JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for CCPEM Archives


CCPEM Archives

CCPEM Archives


CCPEM@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

CCPEM Home

CCPEM Home

CCPEM  January 2019

CCPEM January 2019

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: ERROR in appending metadata tables with not the same columns!

From:

Takanori Nakane <[log in to unmask]>

Reply-To:

Takanori Nakane <[log in to unmask]>

Date:

Tue, 22 Jan 2019 19:39:43 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (150 lines)

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

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

April 2024
March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager