Sen2cor 2.8 process error

s2tbx sen2cor
#1

today, i using sen2cor to test process data:
S2B_MSIL1C_20190725T031549_N0208_R118_T47MRT_20190725T073609.SAFE

here is linux line

L2A_Process --resolution=10 --output_dir=/home/test/ S2B_MSIL1C_20190725T031549_N0208_R118_T47MRT_20190725T073609.SAFE

this is log

Sentinel-2 Level 2A Processor (Sen2Cor). Version: 2.8.0, created: 2019.02.20, supporting Level-1C product version 14.2 - 14.5 started …
Product version: 14.5
Operation mode: TOOLBOX
Processing baseline: 99.99
Progress[]: 0.00 : Generating datastrip metadata L1C datastrip found, L2A datastrip successfully generated Selected resolution: 10 m Progress[]: 0.05 : PID-22362, L2A_ProcessTile: 20 m resolution must be processed first, elapsed time[s]: 0.971, total: 0:00:05.381348
Progress[]: 0.12 : PID-22362, L2A_ProcessTile: processing with resolution 20 m, elapsed time[s]: 1.153, total: 0:00:06.534253 Progress[]: 0.12 : PID-22362, L2A_ProcessTile: start of pre processing, elapsed time[s]: 0.000, total: 0:00:06.534567
Progress[]: 0.12 : PID-22362, L2A_Tables: start import, elapsed time[s]: 0.050, total: 0:00:06.584926 Progress[]: 0.15 : PID-22362, L2A_Tables: band B01 imported, elapsed time[s]: 0.496, total: 0:00:07.080949
Progress[]: 0.45 : PID-22362, L2A_Tables: band B02 imported, elapsed time[s]: 5.424, total: 0:00:12.505103 Progress[]: 0.76 : PID-22362, L2A_Tables: band B03 imported, elapsed time[s]: 5.727, total: 0:00:18.231629
Progress[]: 1.08 : PID-22362, L2A_Tables: band B04 imported, elapsed time[s]: 5.666, total: 0:00:23.897953 Progress[]: 1.23 : PID-22362, L2A_Tables: band B05 imported, elapsed time[s]: 2.651, total: 0:00:26.548652
Progress[]: 1.36 : PID-22362, L2A_Tables: band B06 imported, elapsed time[s]: 2.513, total: 0:00:29.061894 Progress[]: 1.50 : PID-22362, L2A_Tables: band B07 imported, elapsed time[s]: 2.522, total: 0:00:31.583970
Progress[]: 1.64 : PID-22362, L2A_Tables: band B8A imported, elapsed time[s]: 2.519, total: 0:00:34.103405 Progress[]: 1.67 : PID-22362, L2A_Tables: band B09 imported, elapsed time[s]: 0.501, total: 0:00:34.604130
Progress[]: 1.69 : PID-22362, L2A_Tables: band B10 imported, elapsed time[s]: 0.415, total: 0:00:35.019489 Progress[]: 1.83 : PID-22362, L2A_Tables: band B11 imported, elapsed time[s]: 2.521, total: 0:00:37.540530
Progress[]: 1.98 : PID-22362, L2A_Tables: band B12 imported, elapsed time[s]: 2.578, total: 0:00:40.118686 Progress[]: 1.98 : PID-22362, L2A_ProcessTile: start of Scene Classification, elapsed time[s]: 0.004, total: 0:00:40.123066
Progress[]: 1.99 : PID-22362, L2A_Tables: band B02 must be resampled, elapsed time[s]: 0.188, total: 0:00:40.311365 Progress[]: 2.12 : PID-22362, Pre process , elapsed time[s]: 2.389, total: 0:00:42.700527
Progress[]: 2.12 : PID-22362, L2A_Tables: band B01 must be resampled, elapsed time[s]: 0.007, total: 0:00:42.707580 Progress[]: 2.32 : PID-22362, L2A_Tables: band B03 must be resampled, elapsed time[s]: 3.693, total: 0:00:46.400765
Progress[]: 2.45 : PID-22362, L2A_Tables: band B04 must be resampled, elapsed time[s]: 2.190, total: 0:00:48.591029 Progress[]: 2.59 : PID-22362, L2A_Tables: band B09 must be resampled, elapsed time[s]: 2.607, total: 0:00:51.197544
Progress[]: 2.68 : PID-22362, L2A_Tables: band B10 must be resampled, elapsed time[s]: 1.649, total: 0:00:52.846570 Progress[]: 2.79 : PID-22362, L2A_SC init , elapsed time[s]: 1.955, total: 0:00:54.801610
