V1: problems #11
Comments
|
Hi，
I saw that you have 2219 tile for MiSeq. But I believe for MiSeq, there is
no tile 2219. Do you mind taking a look at what is your unique lane and
tiles? At the same time I will test something by myself.
Thanks!
BR,
Jingyue
…On Sat, Mar 5, 2022 at 2:04 PM t221f ***@***.***> wrote:
Hi again,
when running V1 step with your sample dataset, I get the error output
below.
From what I understand, there seems to be a problem with the nrow and ncol
counting in this step. When I checked this further, I noticed that the
script does not allow to give --nrow or --ncol values at all.
Thanks a lot for all your amazing work!
Input
python3 $STHOME/sttools.py --run-steps V1
--STtools $STHOME
--predir $STOUT-test/visualization
--spatial $STOUT-test/spatialcoordinates.txt.gz
--ncpus 6
--DGEdir $STDGEtest
--layout MiSeq
--green Alb
--red Mup20,Cyp2f2,Mup3,Serpina1e,Hsd17b13,Hpx,Hsd17b6,Pck1,Pigr,Ambp
--blue Cyp2e1,Cyp2c29,Cyp1a2,Mup11,Cyp2a5,Cyp2a50,Rgn,Hamp,Pon1,Slco1b2
--tmpdir $STOUT-test/visualization
--buffer-size 10G;
Error output:
Processing (0,75) : 1_2219
here
/home/t141g/STtools/out-test/visualization/1/2219/features.tsv.gz
not exist
Calculate mean intensity of each color
Scale_factors = (200000000000.0, 200000000000.0, 200000000000.0)
Constructing an image of -115292150460684696 x -8762203435012036896
Traceback (most recent call last):
File "/home/t141g/STtools/visualization/rgb-gene-image.py", line 223, in
data = np.zeros( (total_h, total_w, 3), dtype=np.uint8 )
ValueError: negative dimensions are not allowed
Traceback (most recent call last):
File "/home/t141g/STtools/sttools.py", line 566, in
func()
File "/home/t141g/STtools/sttools.py", line 528, in stepV1
raise ValueError(f"ERROR in running {cmd7}, returning exit code {ret}")
ValueError: ERROR in running /usr/bin/python3
/home/t141g/STtools/visualization/rgb-gene-image.py -o /root/Sample_vis -d
/home/t141g/STtools/out-test/visualization -g Alb -b
Cyp2e1,Cyp2c29,Cyp1a2,Mup11,Cyp2a5,Cyp2a50,Rgn,Hamp,Pon1,Slco1b2 -r
Mup20,Cyp2f2,Mup3,Serpina1e,Hsd17b13,Hpx,Hsd17b6,Pck1,Pigr,Ambp --scale
20.0 --min-tpm 1000 --res 80 --layout
/home/t141g/STtools/visualization/miseq_layout.tsv, returning exit code 256
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Hi and thanks for the fast reply,
Isn't the tile in the dataset 2106? Or is the dataset from HiSeq and not MiSeq?
Besides, the not exist error also occurred with a lot of other tiles before that.
I edited the initial comment with the full error output.
Thanks and best wishes
Tobias
… Am 05.03.2022 um 20:14 schrieb jyxi7676 ***@***.***>:
Hi，
I saw that you have 2219 tile for MiSeq. But I believe for MiSeq, there is
no tile 2219. Do you mind taking a look at what is your unique lane and
tiles? At the same time I will test something by myself.
Thanks!
BR,
Jingyue
On Sat, Mar 5, 2022 at 2:04 PM t221f ***@***.***> wrote:
> Hi again,
> when running V1 step with your sample dataset, I get the error output
> below.
> From what I understand, there seems to be a problem with the nrow and ncol
> counting in this step. When I checked this further, I noticed that the
> script does not allow to give --nrow or --ncol values at all.
> Thanks a lot for all your amazing work!
