Error Exceeded Limit of Size on Disk While Running vg index

[AishaAlsuwaidi]

Description: While attempting to run the vg index command to generate GCSA index files from multiple .vg files, the process terminated due to a size limit being exceeded. The error message and crash report are detailed below.

Command Executed:

vg index -g wg.gcsa -Z 200 $(for i in $(seq 22; echo X; echo Y); do echo chr${i}.pruned.vg; done)

Error Message:

error: [write_gcsa_kmers()] size limit of 3485932160 bytes exceeded                                                                                                                    terminate called after throwing an instance of 'vg::SizeLimitExceededException'                                                                                                          what():  error: exceeded limit of size on disk

Crash Report:

━━━━━━━━━━━━━━━━━━━━
Crash report for vg v1.56.0 "Collalto"
Stack trace (most recent call last):
#13   Object "/vg/bin/vg", at 0x5f470d, in _start
#12   Object "/vg/bin/vg", at 0x1f686ff, in __libc_start_main
#11   Object "/vg/bin/vg", at 0x5c44be, in main
#10   Object "/vg/bin/vg", at 0xd72beb, in vg::subcommand::Subcommand::operator()(int, char**) const
#9    Object "/vg/bin/vg", at 0xcad87a, in main_index(int, char**)
#8    Object "/vg/bin/vg", at 0x12f459c, in vg::VGset::write_gcsa_kmers_binary[abi:cxx11](int, unsigned long&, long long, long long)
#7    Object "/vg/bin/vg", at 0x12f3ac3, in vg::VGset::for_each(std::function<void (handlegraph::HandleGraph*)>)
#6    Object "/vg/bin/vg", at 0x5617bc, in vg::VGset::write_gcsa_kmers_binary[abi:cxx11](int, unsigned long&, long long, long long)::{lambda(handlegraph::HandleGraph*)#1}::operator()(handlegraph::HandleGraph*) const [clone .cold]
#5    Object "/vg/bin/vg", at 0x1ea4778, in __cxa_throw
#4    Object "/vg/bin/vg", at 0x1ea4616, in std::terminate()
#3    Object "/vg/bin/vg", at 0x1ea45ab, in __cxxabiv1::__terminate(void (*)())
#2    Object "/vg/bin/vg", at 0x5c104a, in __gnu_cxx::__verbose_terminate_handler() [clone .cold]
#1    Object "/vg/bin/vg", at 0x5c39e7, in abort
#0    Object "/vg/bin/vg", at 0x14dfd1b, in raise
ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug.
Please include this entire error log in your bug report!

### Environment:

VG Version: 1.56.0 "Collalto" Operating System: Ubuntu 20.04.6 LTS (Focal Fossa) Kernel Version: 6.5.0-27-generic Memory: Free: 216Gi

[adamnovak]

Some graph structures, especially those with many variants in quick succession, are impractical to index with GCSA indexing. If the default pruning settings of vg prune aren't enough to make your graph indexable on the computer you have, you can try passing a larger -k to vg prune to make it prune out more variation.