Progress[]: 2.84 : PID-22362, L2A_CSND_1_1 , elapsed time[s]: 0.958, total: 0:00:55.759538 Progress[]: 2.90 : PID-22362, L2A_CSND_1_2 , elapsed time[s]: 1.095, total: 0:00:56.854314
Progress[]: 3.00 : PID-22362, L2A_CSND_3 , elapsed time[s]: 1.736, total: 0:00:58.590775 Progress[]: 3.08 : PID-22362, L2A_CSND_5_1 , elapsed time[s]: 1.426, total: 0:01:00.016414
Progress[]: 3.19 : PID-22362, L2A_CSND_5_2 , elapsed time[s]: 2.038, total: 0:01:02.054178 Progress[]: 3.27 : PID-22362, L2A_CSND_6 , elapsed time[s]: 1.476, total: 0:01:03.529935
Progress[]: 3.33 : PID-22362, L2A_CSND_6_2 , elapsed time[s]: 0.985, total: 0:01:04.515115 Progress[]: 3.39 : PID-22362, L2A_CSND_7 , elapsed time[s]: 1.159, total: 0:01:05.674585
Progress[]: 5.40 : PID-22362, L2A_SHD , elapsed time[s]: 36.263, total: 0:01:41.937500 Progress[]: 5.47 : PID-22362, DV recovery , elapsed time[s]: 1.266, total: 0:01:43.203121
Progress[]: 5.54 : PID-22362, WP recovery , elapsed time[s]: 1.259, total: 0:01:44.462175 Progress[]: 5.54 : PID-22362, WP recovery with CCI Water Bodies at 150m , elapsed time[s]: 0.001, total: 0:01:44.463416
Progress[]: 5.63 : PID-22362, Snow recovery , elapsed time[s]: 1.677, total: 0:01:46.140287 Progress[]: 5.66 : PID-22362, Soil recovery , elapsed time[s]: 0.619, total: 0:01:46.759316
Progress[]: 5.66 : PID-22362, Land recovery with B10, B09 and B8A , elapsed time[s]: 0.001, total: 0:01:46.760540 Progress[]: 5.66 : PID-22362, Soil recovery , elapsed time[s]: 0.619, total: 0:01:46.759316 [51/1489]
Progress[]: 5.66 : PID-22362, Land recovery with B10, B09 and B8A , elapsed time[s]: 0.001, total: 0:01:46.760540 Progress[]: 5.66 : PID-22362, Cirrus recovery with B10 , elapsed time[s]: 0.001, total: 0:01:46.762011
Progress[]: 5.66 : PID-22362, Urban and Bare pixel recovery with CCI Land Cover Map at 300 m , elapsed time[s]: 0.001, total: 0:01:46.762976 Progress[]: 5.66 : PID-22362, Post process , elapsed time[s]: 0.000, total: 0:01:46.763222
Progress[]: 5.84 : PID-22362, L2A_ProcessTile: start of Atmospheric Correction, elapsed time[s]: 3.082, total: 0:01:49.845332 Progress[]: 5.91 : PID-22362, L2A_AtmCorr: end of calculation terrain maps, elapsed time[s]: 1.272, total: 0:01:51.117133
Progress[]: 5.91 : PID-22362, L2A_AtmCorr: start of AOT retrieval at 550nm, elapsed time[s]: 0.000, total: 0:01:51.117609 Progress[]: 6.19 : PID-22362, L2A_AtmCorr: end of internal classification, elapsed time[s]: 5.057, total: 0:01:56.174282
Progress[]: 6.21 : PID-22362, L2A_AtmCorr: end of interpolation LUTs, elapsed time[s]: 0.473, total: 0:01:56.646891 Progress[]: 7.06 : PID-22362, L2A_AtmCorr: end retrieving reference pixels for dark areas, elapsed time[s]: 15.249, total: 0:02:11.896377
Progress[]: 12.90 : PID-22362, L2A_AtmCorr: end of check for negative reflectance pixels, elapsed time[s]: 105.684, total: 0:03:57.580359 Progress[]: 13.04 : PID-22362, L2A_AtmCorr: the rescaling of path radiance in blue band has been disabled by configuration, elapsed time[s]: 2.463, total: 0:04:00.042908
Progress[]: 15.08 : PID-22362, L2A_AtmCorr: end of visibility index calculation, elapsed time[s]: 36.908, total: 0:04:36.951101 Progress[]: 15.08 : PID-22362, L2A_AtmCorr: end of AOT retrieval at 550nm, elapsed time[s]: 0.000, total: 0:04:36.951590
