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YangLab / CIRCexplorer2

circular RNA analysis toolset
http://circexplorer2.readthedocs.org/
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can't continue 'Annotating' #4

Closed gnilihzeux closed 7 years ago

gnilihzeux commented 7 years ago

I followed the manual and couldn't continue the 'Annotating' with a reply from the error file: Usage: CIRCexplorer2 annotate [options] -r REF -g GENOME <circ_dir>

Then I checked my input and found no incompatibility.

The REF is from Ensembl GRCh38 gtf consistent with Ref_genome by using gtfToGenePred . The header is:

TSPAN6  ENST00000373020 X       -       100628669       100636806       100630797       100636694       8  100628669,100630758,100632484,100633404,100633930,100635177,100635557,100636607, 100629986,100630866,100632568,100633539,100634029,100635252,100635746,100636806,
TSPAN6  ENST00000494424 X       -       100633441       100639991       100639991       100639991       6  100633441,100633930,100635177,100635557,100636792,100639944,     100633539,100634029,100635252,100635746,100637104,100639991,
TSPAN6  ENST00000496771 X       -       100632540       100636689       100636689       100636689       6  100632540,100633404,100633930,100635177,100635557,100636190,     100632568,100633539,100634029,100635252,100635746,100636689,
TSPAN6  ENST00000612152 X       -       100627108       100637104       100630797       100635569       7  100627108,100630758,100633404,100633930,100635177,100635557,100636792,   100629986,100630866,100633539,100634029,100635252,100635746,100637104,
TSPAN6  ENST00000614008 X       -       100632062       100637104       100632062       100635569       7  100632062,100632484,100633404,100633930,100635177,100635557,100636792,   100632068,100632568,100633539,100634029,100635252,100635746,100637104,
TNMD    ENST00000373031 X       +       100584801       100599885       100585018       100599717       7  100584801,100585230,100593894,100594260,100597503,100599015,100599507,   100585066,100585362,100594035,100594362,100597657,100599182,100599885,
TNMD    ENST00000485971 X       +       100593623       100597531       100597531       100597531       3  100593623,100594260,100597503,   100594035,100594362,100597531,
DPM1    ENST00000371582 20      -       50934866        50958555        50935131        50958523        10 50934866,50936147,50940864,50941128,50942030,50945736,50945846,50948628,50955185,50958362,       50935236,50936262,50940933,50941209,50942126,50945762,50945923,50948662,50955285,50958555,
DPM1    ENST00000371584 20      -       50934944        50958521        50935131        50958521        10 50934944,50936147,50940864,50941104,50942030,50945736,50945846,50948628,50955185,50958362,       50935236,50936262,50940933,50941209,50942126,50945762,50945923,50948662,50955285,50958521,
DPM1    ENST00000371588 20      -       50934866        50958550        50935131        50958523        9  50934866,50936147,50940864,50942030,50945736,50945846,50948628,50955185,50958362,        50935236,50936262,50940933,50942126,50945762,50945923,50948662,50955285,50958550,

And my Ref genome is Ensembl GRCh38, headers are:

>1 dna:chromosome chromosome:GRCh38:1:1:248956422:1 REF
>2 dna:chromosome chromosome:GRCh38:2:1:242193529:1 REF
>3 dna:chromosome chromosome:GRCh38:3:1:198295559:1 REF
>4 dna:chromosome chromosome:GRCh38:4:1:190214555:1 REF
>5 dna:chromosome chromosome:GRCh38:5:1:181538259:1 REF
>6 dna:chromosome chromosome:GRCh38:6:1:170805979:1 REF
>7 dna:chromosome chromosome:GRCh38:7:1:159345973:1 REF
>8 dna:chromosome chromosome:GRCh38:8:1:145138636:1 REF
>9 dna:chromosome chromosome:GRCh38:9:1:138394717:1 REF
>10 dna:chromosome chromosome:GRCh38:10:1:133797422:1 REF
>11 dna:chromosome chromosome:GRCh38:11:1:135086622:1 REF
>12 dna:chromosome chromosome:GRCh38:12:1:133275309:1 REF
>13 dna:chromosome chromosome:GRCh38:13:1:114364328:1 REF
>14 dna:chromosome chromosome:GRCh38:14:1:107043718:1 REF
>15 dna:chromosome chromosome:GRCh38:15:1:101991189:1 REF
>16 dna:chromosome chromosome:GRCh38:16:1:90338345:1 REF
>17 dna:chromosome chromosome:GRCh38:17:1:83257441:1 REF
>18 dna:chromosome chromosome:GRCh38:18:1:80373285:1 REF
>19 dna:chromosome chromosome:GRCh38:19:1:58617616:1 REF
>20 dna:chromosome chromosome:GRCh38:20:1:64444167:1 REF
>21 dna:chromosome chromosome:GRCh38:21:1:46709983:1 REF
>22 dna:chromosome chromosome:GRCh38:22:1:50818468:1 REF
>X dna:chromosome chromosome:GRCh38:X:1:156040895:1 REF
>Y dna:chromosome chromosome:GRCh38:Y:2781480:56887902:1 REF

and <circ_dir> is directory circ_out with file fusion_junction.bed and its header is:

15      83885100        83891379        FUSIONJUNC_0/1  0       +
16      15001838        70036578        FUSIONJUNC_1/1  0       +
17      46475199        46694662        FUSIONJUNC_2/1  0       +
19      3586648 14480485        FUSIONJUNC_3/4  0       +
3       73047269        197634612       FUSIONJUNC_4/1  0       +
21      8206731 8433925 FUSIONJUNC_5/1  0       +
21      5121790 44137296        FUSIONJUNC_6/1  0       +
3       158652095       158666386       FUSIONJUNC_7/2  0       +
5       94569462        134924198       FUSIONJUNC_8/15 0       +
5       94569462        134924197       FUSIONJUNC_9/1  0       +

Thanks for your attention!

xingma commented 7 years ago

Can you show the detailed commands and error information?

gnilihzeux commented 7 years ago

Sorry for my unclear meaning. The commands is:

CIRCexplorer2 annotate -r ~/hg38_ens.txt -g ~/ensembl_grch38.fa ~/circ_out > CIRCexplorer2_annotate.log

and the error is:

Usage: CIRCexplorer2 annotate [options] -r REF -g GENOME <circ_dir>

And the content of files were described above.

xingma commented 7 years ago

The error message is saying that there is something wrong with your command. But I can't find it out with

CIRCexplorer2 annotate -r ~/hg38_ens.txt -g ~/ensembl_grch38.fa ~/circ_out > CIRCexplorer2_annotate.log

May there are some problems when you type in the terminal. Can you provide a screenshots with the command and error?

gnilihzeux commented 7 years ago

Thank you for your attention! It seems work after adjusting my input format. Before:

CIRCexplorer2 annotate -r ~/hg38_ens.txt \
-g -g ~/ensembl_grch38.fa \
~/circ_out \
> CIRCexplorer2_annotate.log
xingma commented 7 years ago

I think the problem is double "-g" in your command before.

gnilihzeux commented 7 years ago

Eh, it's a wrong handling. Actually I find CIRCexplorer2 annotate seems not support linux continue operater '\' just as below:

CIRCexplorer2 annotate -r ~/hg38_ens.txt \
-g ~/ensembl_grch38.fa \
~/circ_out \
> CIRCexplorer2_annotate.log

Even just one \. I wish this could be solved because of the ugly format of full path. Maybe mine is an exception.