>
> Input
> python3 $STHOME/sttools.py --run-steps V1
> --STtools $STHOME
> --predir $STOUT-test/visualization
> --spatial $STOUT-test/spatialcoordinates.txt.gz
> --ncpus 6
> --DGEdir $STDGEtest
> --layout MiSeq
> --green Alb
> --red Mup20,Cyp2f2,Mup3,Serpina1e,Hsd17b13,Hpx,Hsd17b6,Pck1,Pigr,Ambp
> --blue Cyp2e1,Cyp2c29,Cyp1a2,Mup11,Cyp2a5,Cyp2a50,Rgn,Hamp,Pon1,Slco1b2
> --tmpdir $STOUT-test/visualization
> --buffer-size 10G;
>
> Error output:
> Processing (0,75) : 1_2219
> here
> /home/t141g/STtools/out-test/visualization/1/2219/features.tsv.gz
> not exist
> Calculate mean intensity of each color
> Scale_factors = (200000000000.0, 200000000000.0, 200000000000.0)
> Constructing an image of -115292150460684696 x -8762203435012036896
> Traceback (most recent call last):
> File "/home/t141g/STtools/visualization/rgb-gene-image.py", line 223, in
> data = np.zeros( (total_h, total_w, 3), dtype=np.uint8 )
> ValueError: negative dimensions are not allowed
> Traceback (most recent call last):
> File "/home/t141g/STtools/sttools.py", line 566, in
> func()
> File "/home/t141g/STtools/sttools.py", line 528, in stepV1
> raise ValueError(f"ERROR in running {cmd7}, returning exit code {ret}")
> ValueError: ERROR in running /usr/bin/python3
> /home/t141g/STtools/visualization/rgb-gene-image.py -o /root/Sample_vis -d
> /home/t141g/STtools/out-test/visualization -g Alb -b
> Cyp2e1,Cyp2c29,Cyp1a2,Mup11,Cyp2a5,Cyp2a50,Rgn,Hamp,Pon1,Slco1b2 -r
> Mup20,Cyp2f2,Mup3,Serpina1e,Hsd17b13,Hpx,Hsd17b6,Pck1,Pigr,Ambp --scale
> 20.0 --min-tpm 1000 --res 80 --layout
> /home/t141g/STtools/visualization/miseq_layout.tsv, returning exit code 256
>
> —
> Reply to this email directly, view it on GitHub
> <#11>, or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AL45UCKILSTIE6YWCILBOEDU6OV3LANCNFSM5QABINYA>
> .
> Triage notifications on the go with GitHub Mobile for iOS
> <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675>
> or Android
> <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.
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@t221f |
OK, I got it~ the example data is in */SampleSolo.out/GeneFull/ordered ~ |
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Hi again,
when running V1 step with your sample dataset, I get the error output below.
From what I understand, there seems to be a problem with the nrow and ncol counting in this step. When I checked this further, I noticed that the script does not allow to give --nrow or --ncol values at all.
Thanks a lot for all your amazing work!
Input
python3 $STHOME/sttools.py --run-steps V1
--STtools $STHOME
--predir $STOUT-test/visualization
--spatial $STOUT-test/spatialcoordinates.txt.gz
--ncpus 6
--DGEdir $STDGEtest
--layout MiSeq
--green Alb
--red Mup20,Cyp2f2,Mup3,Serpina1e,Hsd17b13,Hpx,Hsd17b6,Pck1,Pigr,Ambp
--blue Cyp2e1,Cyp2c29,Cyp1a2,Mup11,Cyp2a5,Cyp2a50,Rgn,Hamp,Pon1,Slco1b2
--tmpdir $STOUT-test/visualization
--buffer-size 10G;
Error output:
Run step V1
Start Visualization!