Progress[]: 15.08 : PID-22362, L2A_AtmCorr: start of water vapour retrieval, elapsed time[s]: 0.000, total: 0:04:36.951909 Progress[]: 15.12 : PID-22362, L2A_AtmCorr: end of water vapour retrieval preparation, elapsed time[s]: 0.672, total: 0:04:37.623949
Progress[]: 22.49 : PID-22362, L2A_AtmCorr: end of water vapour retrieval, elapsed time[s]: 133.100, total: 0:06:50.723667 Progress[]: 22.49 : PID-22362, L2A_AtmCorr: preparation of surface reflectance retrieval, elapsed time[s]: 0.001, total: 0:06:50.724236
Progress[]: 22.71 : PID-22362, L2A_AtmCorr: end of surface reflectance retrieval preparation, elapsed time[s]: 4.055, total: 0:06:54.778991 Progress[]: 22.71 : PID-22362, L2A_AtmCorr: start of surface reflectance retrieval, elapsed time[s]: 0.002, total: 0:06:54.780988
Progress[]: 28.77 : PID-22362, L2A_AtmCorr: end of surface reflectance retrieval, elapsed time[s]: 109.440, total: 0:08:44.220956 Progress[]: 28.77 : PID-22362, L2A_AtmCorr: start of rho retrieval step 2, elapsed time[s]: 0.005, total: 0:08:44.225887
Progress[]: 29.94 : PID-22362, L2A_AtmCorr: end of rho retrieval step 2, elapsed time[s]: 21.087, total: 0:09:05.313090 Progress[]: 29.94 : PID-22362, L2A_ProcessTile: start of post processing, elapsed time[s]: 0.020, total: 0:09:05.332795
Progress[]: 29.94 : PID-22362, L2A_Tables: start export for 20 m resolution, elapsed time[s]: 0.000, total: 0:09:05.333280 Progress[]: 30.35 : PID-22362, L2A_Tables: band B02 exported, elapsed time[s]: 7.547, total: 0:09:12.880707
Progress[]: 30.79 : PID-22362, L2A_Tables: band B03 exported, elapsed time[s]: 7.889, total: 0:09:20.769607 Progress[]: 31.22 : PID-22362, L2A_Tables: band B04 exported, elapsed time[s]: 7.780, total: 0:09:28.549595
Progress[]: 31.67 : PID-22362, L2A_Tables: band B05 exported, elapsed time[s]: 8.016, total: 0:09:36.565704 Progress[]: 32.14 : PID-22362, L2A_Tables: band B06 exported, elapsed time[s]: 8.616, total: 0:09:45.181605
Progress[]: 32.63 : PID-22362, L2A_Tables: band B07 exported, elapsed time[s]: 8.782, total: 0:09:53.963451 Progress[]: 33.12 : PID-22362, L2A_Tables: band B8A exported, elapsed time[s]: 8.919, total: 0:10:02.882173
Progress[]: 33.58 : PID-22362, L2A_Tables: band B11 exported, elapsed time[s]: 8.304, total: 0:10:11.186523 Progress[]: 34.02 : PID-22362, L2A_Tables: band B12 exported, elapsed time[s]: 8.002, total: 0:10:19.188805
Progress[]: 34.09 : PID-22362, L2A_Tables: band SCL exported, elapsed time[s]: 1.175, total: 0:10:20.363578 Progress[]: 34.12 : PID-22362, L2A_Tables: band SNW exported, elapsed time[s]: 0.529, total: 0:10:20.892460
Progress[]: 34.23 : PID-22362, L2A_Tables: band CLD exported, elapsed time[s]: 2.074, total: 0:10:22.966265 Progress[]: 34.27 : PID-22362, L2A_Tables: band AOT exported, elapsed time[s]: 0.729, total: 0:10:23.695154
Progress[]: 34.71 : PID-22362, L2A_Tables: band WVP exported, elapsed time[s]: 7.795, total: 0:10:31.490571 Progress[]: 34.74 : PID-22362, L2A_Tables: band VIS exported, elapsed time[s]: 0.605, total: 0:10:32.095705
Progress[]: 34.75 : PID-22362, L2A_Tables: band PVI exported, elapsed time[s]: 0.229, total: 0:10:32.324643 Progress[]: 34.75 : PID-22362, L2A_Tables: stop export, elapsed time[s]: 0.000, total: 0:10:32.325049
Module L2A_T47MRT_A012442_20190725T032858 failed
Progress[%]: 100.00 : Application terminated with at least one error.

