Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. lmbwide.login complete /public/xtal/CCP4/ccp4-64/Prerelease ccp4_base /public/xtal lmbbase +------------------------------------------------ LMB crystallography software CCP4 release 7.1 installed 23/04/2020 (DB) Type "ccp4i2" to get the new improved interface for new projects NOW IMPROVED WITH ACCESS TO ccp4i1 projects **** If you really want to use the older (7.0) version, edit your .login to "source /public/xtal/ccp4/xtal-7.0.login" and login again ------------------------------------------------------------------------------ phenix release 1.18 (3874) 20 5 20 (JL) "phenix &" for GUI ------------------------------------------------------------------------------ sharp server is on hal:8081, Sharp version 2.9.0 7/2/20 (DB) ------------------------------------------------------------------------------ XDS 4/2020 (DB), generate_XDS.INP / eiger_XDS.INP 5/2019 (JL) ------------------------------------------------------------------------------ MAIN 2019 JL 3/2019 ------------------------------------------------------------------------------ iMosflm will now read "master" hdf5 files, including the Eiger2 detector at DLS AGWL 5/2019 ------------------------------------------------------------------------------ Buster and autoPROC update 19/3/20 (DB) ------------------------------------------------------------------------------ MoRDa database updated to version 31 13/04/2020 (DB/JL) ------------------------------------------------------------------------------ ************************************************** MRC image processing programs have moved. You are using image2010 by default. If you wish to use the frozen image2000 you need to : source /public/EM/image2000/com/image.login and source /public/EM/image2000/com/image.cshrc Jude Short (F46 x2039 jms@mrc-lmb.cam.ac.uk) 09.03.2011 ************************************************** Path to mpiexec: /public/EM/OpenMPI/openmpi-2.0.1/build/bin/mpiexec Path to relion_refine_mpi: /lmb/home/tnakane/prog/relion-devel-lmb/build-test/bin/relion_refine_mpi Libraries for relion_refine_mpi: linux-vdso.so.1 => (0x00007ffd8f2a8000) libcufft.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcufft.so.9.0 (0x00002b5ce2ec8000) libmpi.so.20 => /public/EM/OpenMPI/openmpi-2.0.1/build/lib/libmpi.so.20 (0x00002b5ceaf69000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b5ceb248000) libtiff.so.5 => /lib64/libtiff.so.5 (0x00002b5ceb44c000) libfftw3.so.3 => /lmb/home/tnakane/prog/relion-devel-lmb/external/fftw/lib/libfftw3.so.3 (0x00002b5ceb6c0000) libfftw3f.so.3 => /lmb/home/tnakane/prog/relion-devel-lmb/external/fftw/lib/libfftw3f.so.3 (0x00002b5ceba3f000) libcurand.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcurand.so.9.0 (0x00002b5cebe4a000) libpng15.so.15 => /lib64/libpng15.so.15 (0x00002b5cefdae000) libcudart.so.9.0 => /net/nfs1/public/EM/CUDA/cuda-9.0/lib64/libcudart.so.9.0 (0x00002b5ceffd9000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00002b5cf0246000) libm.so.6 => /lib64/libm.so.6 (0x00002b5cf054e000) libgomp.so.1 => /lib64/libgomp.so.1 (0x00002b5cf0850000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b5cf0a76000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b5cf0c8c000) libc.so.6 => /lib64/libc.so.6 (0x00002b5cf0ea8000) librt.so.1 => /lib64/librt.so.1 (0x00002b5cf1275000) libopen-rte.so.20 => /net/nfs1/public/EM/OpenMPI/openmpi-2.0.1/build/lib/libopen-rte.so.20 (0x00002b5cf147d000) libopen-pal.so.20 => /net/nfs1/public/EM/OpenMPI/openmpi-2.0.1/build/lib/libopen-pal.so.20 (0x00002b5cf16fc000) libutil.so.1 => /lib64/libutil.so.1 (0x00002b5cf19e2000) /lib64/ld-linux-x86-64.so.2 (0x00002b5ce2ca4000) libjbig.so.2.0 => /lib64/libjbig.so.2.0 (0x00002b5cf1be5000) libjpeg.so.62 => /lib64/libjpeg.so.62 (0x00002b5cf1df1000) libz.so.1 => /lib64/libz.so.1 (0x00002b5cf2046000) RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE = /public/EM/SIDESPLITTER/sidesplitter_wrapper.sh SIDESPLITTER = /public/EM/SIDESPLITTER/sidesplitter RUN STARTED AT 1594080632 ----------------------------------------------------------- Reading in optimiser.star ... + Reading in mask ... + The subtracted particles will be re-centred on projections of 3D-coordinate: (84 , -41 , -3) + Calculating Fourier transforms of the maps ... + Subtracting all particles ... 000/??? sec ~~(,_,"> [oo] 0.01/1.14 hrs ~~(,_,"> 0.02/1.09 hrs ~~(,_,"> 0.03/1.08 hrs .~~(,_,"> 0.04/1.07 hrs .~~(,_,"> 0.04/1.08 hrs ..~~(,_,"> 0.05/1.09 hrs ..~~(,_,"> 0.06/1.09 hrs ...~~(,_,"> 0.07/1.09 hrs ...~~(,_,"> 0.08/1.09 hrs ....~~(,_,"> 0.09/1.08 hrs ....~~(,_,"> 0.10/1.08 hrs .....~~(,_,"> 0.11/1.09 hrs .....~~(,_,"> 0.12/1.09 hrs ......~~(,_,"> 0.13/1.09 hrs ......~~(,_,"> 0.14/1.10 hrs .......~~(,_,"> 0.15/1.15 hrs .......~~(,_,"> 0.17/1.19 hrs ........~~(,_,"> 0.18/1.22 hrs ........~~(,_,"> 0.20/1.25 hrs .........~~(,_,"> 0.21/1.27 hrs .........~~(,_,"> 0.22/1.28 hrs ..........~~(,_,"> 0.24/1.30 hrs ..........~~(,_,"> 0.25/1.32 hrs ...........~~(,_,"> 0.26/1.33 hrs ...........~~(,_,"> 0.28/1.34 hrs ............~~(,_,"> 0.29/1.35 hrs ............~~(,_,"> 0.30/1.36 hrs .............~~(,_,"> 0.32/1.36 hrs .............~~(,_,"> 0.33/1.37 hrs ..............~~(,_,"> 0.34/1.38 hrs ..............~~(,_,"> 0.36/1.38 hrs ...............~~(,_,"> 0.37/1.39 hrs ...............~~(,_,"> 0.38/1.39 hrs ................~~(,_,"> 0.40/1.40 hrs ................~~(,_,"> 0.41/1.41 hrs .................~~(,_,"> 0.43/1.43 hrs .................~~(,_,"> 0.44/1.43 hrs ..................~~(,_,"> 0.45/1.43 hrs ..................~~(,_,"> 0.46/1.43 hrs ...................~~(,_,"> 0.48/1.43 hrs ...................~~(,_,"> 0.49/1.43 hrs ....................~~(,_,"> 0.50/1.43 hrs ....................~~(,_,"> 0.51/1.43 hrs .....................~~(,_,"> 0.52/1.43 hrs .....................~~(,_,"> 0.53/1.43 hrs ......................~~(,_,"> 0.55/1.43 hrs ......................~~(,_,"> 0.56/1.43 hrs .......................~~(,_,"> 0.57/1.43 hrs .......................~~(,_,"> 0.58/1.42 hrs ........................~~(,_,"> 0.59/1.41 hrs ........................~~(,_,"> 0.60/1.40 hrs .........................~~(,_,"> 0.60/1.40 hrs .........................~~(,_,"> 0.61/1.39 hrs ..........................~~(,_,"> 0.62/1.38 hrs ..........................~~(,_,"> 0.63/1.38 hrs ...........................~~(,_,"> 0.64/1.38 hrs ...........................~~(,_,"> 0.65/1.37 hrs ............................~~(,_,"> 0.66/1.37 hrs ............................~~(,_,"> 0.67/1.37 hrs .............................~~(,_,"> 0.68/1.37 hrs .............................~~(,_,"> 0.69/1.36 hrs ..............................~~(,_,"> 0.70/1.36 hrs ..............................~~(,_,"> 0.71/1.35 hrs ...............................~~(,_,"> 0.72/1.35 hrs ...............................~~(,_,"> 0.73/1.35 hrs ................................~~(,_,"> 0.74/1.34 hrs ................................~~(,_,"> 0.75/1.34 hrs .................................~~(,_,"> 0.76/1.34 hrs .................................~~(,_,"> 0.77/1.34 hrs ..................................~~(,_,"> 0.78/1.34 hrs ..................................~~(,_,"> 0.79/1.33 hrs ...................................~~(,_,"> 0.80/1.33 hrs ...................................~~(,_,"> 0.80/1.32 hrs ....................................~~(,_,"> 0.81/1.32 hrs ....................................