a
b
/home/t141g/STtools/out-test/visualization
/root/Sample_vis
/home/t141g/STtools/visualization/miseq_layout.tsv
Processing (0,0) : 1_1101
here
/home/t141g/STtools/out-test/visualization/1/1101/features.tsv.gz
not exist
Processing (0,1) : 1_1102
here
/home/t141g/STtools/out-test/visualization/1/1102/features.tsv.gz
not exist
Processing (0,2) : 1_1103
here
/home/t141g/STtools/out-test/visualization/1/1103/features.tsv.gz
not exist
Processing (0,3) : 1_1104
here
/home/t141g/STtools/out-test/visualization/1/1104/features.tsv.gz
not exist
Processing (0,4) : 1_1105
here
/home/t141g/STtools/out-test/visualization/1/1105/features.tsv.gz
not exist
Processing (0,5) : 1_1106
here
/home/t141g/STtools/out-test/visualization/1/1106/features.tsv.gz
not exist
Processing (0,6) : 1_1107
here
/home/t141g/STtools/out-test/visualization/1/1107/features.tsv.gz
not exist
Processing (0,7) : 1_1108
here
/home/t141g/STtools/out-test/visualization/1/1108/features.tsv.gz
not exist
Processing (0,8) : 1_1109
here
/home/t141g/STtools/out-test/visualization/1/1109/features.tsv.gz
not exist
Processing (0,9) : 1_1110
here
/home/t141g/STtools/out-test/visualization/1/1110/features.tsv.gz
not exist
Processing (0,10) : 1_1111
here
/home/t141g/STtools/out-test/visualization/1/1111/features.tsv.gz
not exist
Processing (0,11) : 1_1112
here
/home/t141g/STtools/out-test/visualization/1/1112/features.tsv.gz
not exist
Processing (0,12) : 1_1113
here
/home/t141g/STtools/out-test/visualization/1/1113/features.tsv.gz
not exist
Processing (0,13) : 1_1114
here
/home/t141g/STtools/out-test/visualization/1/1114/features.tsv.gz
not exist
Processing (0,14) : 1_1115
here
/home/t141g/STtools/out-test/visualization/1/1115/features.tsv.gz
not exist
Processing (0,15) : 1_1116
here
/home/t141g/STtools/out-test/visualization/1/1116/features.tsv.gz
not exist
Processing (0,16) : 1_1117
here
/home/t141g/STtools/out-test/visualization/1/1117/features.tsv.gz
not exist
Processing (0,17) : 1_1118
here
/home/t141g/STtools/out-test/visualization/1/1118/features.tsv.gz
not exist
Processing (0,18) : 1_1119
here
/home/t141g/STtools/out-test/visualization/1/1119/features.tsv.gz
not exist
Processing (0,19) : 1_1201
here
/home/t141g/STtools/out-test/visualization/1/1201/features.tsv.gz
not exist
Processing (0,20) : 1_1202
here
/home/t141g/STtools/out-test/visualization/1/1202/features.tsv.gz
not exist
Processing (0,21) : 1_1203
here
/home/t141g/STtools/out-test/visualization/1/1203/features.tsv.gz
not exist
Processing (0,22) : 1_1204
here
/home/t141g/STtools/out-test/visualization/1/1204/features.tsv.gz
not exist
Processing (0,23) : 1_1205
here
/home/t141g/STtools/out-test/visualization/1/1205/features.tsv.gz
not exist
Processing (0,24) : 1_1206
here
/home/t141g/STtools/out-test/visualization/1/1206/features.tsv.gz
not exist
Processing (0,25) : 1_1207
here
/home/t141g/STtools/out-test/visualization/1/1207/features.tsv.gz
not exist
Processing (0,26) : 1_1208
here
/home/t141g/STtools/out-test/visualization/1/1208/features.tsv.gz
not exist
Processing (0,27) : 1_1209
here
/home/t141g/STtools/out-test/visualization/1/1209/features.tsv.gz
not exist
