the problem in vg surject

[xuxingyubio]

I'm very sorry to bother you again.

My command goes like this: vg surject -x "$GRAPH" -t "$NUMCPU" -m -b -S -A -F "$REF_PATHS" "$GAMP" > "$BAM" I try to use 'vg surject' to project down to linear reference.

I don't know if the following error is due to the command requiring a large amount of memory space, or if there are some issues with my input file, or some other issue. How can I solve this problem?

The error is as follows: ... warning[vg::Watchdog]: Thread 7 has been checked in for 10 seconds processing: SRR1153470.16621002 warning[vg::Watchdog]: Thread 1 finally checked out after 26 seconds and 38447248 kb memory growth processing: SRR1153470.16349503 [BAMatrix::fill_matrix]: failed to allocate matrices of height 14978670 and width 32 for a total cell count of 479317440 [BAMatrix::fill_matrix]: is alignment problem too big for your virtual or physical memory? warning[vg::Watchdog]: Thread 7 finally checked out after 16 seconds and 46538040 kb memory growth processing: SRR1153470.16621002 Unhandled exception: std::bad_alloc Exception context: SRR1153470.16376079 ━━━━━━━━━━━━━━━━━━━━ Crash report for vg v1.48.0 "Gallipoli" Stack trace (most recent call last) in thread 2315526: #11 Object "", at 0xffffffffffffffff, in #10 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0x1f8f7f2, in __clone #9 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0x1492898, in start_thread #8 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0x1ec3ffd, in gomp_thread_start #7 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0xca1d43, in void vg::io::for_each_parallel_implvg::MultipathAlignment(std::istream&, std::function<void (vg::MultipathAlignment&, vg::MultipathAlignment&)> const&, std::function<void (vg::MultipathAlignment&)> const&, std::function<bool ()> const&, unsigned long) [clone ._omp_fn.0] #6 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0x1ec68d7, in gomp_team_barrier_wait_end #5 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0x1ebdf9b, in gomp_barrier_handle_tasks #4 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0xca16c1, in void vg::io::for_each_parallel_implvg::MultipathAlignment(std::istream&, std::function<void (vg::MultipathAlignment&, vg::MultipathAlignment&)> const&, std::function<void (vg::MultipathAlignment&)> const&, std::function<bool ()> const&, unsigned long) [clone ._omp_fn.1] #3 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0x506970, in main_surject(int, char**)::{lambda(std::istream&)#9}::operator()(std::istream&) const::{lambda(vg::MultipathAlignment&)#2}::operator()(vg::MultipathAlignment) const [clone .cold] #2 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0x5618ac, in vg::report_exception(std::exception const&) [clone .cold] #1 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0x5c0007, in abort #0 Object "/home/users/xyxu/pantools/cactus-bin-v2.5.2/bin/vg", at 0x149611b, 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!