open the log find the error

inspection execution=“2019-08-08T07:14:45.668” level=“FATAL” process=“22362” module=“L2A_ProcessTileToolbox” function="_process" line=“193”/
message contentType=“Text”>Module L2A_T47MRT_A012442_20190725T032858 failed</message

how can fix this error?

#2

why do you define --output_dir at all? It looks like you want to write the corrected data into the original L1C product (was a misunderstanding, there is a space between /test/ and the SAFE folder)

#3

i want to write corrected data to /home/test/S2B_MSIL2A_20190725T031549_*.SAFE not into the original L1C product.

#4

if you do not define an output directory it is automatically created at the location of the input image. Give it a try to see if the error persists.

#5

ok, i will try. Thanks!

test

L2A_Process --resolution 10 S2B_MSIL1C_20190725T031549_N0208_R118_T47MRT_20190725T073609.SAFE

log same as above

Progress[]: 35.49 : PID-13923, L2A_Tables: stop export, elapsed time[s]: 0.000, total: 0:10:50.563415 Module L2A_T47MRT_A012442_20190725T032858 failed Progress[]: 100.00 : Application terminated with at least one error.

#6

hm, that means at least the output directory is not the problem.

Please delete all output files and run again without specifying the output resolution

L2A_Process S2B_MSIL1C_20190725T031549_N0208_R118_T47MRT_20190725T073609.SAFE

#7

I delete all output file , and run L2A_Process S2B_MSIL1C_20190725T031549_N0208_R118_T47MRT_20190725T073609.SAFE, but It also the same error.
how can i change “Operation mode: TOOLBOX” to PDGS in version 2.8.8?
Now i will test this tile using sen2cor 2.5.5 by PDGS, after test i will give the result.

#8

@ABraun i test using sen2cor 2.5.5 PDGS mode,

log about some errror

Progress[]: 34.93 : PID-10886, L2A_Tables: stop export, elapsed time[s]: 0.252, total: 0:23:21.415773 Syntax error in metadata, see report file for details. [ERROR] L2A_XmlParse: 120 Schema file: S2-PDGS-TAS-DI-PSD-V14.5_Schema/S2_PDI_Level-2A_Tile_Metadata.xsd [ERROR] L2A_XmlParse: 120 Schema file: S2-PDGS-TAS-DI-PSD-V14.5_Schema/S2_PDI_Level-2A_Tile_Metadata.xsd [ERROR] L2A_XmlParse: 121 Details: Element 'PVI_FILENAME': [facet 'pattern'] The value 'GRANULE/L1C_T47MRT_A012442_20190725T032858/QI_DATA/T47MRT_20190725T031549_PVI.jp2' is not accepted by the pattern 'GRANULE/L2A_T[\w{Lu}_]{5}_A\d{6}_\d{8}T\d{6}/QI_DATA/T[\w{Lu}_]{5}_\d{8}T\d{6}_PVI.jp2'. [ERROR] L2A_XmlParse: 121 Details: Element 'PVI_FILENAME': [facet 'pattern'] The value 'GRANULE/L1C_T47MRT_A012442_20190725T032858/QI_DATA/T47MRT_20190725T031549_PVI.jp2' is not accepted by the pattern 'GRANULE/L2A_T[\w{Lu}_]{5}_A\d{6}_\d{8}T\d{6}/QI_DATA/T[\w{Lu}_]{5}_\d{8}T\d{6}_PVI.jp2'. Parsing error: Schema file: S2-PDGS-TAS-DI-PSD-V14.5_Schema/S2_PDI_Level-2A_Tile_Metadata.xsd Details: Element 'PVI_FILENAME': [facet 'pattern'] The value 'GRANULE/L1C_T47MRT_A012442_20190725T032858/QI_DATA/T47MRT_20190725T031549_PVI.jp2' is not accepted by the pattern 'GRANULE/L2A_T[\w{Lu}_]{5}_A\d{6}_\d{8}T\d{6}/QI_DATA/T[\w{Lu}_]{5}_\d{8}T\d{6}_PVI.jp2'. Progress[]: 34.99 : PID-10886, L2A_ProcessTile: processing with resolution 10 m, elapsed time[s]: 2.219, total: 0:23:23.635257
Progress[]: 34.99 : PID-10886, L2A_ProcessTile: start of pre processing, elapsed time[s]: 0.000, total: 0:23:23.635590 Progress[]: 34.99 : PID-10886, L2A_Tables: start import, elapsed time[s]: 0.056, total: 0:23:23.691390

But it will continue to process the 10m. at last , I can get 10m and 20m data.
I think sen2cor 2.8.8 error.

#9

Did you take a look at the following posts,

How to install and implement sen2cor version 2.08 please take a look the following thread,

Source of the thread

you could implement it from the command shell,

Take a look at the following post,

Source of the post

#10

I have read all about post. this tile using sen2cor 2.8.0 can not get 10m result, but I have get result by sen2cor 2.5.5 by PDGS mode. more tile i have no test.