> I am not able to reproduce the error. Unfortunately there is a glitch
> in
> the error handling which causes a second error to hide the original
> one.
> If you turn on debugging there might be some more information
> displayed. You turn on debugging by editing the
> /www/WEB-INF/classes/log4j.properties file.
>
> In the "Base 2 CORE loggers" section change the line:
> log4j.logger.net.sf.basedb.core=warn
>
> to:
> log4j.logger.net.sf.basedb.core=debug
>
> and run the initdb.sh script again.
>
> /Nicklas
OK, here are the last lines of the debug output. Let me know if you
want more (full log is 200K+)!
Thx, Emil
15:26:07,926 INFO core:108 - Loaded predefined queries from file:
/common-queries.xml
15:26:07,933 INFO core:112 - Loaded predefined queries from file:
/mysql-queries.xml
15:26:07,935 DEBUG sql:392 - INSERT SQL for entity = rawdata_agilent:
INSERT INTO `RawDataAgilent` (`version`, `rawbioassay_id`,
`feature_id`, `reporter_id`, `position`, `x`, `y`, `block`,
`metagrid_x`, `metagrid_y`, `row`, `column`, `log_ratio`,
`pvalue_log_ratio`, `g_surrogate_used`, `r_surrogate_used`,
`g_is_found`, `r_is_found`, `g_processed_signal`, `r_processed_signal`,
`g_high_outlier_pixels`, `r_high_outlier_pixels`,
`g_low_outlier_pixels`, `r_low_outlier_pixels`, `g_pixels`, `r_pixels`,
`g_mean_signal`, `r_mean_signal`, `g_median_signal`, `r_median_signal`,
`g_bg_pixels`, `r_bg_pixels`, `g_bg_mean_signal`, `r_bg_mean_signal`,
`g_bg_median_signal`, `r_bg_median_signal`, `g_sat_pixels`,
`r_sat_pixels`, `g_is_saturated`, `r_is_saturated`, `pix_correlation`,
`bg_pix_correlation`, `g_nonuniform_outlier`, `r_nonuniform_outlier`,
`g_bg_nonuniform_outlier`, `r_bg_nonuniform_outlier`,
`g_population_outlier`, `r_population_outlier`,
`g_bg_population_outlier`, `r_bg_population_outlier`, `manual_flag`,
`g_net_signal`, `r_net_signal`, `bg_correlation`, `g_significant`,
`r_significant`, `g_pvalue`, `r_pvalue`, `g_numbg_used`,
`r_numbg_used`, `g_above_bg`, `r_above_bg`, `g_bg_used`, `r_bg_used`,
`is_normalization`, `g_normalized`, `r_normalized`, `norm_correlation`,
`error_model`, `x_dev`, `g_spatial_trend`, `r_spatial_trend`,
`g_surface_value`, `r_surface_value`) VALUES (?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
15:26:07,937 DEBUG sql:439 - UPDATE SQL for entity = rawdata_agilent:
UPDATE `RawDataAgilent` SET `version` = ?, `log_ratio` = ?,
`pvalue_log_ratio` = ?, `g_surrogate_used` = ?, `r_surrogate_used` = ?,
`g_is_found` = ?, `r_is_found` = ?, `g_processed_signal` = ?,
`r_processed_signal` = ?, `g_high_outlier_pixels` = ?,
`r_high_outlier_pixels` = ?, `g_low_outlier_pixels` = ?,
`r_low_outlier_pixels` = ?, `g_pixels` = ?, `r_pixels` = ?,
`g_mean_signal` = ?, `r_mean_signal` = ?, `g_median_signal` = ?,
`r_median_signal` = ?, `g_bg_pixels` = ?, `r_bg_pixels` = ?,
`g_bg_mean_signal` = ?, `r_bg_mean_signal` = ?, `g_bg_median_signal` =
?, `r_bg_median_signal` = ?, `g_sat_pixels` = ?, `r_sat_pixels` = ?,
`g_is_saturated` = ?, `r_is_saturated` = ?, `pix_correlation` = ?,
`bg_pix_correlation` = ?, `g_nonuniform_outlier` = ?,
`r_nonuniform_outlier` = ?, `g_bg_nonuniform_outlier` = ?,
`r_bg_nonuniform_outlier` = ?, `g_population_outlier` = ?,
`r_population_outlier` = ?, `g_bg_population_outlier` = ?,
`r_bg_population_outlier` = ?, `manual_flag` = ?, `g_net_signal` = ?,
`r_net_signal` = ?, `bg_correlation` = ?, `g_significant` = ?,
`r_significant` = ?, `g_pvalue` = ?, `r_pvalue` = ?, `g_numbg_used` =
?, `r_numbg_used` = ?, `g_above_bg` = ?, `r_above_bg` = ?, `g_bg_used`
= ?, `r_bg_used` = ?, `is_normalization` = ?, `g_normalized` = ?,
`r_normalized` = ?, `norm_correlation` = ?, `error_model` = ?, `x_dev`
= ?, `g_spatial_trend` = ?, `r_spatial_trend` = ?, `g_surface_value` =
?, `r_surface_value` = ? WHERE `id` = ? AND `version` = ?