Processing (0,28) : 1_1210
here
/home/t141g/STtools/out-test/visualization/1/1210/features.tsv.gz
not exist
Processing (0,29) : 1_1211
here
/home/t141g/STtools/out-test/visualization/1/1211/features.tsv.gz
not exist
Processing (0,30) : 1_1212
here
/home/t141g/STtools/out-test/visualization/1/1212/features.tsv.gz
not exist
Processing (0,31) : 1_1213
here
/home/t141g/STtools/out-test/visualization/1/1213/features.tsv.gz
not exist
Processing (0,32) : 1_1214
here
/home/t141g/STtools/out-test/visualization/1/1214/features.tsv.gz
not exist
Processing (0,33) : 1_1215
here
/home/t141g/STtools/out-test/visualization/1/1215/features.tsv.gz
not exist
Processing (0,34) : 1_1216
here
/home/t141g/STtools/out-test/visualization/1/1216/features.tsv.gz
not exist
Processing (0,35) : 1_1217
here
/home/t141g/STtools/out-test/visualization/1/1217/features.tsv.gz
not exist
Processing (0,36) : 1_1218
here
/home/t141g/STtools/out-test/visualization/1/1218/features.tsv.gz
not exist
Processing (0,37) : 1_1219
here
/home/t141g/STtools/out-test/visualization/1/1219/features.tsv.gz
not exist
Processing (0,38) : 1_2101
here
/home/t141g/STtools/out-test/visualization/1/2101/features.tsv.gz
not exist
Processing (0,39) : 1_2102
here
/home/t141g/STtools/out-test/visualization/1/2102/features.tsv.gz
not exist
Processing (0,40) : 1_2103
here
/home/t141g/STtools/out-test/visualization/1/2103/features.tsv.gz
not exist
Processing (0,41) : 1_2104
here
/home/t141g/STtools/out-test/visualization/1/2104/features.tsv.gz
not exist
Processing (0,42) : 1_2105
here
/home/t141g/STtools/out-test/visualization/1/2105/features.tsv.gz
not exist
Processing (0,43) : 1_2106
here
/home/t141g/STtools/out-test/visualization/1/2106/features.tsv.gz
not exist
Processing (0,44) : 1_2107
here
/home/t141g/STtools/out-test/visualization/1/2107/features.tsv.gz
not exist
Processing (0,45) : 1_2108
here
/home/t141g/STtools/out-test/visualization/1/2108/features.tsv.gz
not exist
Processing (0,46) : 1_2109
here
/home/t141g/STtools/out-test/visualization/1/2109/features.tsv.gz
not exist
Processing (0,47) : 1_2110
here
/home/t141g/STtools/out-test/visualization/1/2110/features.tsv.gz
not exist
Processing (0,48) : 1_2111
here
/home/t141g/STtools/out-test/visualization/1/2111/features.tsv.gz
not exist
Processing (0,49) : 1_2112
here
/home/t141g/STtools/out-test/visualization/1/2112/features.tsv.gz
not exist
Processing (0,50) : 1_2113
here
/home/t141g/STtools/out-test/visualization/1/2113/features.tsv.gz
not exist
Processing (0,51) : 1_2114
here
/home/t141g/STtools/out-test/visualization/1/2114/features.tsv.gz
not exist
Processing (0,52) : 1_2115
here
/home/t141g/STtools/out-test/visualization/1/2115/features.tsv.gz
not exist
Processing (0,53) : 1_2116
here
/home/t141g/STtools/out-test/visualization/1/2116/features.tsv.gz
not exist
Processing (0,54) : 1_2117
here
/home/t141g/STtools/out-test/visualization/1/2117/features.tsv.gz
not exist
Processing (0,55) : 1_2118
here
/home/t141g/STtools/out-test/visualization/1/2118/features.tsv.gz
not exist
Processing (0,56) : 1_2119
here
/home/t141g/STtools/out-test/visualization/1/2119/features.tsv.gz
not exist
