[wgs-assembler-users] appending to a gkpStore?

[Langhorst, B. <Lan...@ne...>]

Hi:

I ran into a problem creating a gkpStore from 3 frg files (pointing to PE fastq files, each about 500M reads)
It failed due to a memory allocation error when i tried to import all 3 at once, so I thought I’d try to append to the store like this:
$gatekeeper -o $store -T -F $frg_path/run15.frg
$gatekeeper -a -o $store -T -F $frg_path/run16.frg
$gatekeeper -a -o $store -T -F $frg_path/run17.frg

The first one succeeds, but the append fails immediately.

Seems like the store is somehow marked read-only. I didn’t expect that since the first command succeeded.
Should appending to a store work?
Should I try an older gatekeeper? Will that cause trouble later if i try to use 8.3 for following steps?

Here’s the log:

Starting file '/mnt/galaxy/data/langhorst/deer_unitigs/run15.frg'.

Processing INNIE SANGER QV encoding reads from:
      '/mnt/ngswork/langhorst/deer_assembly/ovi_run15.1.fastq'
  and '/mnt/ngswork/langhorst/deer_assembly/ovi_run15.2.fastq'


GKP finished with 1 alerts or errors:
1	# LIB Alert: stddev too big for mean; reset stddev to 0.1 * mean.


Starting file '/mnt/galaxy/data/langhorst/deer_unitigs/run16.frg'.
gatekeeper: AS_PER_genericStore.C:425: int64 appendStringStore(StoreStruct*, char*, uint32): Assertion `s->readOnly == false' failed.

…

[0] /home/NEB/langhorst/wgs-8.3rc1/Linux-amd64/bin/gatekeeper::AS_UTL_catchCrash(int, siginfo*, void*) + 0x2a  [0x42587a]
[1] /lib/x86_64-linux-gnu/libpthread.so.0::(null) + 0x10340  [0x7ffb82749340]
[2] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x39  [0x7ffb823aacc9]
[3] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x148  [0x7ffb823ae0d8]
[4] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x2fb86  [0x7ffb823a3b86]
[5] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0x2fc32  [0x7ffb823a3c32]
[6] /home/NEB/langhorst/wgs-8.3rc1/Linux-amd64/bin/gatekeeper() [0x43129d]
[7] /home/NEB/langhorst/wgs-8.3rc1/Linux-amd64/bin/gatekeeper::gkStore::gkStore_addUID(char*) + 0x13f  [0x436d6f]
[8] /home/NEB/langhorst/wgs-8.3rc1/Linux-amd64/bin/gatekeeper::AS_UID_load(char*) + 0x196  [0x4254b6]
[9] /home/NEB/langhorst/wgs-8.3rc1/Linux-amd64/bin/gatekeeper::GetUID(char*, _IO_FILE*) + 0x11  [0x4264d1]
[10] /home/NEB/langhorst/wgs-8.3rc1/Linux-amd64/bin/gatekeeper() [0x42f902]
[11] /home/NEB/langhorst/wgs-8.3rc1/Linux-amd64/bin/gatekeeper::ReadProtoMesg_AS(_IO_FILE*, GenericMesg**) + 0x4aa  [0x42719a]
[12] /home/NEB/langhorst/wgs-8.3rc1/Linux-amd64/bin/gatekeeper::(null) + 0x5c1  [0x4087b1]
[13] /lib/x86_64-linux-gnu/libc.so.6::(null) + 0xf5  [0x7ffb82395ec5]
[14] /home/NEB/langhorst/wgs-8.3rc1/Linux-amd64/bin/gatekeeper::(null) + 0xf1  [0x406949]