15:26:07,937 DEBUG sql:465 - DELETE SQL for entity = rawdata_agilent:
DELETE FROM `RawDataAgilent` WHERE `id` = ?
15:26:07,939 DEBUG sql:392 - INSERT SQL for entity =
rawdata_chipskipper: INSERT INTO `RawDataChipSkipper` (`version`,
`rawbioassay_id`, `feature_id`, `reporter_id`, `position`, `x`, `y`,
`block`, `metagrid_x`, `metagrid_y`, `row`, `column`, `line_counter`,
`flags`, `gs_flags`, `cy3_volume`, `cy3_avg`, `cy3_bg_arith`,
`cy3_bg_geom`, `cy3_bg_median`, `cy3_bg_total`, `cy3_reduced`,
`cy3_area`, `cy3_saturated`, `cy5_volume`, `cy5_avg`, `cy5_bg_arith`,
`cy5_bg_geom`, `cy5_bg_median`, `cy5_bg_total`, `cy5_reduced`,
`cy5_area`, `cy5_saturated`, `rep_vol`, `ratio`, `directional_ratio`,
`log2_ratio`, `cy3_normalised`, `cy5_normalised`, `compensated_ratio`,
`comp_dir_ratio`, `comp_log2_ratio`, `comment`, `snr_tot`,
`snr_tot_score`, `sat_pixels`, `replicas`, `regulation`, `group_name`,
`median_ratios`, `median_ratios_sdev`, `ratio_medians`,
`ratio_medians_sdev`) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
15:26:07,940 DEBUG sql:439 - UPDATE SQL for entity =
rawdata_chipskipper: UPDATE `RawDataChipSkipper` SET `version` = ?,
`line_counter` = ?, `flags` = ?, `gs_flags` = ?, `cy3_volume` = ?,
`cy3_avg` = ?, `cy3_bg_arith` = ?, `cy3_bg_geom` = ?, `cy3_bg_median` =
?, `cy3_bg_total` = ?, `cy3_reduced` = ?, `cy3_area` = ?,
`cy3_saturated` = ?, `cy5_volume` = ?, `cy5_avg` = ?, `cy5_bg_arith` =
?, `cy5_bg_geom` = ?, `cy5_bg_median` = ?, `cy5_bg_total` = ?,
`cy5_reduced` = ?, `cy5_area` = ?, `cy5_saturated` = ?, `rep_vol` = ?,
`ratio` = ?, `directional_ratio` = ?, `log2_ratio` = ?,
`cy3_normalised` = ?, `cy5_normalised` = ?, `compensated_ratio` = ?,
`comp_dir_ratio` = ?, `comp_log2_ratio` = ?, `comment` = ?, `snr_tot` =
?, `snr_tot_score` = ?, `sat_pixels` = ?, `replicas` = ?, `regulation`
= ?, `group_name` = ?, `median_ratios` = ?, `median_ratios_sdev` = ?,
`ratio_medians` = ?, `ratio_medians_sdev` = ? WHERE `id` = ? AND
`version` = ?
15:26:07,940 DEBUG sql:465 - DELETE SQL for entity =
rawdata_chipskipper: DELETE FROM `RawDataChipSkipper` WHERE `id` = ?
