std::bad_alloc for subtomo averaging

[DrJesseHansen]

hi,

I am using RELION for subtomo averaging after exporting the extracted subvolumes from WARP. My box is 200 pix at 4.2A/pix. I have 4000 particles. This doesnt seem excessive. I have a subtomo star file and the subtomos subfolder with the subvolumes.

I have checked the data by doing a relion_reconstruct with --3d_rot and it worked well.

However when I try to do either 3D refine or 3D classification then I get the error below "std::bad_alloc. My command is below. I have tried different GPUs or CPUs on our cluster, interactively or through SLURM. It hardly processes anything it just goes straight to this error immediately.

Note that I am running RELION/3.0.8 since we have the old WARP which can not export optics table to my understanding.

I am used to doing SPA with RELION, I don't often use it for subtomo averaging. Is there something else I should be doing that I am unaware of?

thank you

---

relion_refine_mpi --o Refine3D/job001/run --auto_refine --split_random_halves --i subtomos.star --ref output.mrc --firstiter_cc --ini_high 60 --dont_combine_weights_via_disc --pool 3 --pad 2 --ctf --particle_diameter 200 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 10 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale --j 1

Running CPU instructions in double precision. terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted

[DrJesseHansen]

i think I sorted it out. it was the relion_Reconstruct output volume which was causing the error... evem though the volume looked fine. I re-saved in chimera and now it works. weird.