datalad error

[satra]

first: known error - see datalad/datalad-container#43)
second: see after this error

$ datalad containers-run -m "sub-02 1st-level GLM" \
>     --input sub-02/onsets \
>     --input sub-02/1stlvl_design.fsf \
>     --input inputs/rawdata/sub-02/func/sub-02_task-oneback_run-01_bold.nii.gz \
>     --output sub-02/1stlvl_glm.feat \
>     feat sub-02/1stlvl_design.fsf
[INFO   ] == Command start (output follows) =====                                                                                                                            
grep: /home/satra/sub-02/1stlvl_design.fsf: No such file or directory
    while executing
"exec sh -c "grep -a 'fmri(inmelodic)' $filename | tail -n 1 | awk '{ print \$3 }'" "
    (procedure "feat5:load" line 5)
    invoked from within
"feat5:load -1 1 ${fsfroot}.fsf"
    (file "/usr/lib/fsl/5.0/feat" line 306)
[INFO   ] == Command exit (modification check follows) ===== 
[INFO   ] The command had a non-zero exit code. If this is expected, you can save the changes with 'datalad save -r -F.git/COMMIT_EDITMSG .' 
Failed to run 'singularity exec .datalad/environments/fsl/image feat sub-02/1stlvl_design.fsf' under '/om/scratch/Fri/satra/training/test-exercises/glm_analysis'. Exit code=
1. out= err=SDEV[00:04][0.15][1%]satra@node025:gl                                                                                                                            

git-annex has modified changes, therefore the following does not run:

$ datalad run singularity exec -c -B /tmp -H `pwd` .datalad/environments/fsl/image feat sub-02/1stlvl_design.fsf
run(impossible): /om/scratch/Fri/satra/training/test-exercises/glm_analysis (dataset) [unsaved modifications present, cannot detect changes by command]

how should i reset the state?

[satra]

did not read: datalad save -r -F.git/COMMIT_EDITMSG .

[satra]

@mih - this actually didn't work. i still got a state i don't know how to get rid of

$ datalad containers-run -n fsl2  -m "sub-02 1st-level GLM"   --input sub-02/onsets   --input sub-02/1stlvl_design.fsf   --input inputs/rawdata/sub-02/func/sub-02_task-oneback_run-01_bold.nii.gz   --output sub-02/1stlvl_glm.feat   feat sub-02/1stlvl_design.fsf
run(impossible): /nobackup/scratch/Fri/satra/training/test-exercises/glm_analysis (dataset) [unsaved modifications present, cannot detect changes by command]

also i don't think this command is proper (even with a space added between F and .git/COMMIT_EDITMSG

[mih]

Just git reset --hard? it should do or need any magic.

If I am missing something, please post the git status output.

[satra]

i don't have a copy of it, but i saw a:

T /path/to/staged/file

[mih]

That was likely the unlocked container image. The is normal, given the command that specifies `--output .`

…

On Sun, Jun 10, 2018, 15:02 Satrajit Ghosh ***@***.***> wrote: i don't have a copy of it, but i saw a: T /path/to/staged/file — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAIVH5c-EvTzeEXwwxF8_w2RC1_zPubGks5t7Rj8gaJpZM4Uhk1S> .