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Hi, This error occurs when some of coordinate STAR files contains more or fewer columns than others. Please examine carefully the STAR files from Warp. I cannot test myself, as I don't have a Windows machine to run Warp. Best regards, Takanori Nakane On 2019/01/22 17:46, Tomas KOUBA wrote: > Hi Takanori, > > Hope you are well and things go well at LMB. > > I am using Warp coordinates, which we get on-fly during data collection > to speed up the whole process (not really works in this case:). > > I moved *_ali_BoxNet2Mask_20180918.star file coordinates to the > MotionCorr/job004/data/ folder, then imported them. > Then one can see the coordinates by displaying > coords_suffix_ali_BoxNet2Mask_20180918.star. > > Then I do extraction, which works in one case from three. > > Bizarre > > I mean I can repick, but it should work...I used to make this approach > so many times before with Gautomach. > > > T. > > > > > On 2019-01-22 17:15, Takanori Nakane wrote: >> Hi, >> >> Did you manually modify the result from AutoPick? >> >> This used to be a problem in RELION 2.1, but should not cause >> problems in 3.0. >> >> Best regards, >> >> Takanori Nakane >> >>> Dear All, >>> >>> Has anybody experienced an "ERROR in appending metadata tables with not >>> the same columns!" during particle extraction? >>> >>> First I thought it might have been because of some of the mics failed in >>> MotionCor2: >>> data/92-36_000.tif: too few valid local trajectories to fit local motion >>> model. >>> >>> But then I split the mics into batches and in one I got the ERROR and in >>> one I did not, even when the MotionCor2 fail was present in both. >>> >>> Any advice will be appreciated. >>> >>> Best wishes >>> >>> Tomas >>> >>> >>> >>> >>> The full log: >>> >>> === Backtrace === >>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_preprocess_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) >>> >>> [0x429651] >>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_preprocess_mpi(_ZN13MetaDataTable6appendERKS_+0x181) >>> >>> [0x432761] >>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_preprocess_mpi(_ZN13Preprocessing16joinAllStarFilesEv+0x421) >>> >>> [0x44b611] >>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi19runExtractParticlesEv+0x3f3) >>> >>> [0x46a243] >>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_preprocess_mpi(_ZN16PreprocessingMpi3runEv+0x27) >>> >>> [0x46a637] >>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_preprocess_mpi(main+0x3b) >>> >>> [0x4209ab] >>> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5) [0x2ab3de51cb45] >>> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_preprocess_mpi() >>> [0x4210c1] >>> ================== >>> ERROR: >>> ERROR in appending metadata tables with not the same columns! >>> [warn] Epoll ADD(4) on fd 104 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 85 failed. Old events were 0; read change was >>> 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 83 failed. Old events were 0; read change was >>> 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 147 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 128 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 71 failed. Old events were 0; read change was >>> 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 105 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 87 failed. Old events were 0; read change was >>> 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 138 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 130 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 136 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 119 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 91 failed. Old events were 0; read change was >>> 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 80 failed. Old events were 0; read change was >>> 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 139 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 74 failed. Old events were 0; read change was >>> 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 137 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 145 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> [warn] Epoll ADD(4) on fd 111 failed. Old events were 0; read change >>> was 0 (none); write change was 1 (add): Bad file descriptor >>> >>> ######################################################################## >>> >>> To unsubscribe from the CCPEM list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 >>> ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1