Processing (0,57) : 1_2201
here
/home/t141g/STtools/out-test/visualization/1/2201/features.tsv.gz
not exist
Processing (0,58) : 1_2202
here
/home/t141g/STtools/out-test/visualization/1/2202/features.tsv.gz
not exist
Processing (0,59) : 1_2203
here
/home/t141g/STtools/out-test/visualization/1/2203/features.tsv.gz
not exist
Processing (0,60) : 1_2204
here
/home/t141g/STtools/out-test/visualization/1/2204/features.tsv.gz
not exist
Processing (0,61) : 1_2205
here
/home/t141g/STtools/out-test/visualization/1/2205/features.tsv.gz
not exist
Processing (0,62) : 1_2206
here
/home/t141g/STtools/out-test/visualization/1/2206/features.tsv.gz
not exist
Processing (0,63) : 1_2207
here
/home/t141g/STtools/out-test/visualization/1/2207/features.tsv.gz
not exist
Processing (0,64) : 1_2208
here
/home/t141g/STtools/out-test/visualization/1/2208/features.tsv.gz
not exist
Processing (0,65) : 1_2209
here
/home/t141g/STtools/out-test/visualization/1/2209/features.tsv.gz
not exist
Processing (0,66) : 1_2210
here
/home/t141g/STtools/out-test/visualization/1/2210/features.tsv.gz
not exist
Processing (0,67) : 1_2211
here
/home/t141g/STtools/out-test/visualization/1/2211/features.tsv.gz
not exist
Processing (0,68) : 1_2212
here
/home/t141g/STtools/out-test/visualization/1/2212/features.tsv.gz
not exist
Processing (0,69) : 1_2213
here
/home/t141g/STtools/out-test/visualization/1/2213/features.tsv.gz
not exist
Processing (0,70) : 1_2214
here
/home/t141g/STtools/out-test/visualization/1/2214/features.tsv.gz
not exist
Processing (0,71) : 1_2215
here
/home/t141g/STtools/out-test/visualization/1/2215/features.tsv.gz
not exist
Processing (0,72) : 1_2216
here
/home/t141g/STtools/out-test/visualization/1/2216/features.tsv.gz
not exist
Processing (0,73) : 1_2217
here
/home/t141g/STtools/out-test/visualization/1/2217/features.tsv.gz
not exist
Processing (0,74) : 1_2218
here
/home/t141g/STtools/out-test/visualization/1/2218/features.tsv.gz
not exist
Processing (0,75) : 1_2219
here
/home/t141g/STtools/out-test/visualization/1/2219/features.tsv.gz
not exist
Calculate mean intensity of each color
Scale_factors = (200000000000.0, 200000000000.0, 200000000000.0)
Constructing an image of -115292150460684696 x -8762203435012036896
Traceback (most recent call last):
File "/home/t141g/STtools/visualization/rgb-gene-image.py", line 223, in
data = np.zeros( (total_h, total_w, 3), dtype=np.uint8 )
ValueError: negative dimensions are not allowed
Traceback (most recent call last):
File "/home/t141g/STtools/sttools.py", line 566, in
func()
File "/home/t141g/STtools/sttools.py", line 528, in stepV1
raise ValueError(f"ERROR in running {cmd7}, returning exit code {ret}")
ValueError: ERROR in running /usr/bin/python3 /home/t141g/STtools/visualization/rgb-gene-image.py -o /root/Sample_vis -d /home/t141g/STtools/out-test/visualization -g Alb -b Cyp2e1,Cyp2c29,Cyp1a2,Mup11,Cyp2a5,Cyp2a50,Rgn,Hamp,Pon1,Slco1b2 -r Mup20,Cyp2f2,Mup3,Serpina1e,Hsd17b13,Hpx,Hsd17b6,Pck1,Pigr,Ambp --scale 20.0 --min-tpm 1000 --res 80 --layout /home/t141g/STtools/visualization/miseq_layout.tsv, returning exit code 256
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