~~(,_,"> 0.82/1.32 hrs .....................................~~(,_,"> 0.83/1.32 hrs .....................................~~(,_,"> 0.84/1.31 hrs ......................................~~(,_,"> 0.85/1.31 hrs ......................................~~(,_,"> 0.86/1.31 hrs .......................................~~(,_,"> 0.87/1.31 hrs .......................................~~(,_,"> 0.88/1.31 hrs ........................................~~(,_,"> 0.89/1.30 hrs ........................................~~(,_,"> 0.90/1.30 hrs .........................................~~(,_,"> 0.91/1.30 hrs .........................................~~(,_,"> 0.92/1.30 hrs ..........................................~~(,_,"> 0.93/1.30 hrs ..........................................~~(,_,"> 0.94/1.29 hrs ...........................................~~(,_,"> 0.94/1.29 hrs ...........................................~~(,_,"> 0.95/1.29 hrs ............................................~~(,_,"> 0.96/1.29 hrs ............................................~~(,_,"> 0.97/1.28 hrs .............................................~~(,_,"> 0.98/1.28 hrs .............................................~~(,_,"> 0.99/1.28 hrs ..............................................~~(,_,"> 1.00/1.28 hrs ..............................................~~(,_,"> 1.01/1.27 hrs ...............................................~~(,_,"> 1.01/1.27 hrs ...............................................~~(,_,"> 1.02/1.27 hrs ................................................~~(,_,"> 1.03/1.27 hrs ................................................~~(,_,"> 1.04/1.26 hrs .................................................~~(,_,"> 1.05/1.26 hrs .................................................~~(,_,"> 1.06/1.26 hrs ..................................................~~(,_,"> 1.07/1.26 hrs ..................................................~~(,_,"> 1.08/1.26 hrs ...................................................~~(,_,"> 1.08/1.25 hrs ...................................................~~(,_,"> 1.09/1.25 hrs ....................................................~~(,_,"> 1.10/1.25 hrs ....................................................~~(,_,"> 1.11/1.25 hrs .....................................................~~(,_,"> 1.12/1.25 hrs .....................................................~~(,_,"> 1.13/1.25 hrs ......................................................~~(,_,"> 1.14/1.25 hrs ......................................................~~(,_,"> 1.15/1.25 hrs .......................................................~~(,_,"> 1.16/1.24 hrs .......................................................~~(,_,"> 1.17/1.24 hrs ........................................................~~(,_,"> 1.18/1.24 hrs ........................................................~~(,_,"> 1.19/1.24 hrs .........................................................~~(,_,"> 1.20/1.24 hrs .........................................................~~(,_,"> 1.20/1.24 hrs ..........................................................~~(,_,"> 1.21/1.24 hrs ..........................................................~~(,_,"> 1.22/1.23 hrs ...........................................................~~(,_,"> 1.23/1.23 hrs ...........................................................~~(,_,"> 1.24/1.24 hrs ............................................................~~(,_,"> + Saved STAR file with 320770 subtracted particles in Subtract/job092/particles_subtracted.star ----------------------------------------------------------- RUN FINISHED AT 1594086956 ELAPSED WALL CLOCK TIME: 6324 Running epilog script on fmb122.lmb.internal Tue 7 Jul 02:55:56 BST 2020 Removing files owned by mwilkin on /ssd