15:26:07,941 DEBUG sql:392 - INSERT SQL for entity = rawdata_bzscan:
INSERT INTO `RawDataBZScan` (`version`, `rawbioassay_id`, `feature_id`,
`reporter_id`, `position`, `x`, `y`, `block`, `metagrid_x`,
`metagrid_y`, `row`, `column`, `q_image_const`, `q_image_var`,
`q_fit_const`, `q_fit_var`, `fit_correction`, `quality_metric`,
`spot_quality`, `overshining`) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?)
15:26:07,942 DEBUG sql:439 - UPDATE SQL for entity = rawdata_bzscan:
UPDATE `RawDataBZScan` SET `version` = ?, `q_image_const` = ?,
`q_image_var` = ?, `q_fit_const` = ?, `q_fit_var` = ?, `fit_correction`
= ?, `quality_metric` = ?, `spot_quality` = ?, `overshining` = ? WHERE
`id` = ? AND `version` = ?
15:26:07,943 DEBUG sql:465 - DELETE SQL for entity = rawdata_bzscan:
DELETE FROM `RawDataBZScan` WHERE `id` = ?
15:26:07,944 DEBUG sql:392 - INSERT SQL for entity =
rawdata_quantarraybiotin: INSERT INTO `RawDataQuantArrayBiotin`
(`version`, `rawbioassay_id`, `feature_id`, `reporter_id`, `position`,
`x`, `y`, `block`, `metagrid_x`, `metagrid_y`, `row`, `column`,
`number`, `intensity`, `background`, `diameter`, `area`, `footprint`,
`cirularity`, `uniformity`, `bg_uniformity`, `snr`, `confidence`,
`ignore_filter`, `ratio`, `precent`, `diameter_filter`, `area_filter`,
`footprint_filter`, `circularity_filter`, `uniformity_filter`,
`bg_uniformity_filter`, `snr_filter`, `replicate_filter`) VALUES (?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?)
15:26:07,945 DEBUG sql:439 - UPDATE SQL for entity =
rawdata_quantarraybiotin: UPDATE `RawDataQuantArrayBiotin` SET
`version` = ?, `number` = ?, `intensity` = ?, `background` = ?,
`diameter` = ?, `area` = ?, `footprint` = ?, `cirularity` = ?,
`uniformity` = ?, `bg_uniformity` = ?, `snr` = ?, `confidence` = ?,
`ignore_filter` = ?, `ratio` = ?, `precent` = ?, `diameter_filter` = ?,
`area_filter` = ?, `footprint_filter` = ?, `circularity_filter` = ?,
`uniformity_filter` = ?, `bg_uniformity_filter` = ?, `snr_filter` = ?,
`replicate_filter` = ? WHERE `id` = ? AND `version` = ?
15:26:07,945 DEBUG sql:465 - DELETE SQL for entity =
rawdata_quantarraybiotin: DELETE FROM `RawDataQuantArrayBiotin` WHERE
`id` = ?
15:26:07,946 DEBUG sql:392 - INSERT SQL for entity = rawdata_genetac:
INSERT INTO `RawDataGeneTac` (`version`, `rawbioassay_id`,
`feature_id`, `reporter_id`, `position`, `x`, `y`, `block`,
`metagrid_x`, `metagrid_y`, `row`, `column`, `med_cy3`, `med_cy5`,
`med_ratio`, `bg_cy3`, `bg_cy5`, `bg_ratio`) VALUES (?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
15:26:07,947 DEBUG sql:439 - UPDATE SQL for entity = rawdata_genetac:
UPDATE `RawDataGeneTac` SET `version` = ?, `med_cy3` = ?, `med_cy5` =
?, `med_ratio` = ?, `bg_cy3` = ?, `bg_cy5` = ?, `bg_ratio` = ? WHERE
`id` = ? AND `version` = ?
15:26:07,947 DEBUG sql:465 - DELETE SQL for entity = rawdata_genetac:
DELETE FROM `RawDataGeneTac` WHERE `id` = ?
