jyxi7676
commented
2 years ago 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 https://github.com/jyxi7676/STtools/issues/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.
You are receiving this because you are subscribed to this thread.Message ID: @.***>
FaehlingT
liuchang707
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