothur unexpectedly quit:

Segmentation fault (core dumped)

TIA for the help!


#2

Update: I tried running the sub.sample script with the older version of mothur, 1.38.1, and it worked. The segmentation fault only happened with 1.39.5.


#3

If you fire it back up again and re-run the command does it work or does it gag again?


#4

I apologize for the long time in between replies. I reran sub.sample with a test dataset and everything went fine, but when I tried to run it with my full dataset I got the following:

mothur:37536 terminated with signal 11 at PC=134ea17 SP=7ffc194d86a0. Backtrace:
mothur[0x134ea17]
mothur[0x13acd80]
mothur[0x564d1a]
mothur[0x11c819e]
mothur[0x11c6b13]
mothur[0x11ad1e7]
mothur[0x458183]
mothur[0x4ab87d]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x7f3b669ecd1d]
mothur[0x40d369]


#5

Thanks, I’m pretty sure this is a known bug that we’re working through to fix for the next release hopefully in the next few weeks.

Pat