15:26:07,948 DEBUG sql:392 - INSERT SQL for entity =
net.sf.basedb.core.data.ReporterData: INSERT INTO `Reporters`
(`version`, `external_id`, `symbol`, `last_update`, `name`,
`description`, `reportertype_id`, `species`, `clusterId`, `length`,
`sequence`, `vector`, `tissue`, `library`, `accession`, `nid`,
`chromosome`, `cytoband`, `markers`, `antibiotics`, `locuslink`,
`omim`) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?)
15:26:07,949 DEBUG sql:439 - UPDATE SQL for entity =
net.sf.basedb.core.data.ReporterData: UPDATE `Reporters` SET `version`
= ?, `external_id` = ?, `symbol` = ?, `last_update` = ?, `name` = ?,
`description` = ?, `reportertype_id` = ?, `species` = ?, `clusterId` =
?, `length` = ?, `sequence` = ?, `vector` = ?, `tissue` = ?, `library`
= ?, `accession` = ?, `nid` = ?, `chromosome` = ?, `cytoband` = ?,
`markers` = ?, `antibiotics` = ?, `locuslink` = ?, `omim` = ? WHERE
`id` = ? AND `version` = ?
15:26:07,949 DEBUG sql:465 - DELETE SQL for entity =
net.sf.basedb.core.data.ReporterData: DELETE FROM `Reporters` WHERE
`id` = ?
15:26:07,950 DEBUG sql:392 - INSERT SQL for entity =
net.sf.basedb.core.data.FeatureData: INSERT INTO `Features` (`version`,
`column`, `row`, `position`, `arraydesignblock_id`, `well_id`,
`reporter_id`) VALUES (?, ?, ?, ?, ?, ?, ?)
15:26:07,950 DEBUG sql:439 - UPDATE SQL for entity =
net.sf.basedb.core.data.FeatureData: UPDATE `Features` SET `version` =
? WHERE `id` = ? AND `version` = ?
15:26:07,951 DEBUG sql:465 - DELETE SQL for entity =
net.sf.basedb.core.data.FeatureData: DELETE FROM `Features` WHERE `id`
= ?
15:26:07,983 DEBUG sql:392 - INSERT SQL for entity = rawdata_imagene:
INSERT INTO `RawDataImaGene` (`version`, `rawbioassay_id`,
`feature_id`, `reporter_id`, `position`, `x`, `y`, `block`,
`metagrid_x`, `metagrid_y`, `row`, `column`, `field`, `cy3_flag`,
`cy3_mean_signal`, `cy3_mean_bg`, `cy3_median_signal`, `cy3_median_bg`,
`cy3_mode_signal`, `cy3_mode_bg`, `cy3_area_signal`, `cy3_area_bg`,
`cy3_total_signal`, `cy3_total_bg`, `cy3_shape`, `cy3_area_ignored`,
`cy3_area_spot`, `cy3_median_ignored`, `cy3_area_perimeter`,
`cy3_open_perimeter`, `cy3_x`, `cy3_y`, `cy3_diameter`, `cy3_offset`,
`cy3_offset_x`, `cy3_offset_y`, `cy3_x_expected`, `cy3_y_expected`,
`cy3_x_cm`, `cy3_y_cm`, `cy3_offset_cm`, `cy3_offset_x_cm`,
`cy3_offset_y_cm`, `cy3_diameter_min`, `cy3_diameter_max`,
`cy3_control`, `cy3_control_failed`, `cy3_bg_contamination`,
`cy3_signal_contamination`, `cy3_ignored_failed`,
`cy3_perimeter_failed`, `cy3_shape_failed`, `cy3_areapm_failed`,
`cy3_offset_failed`, `cy3_empty_spot`, `cy3_negative_spot`,
`cy3_selected_spot`, `cy3_saturated_spot`, `cy5_mean_signal`,
`cy5_mean_bg`, `cy5_median_signal`, `cy5_median_bg`, `cy5_mode_signal`,
`cy5_mode_bg`, `cy5_area_signal`, `cy5_area_bg`, `cy5_total_signal`,
`cy5_total_bg`, `cy5_shape`, `cy5_area_ignored`, `cy5_area_spot`,
`cy5_median_ignored`, `cy5_area_perimeter`, `cy5_open_perimeter`,
`cy5_x`, `cy5_y`, `cy5_diameter`, `cy5_offset`, `cy5_offset_x`,
`cy5_offset_y`, `cy5_x_expected`, `cy5_y_expected`, `cy5_x_cm`,
`cy5_y_cm`, `cy5_offset_cm`, `cy5_offset_x_cm`, `cy5_offset_y_cm`,
`cy5_diameter_min`, `cy5_diameter_max`, `cy5_control`,
`cy5_control_failed`, `cy5_bg_contamination`,
`cy5_signal_contamination`, `cy5_ignored_failed`,
`cy5_perimeter_failed`, `cy5_shape_failed`, `cy5_areapm_failed`,
`cy5_offset_failed`, `cy5_empty_spot`, `cy5_negative_spot`,
`cy5_selected_spot`, `cy5_saturated_spot`) VALUES (?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
15:26:07,985 DEBUG sql:439 - UPDATE SQL for entity = rawdata_imagene:
UPDATE `RawDataImaGene` SET `version` = ?, `field` = ?, `cy3_flag` = ?,
`cy3_mean_signal` = ?, `cy3_mean_bg` = ?, `cy3_median_signal` = ?,
`cy3_median_bg` = ?, `cy3_mode_signal` = ?, `cy3_mode_bg` = ?,
`cy3_area_signal` = ?, `cy3_area_bg` = ?, `cy3_total_signal` = ?,
`cy3_total_bg` = ?, `cy3_shape` = ?, `cy3_area_ignored` = ?,
`cy3_area_spot` = ?, `cy3_median_ignored` = ?, `cy3_area_perimeter` =
?, `cy3_open_perimeter` = ?, `cy3_x` = ?, `cy3_y` = ?, `cy3_diameter` =
?, `cy3_offset` = ?, `cy3_offset_x` = ?, `cy3_offset_y` = ?,
`cy3_x_expected` = ?, `cy3_y_expected` = ?, `cy3_x_cm` = ?, `cy3_y_cm`
= ?, `cy3_offset_cm` = ?, `cy3_offset_x_cm` = ?, `cy3_offset_y_cm` = ?,
`cy3_diameter_min` = ?, `cy3_diameter_max` = ?, `cy3_control` = ?,
`cy3_control_failed` = ?, `cy3_bg_contamination` = ?,
`cy3_signal_contamination` = ?, `cy3_ignored_failed` = ?,
`cy3_perimeter_failed` = ?, `cy3_shape_failed` = ?, `cy3_areapm_failed`
= ?, `cy3_offset_failed` = ?, `cy3_empty_spot` = ?, `cy3_negative_spot`
= ?, `cy3_selected_spot` = ?, `cy3_saturated_spot` = ?,
`cy5_mean_signal` = ?, `cy5_mean_bg` = ?, `cy5_median_signal` = ?,
`cy5_median_bg` = ?, `cy5_mode_signal` = ?, `cy5_mode_bg` = ?,
`cy5_area_signal` = ?, `cy5_area_bg` = ?, `cy5_total_signal` = ?,
`cy5_total_bg` = ?, `cy5_shape` = ?, `cy5_area_ignored` = ?,
`cy5_area_spot` = ?, `cy5_median_ignored` = ?, `cy5_area_perimeter` =
?, `cy5_open_perimeter` = ?, `cy5_x` = ?, `cy5_y` = ?, `cy5_diameter` =
?, `cy5_offset` = ?, `cy5_offset_x` = ?, `cy5_offset_y` = ?,
`cy5_x_expected` = ?, `cy5_y_expected` = ?, `cy5_x_cm` = ?, `cy5_y_cm`
= ?, `cy5_offset_cm` = ?, `cy5_offset_x_cm` = ?, `cy5_offset_y_cm` = ?,
`cy5_diameter_min` = ?, `cy5_diameter_max` = ?, `cy5_control` = ?,
`cy5_control_failed` = ?, `cy5_bg_contamination` = ?,
`cy5_signal_contamination` = ?, `cy5_ignored_failed` = ?,
`cy5_perimeter_failed` = ?, `cy5_shape_failed` = ?, `cy5_areapm_failed`
= ?, `cy5_offset_failed` = ?, `cy5_empty_spot` = ?, `cy5_negative_spot`
= ?, `cy5_selected_spot` = ?, `cy5_saturated_spot` = ? WHERE `id` = ?
AND `version` = ?
15:26:07,986 DEBUG sql:465 - DELETE SQL for entity = rawdata_imagene:
DELETE FROM `RawDataImaGene` WHERE `id` = ?
15:26:07,987 DEBUG sql:392 - INSERT SQL for entity = rawdata_genepix:
INSERT INTO `RawDataGenePix` (`version`, `rawbioassay_id`,
`feature_id`, `reporter_id`, `position`, `x`, `y`, `block`,
`metagrid_x`, `metagrid_y`, `row`, `column`, `diameter`,
`ch1_fg_median`, `ch1_fg_mean`, `ch1_fg_sd`, `ch1_bg_median`,
`ch1_bg_mean`, `ch1_bg_sd`, `ch1_perc_sd1`, `ch1_perc_sd2`,
`ch1_perc_sat`, `ch2_fg_median`, `ch2_fg_mean`, `ch2_fg_sd`,
`ch2_bg_median`, `ch2_bg_mean`, `ch2_bg_sd`, `ch2_perc_sd1`,
`ch2_perc_sd2`, `ch2_perc_sat`, `ratios_sd`, `rgn_ratio`, `rgn_r2`,
`fg_pixels`, `bg_pixels`, `flags`, `m_value`, `cv`) VALUES (?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
15:26:07,988 DEBUG sql:439 - UPDATE SQL for entity = rawdata_genepix:
UPDATE `RawDataGenePix` SET `version` = ?, `diameter` = ?,
`ch1_fg_median` = ?, `ch1_fg_mean` = ?, `ch1_fg_sd` = ?,
`ch1_bg_median` = ?, `ch1_bg_mean` = ?, `ch1_bg_sd` = ?, `ch1_perc_sd1`
= ?, `ch1_perc_sd2` = ?, `ch1_perc_sat` = ?, `ch2_fg_median` = ?,
`ch2_fg_mean` = ?, `ch2_fg_sd` = ?, `ch2_bg_median` = ?, `ch2_bg_mean`
= ?, `ch2_bg_sd` = ?, `ch2_perc_sd1` = ?, `ch2_perc_sd2` = ?,
`ch2_perc_sat` = ?, `ratios_sd` = ?, `rgn_ratio` = ?, `rgn_r2` = ?,
`fg_pixels` = ?, `bg_pixels` = ?, `flags` = ?, `m_value` = ?, `cv` = ?
WHERE `id` = ? AND `version` = ?
15:26:07,989 DEBUG sql:465 - DELETE SQL for entity = rawdata_genepix:
DELETE FROM `RawDataGenePix` WHERE `id` = ?
15:26:07,990 DEBUG sql:392 - INSERT SQL for entity =
rawdata_quantarraycy: INSERT INTO `RawDataQuantArrayCy` (`version`,
`rawbioassay_id`, `feature_id`, `reporter_id`, `position`, `x`, `y`,
`block`, `metagrid_x`, `metagrid_y`, `row`, `column`, `cy3_mean`,
`cy3_mean_bg`, `cy3_diameter`, `cy3_area`, `cy3_footprint`,
`cy3_circularity`, `cy3_uniformity`, `cy3_bg_uniformity`, `cy3_snr`,
`cy3_confidence`, `cy5_mean`, `cy5_mean_bg`, `cy5_diameter`,
`cy5_area`, `cy5_footprint`, `cy5_circularity`, `cy5_uniformity`,
`cy5_bg_uniformity`, `cy5_snr`, `cy5_confidence`, `ignore_filter`,
`cy3_ratio`, `cy3_percent`, `cy3_snr_filter`, `cy5_ratio`,
`cy5_percent`, `cy5_snr_filter`, `log_normalised`) VALUES (?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
15:26:07,991 DEBUG sql:439 - UPDATE SQL for entity =
rawdata_quantarraycy: UPDATE `RawDataQuantArrayCy` SET `version` = ?,
`cy3_mean` = ?, `cy3_mean_bg` = ?, `cy3_diameter` = ?, `cy3_area` = ?,
`cy3_footprint` = ?, `cy3_circularity` = ?, `cy3_uniformity` = ?,
`cy3_bg_uniformity` = ?, `cy3_snr` = ?, `cy3_confidence` = ?,
`cy5_mean` = ?, `cy5_mean_bg` = ?, `cy5_diameter` = ?, `cy5_area` = ?,
`cy5_footprint` = ?, `cy5_circularity` = ?, `cy5_uniformity` = ?,
`cy5_bg_uniformity` = ?, `cy5_snr` = ?, `cy5_confidence` = ?,
`ignore_filter` = ?, `cy3_ratio` = ?, `cy3_percent` = ?,
`cy3_snr_filter` = ?, `cy5_ratio` = ?, `cy5_percent` = ?,
`cy5_snr_filter` = ?, `log_normalised` = ? WHERE `id` = ? AND `version`
= ?
15:26:07,991 DEBUG sql:465 - DELETE SQL for entity =
rawdata_quantarraycy: DELETE FROM `RawDataQuantArrayCy` WHERE `id` = ?
15:26:07,992 DEBUG sql:392 - INSERT SQL for entity =
rawdata_spotfinder: INSERT INTO `RawDataSpotfinder` (`version`,
`rawbioassay_id`, `feature_id`, `reporter_id`, `position`, `x`, `y`,
`block`, `metagrid_x`, `metagrid_y`, `row`, `column`, `int_a`, `int_b`,
`mean_ratio`, `area`, `saturation`, `median_ratio`, `mode_ratio`,
`bg_a`, `bg_b`, `flag_a`, `flag_b`, `qc_a`, `qc_b`, `qc_total`, `flag`)
VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?)
15:26:07,993 DEBUG sql:439 - UPDATE SQL for entity =
rawdata_spotfinder: UPDATE `RawDataSpotfinder` SET `version` = ?,
`int_a` = ?, `int_b` = ?, `mean_ratio` = ?, `area` = ?, `saturation` =
?, `median_ratio` = ?, `mode_ratio` = ?, `bg_a` = ?, `bg_b` = ?,
`flag_a` = ?, `flag_b` = ?, `qc_a` = ?, `qc_b` = ?, `qc_total` = ?,
`flag` = ? WHERE `id` = ? AND `version` = ?
15:26:07,994 DEBUG sql:465 - DELETE SQL for entity =
rawdata_spotfinder: DELETE FROM `RawDataSpotfinder` WHERE `id` = ?
15:26:07,994 DEBUG sql:392 - INSERT SQL for entity = rawdata_aida:
INSERT INTO `RawDataAida` (`version`, `rawbioassay_id`, `feature_id`,
`reporter_id`, `position`, `x`, `y`, `block`, `metagrid_x`,
`metagrid_y`, `row`, `column`, `area`, `ch1_integral`, `ch1_mean`,
`ch1_median`, `ch1_bkg`, `ch1_sat`, `ch1_hom`, `ch1_quality`,
`ch2_integral`, `ch2_mean`, `ch2_median`, `ch2_bkg`, `ch2_sat`,
`ch2_hom`, `ch2_quality`) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?,
?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
15:26:07,995 DEBUG sql:439 - UPDATE SQL for entity = rawdata_aida:
UPDATE `RawDataAida` SET `version` = ?, `area` = ?, `ch1_integral` = ?,
`ch1_mean` = ?, `ch1_median` = ?, `ch1_bkg` = ?, `ch1_sat` = ?,
`ch1_hom` = ?, `ch1_quality` = ?, `ch2_integral` = ?, `ch2_mean` = ?,
`ch2_median` = ?, `ch2_bkg` = ?, `ch2_sat` = ?, `ch2_hom` = ?,
`ch2_quality` = ? WHERE `id` = ? AND `version` = ?
15:26:07,996 DEBUG sql:465 - DELETE SQL for entity = rawdata_aida:
DELETE FROM `RawDataAida` WHERE `id` = ?
java.lang.NullPointerException
at
net.sf.basedb.core.HibernateUtil.close(HibernateUtil.java:881)
at net.sf.basedb.core.Install.initDatabase(Install.java:605)
at net.sf.basedb.install.InitDB.main(InitDB.java:67)
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