Closed htmonkey closed 1 year ago
Newly, I got twice the same error during the final annotation. Both annotated peak tables are empty. I am happy to share the original data.
2022-05-18|12:56:11|DEBUG: Rscript /pylcmsprocessing/Rscript/annotating_mixed_method.R "/output/datamatrices/datamatrix_153a1ccc4c1afdb4ac706698c52622d6.csv" "/output/temp_processing_db.sqlite" "/output/datamatrices/annotated_peaktable_153a1ccc4c1afdb4ac706698c52622d6_full.csv" "/output/datamatrices/annotated_peaktable_153a1ccc4c1afdb4ac706698c52622d6_reduced.csv" 16 "/pylcmsprocessing/data/xcms_raw_model.RData" "/output/temp/adducts.csv" "/output/temp/main_adducts.csv" "positive" 15.0 0.01 10 2.0 "/pylcmsprocessing/Rscript/cliques_matching.cpp" |======================================================================| 100%
No traceback available 2: createNetworkMultifiles(dm[sel_idx, , drop = FALSE], raw_files, opened_raw_files, match_files, size_batch = size_batch, ref_xcms = ref_xcms, cosFilter = cosFilter, bpp = bpp) 1: groupFeatures(dm, val_int_var, raw_files, opened_raw_files, match_files, adducts, main_adducts, ionization_mode = POLARITY, ppm = PPM, dmz = DMZ, size_batch = NUM_CORES, cut_size = NUM_BY_BATCH, cosFilter = 0.6, ref_xcms = PATH_MODEL, path_matching = PATH_MATCHING, bbp = bpp) 3: seq.default(1, length(annot), by = num_line) 2: seq(1, length(annot), by = num_line) 1: buildDataMatrixSimplified(dm, annot, PATH_OUTPUT_SIMPLE) 2022-05-18|12:56:49|DEBUG: stderr:Processing batch 1 Variables: 1-5001 current cliques size is 10000 Error in if (nrow(alle) == 0) next : argument is of length zero Calls: groupFeatures -> createNetworkMultifiles Error in seq.default(1, length(annot), by = num_line) : object 'annot' not found Calls: buildDataMatrixSimplified -> seq -> seq.default Error in seq.default(1, length(annot), by = num_line) : object 'annot' not found Calls: buildDataMatrixFull -> seq -> seq.default
Newly, I got twice the same error during the final annotation. Both annotated peak tables are empty. I am happy to share the original data.
2022-05-18|12:56:11|DEBUG: Rscript /pylcmsprocessing/Rscript/annotating_mixed_method.R "/output/datamatrices/datamatrix_153a1ccc4c1afdb4ac706698c52622d6.csv" "/output/temp_processing_db.sqlite" "/output/datamatrices/annotated_peaktable_153a1ccc4c1afdb4ac706698c52622d6_full.csv" "/output/datamatrices/annotated_peaktable_153a1ccc4c1afdb4ac706698c52622d6_reduced.csv" 16 "/pylcmsprocessing/data/xcms_raw_model.RData" "/output/temp/adducts.csv" "/output/temp/main_adducts.csv" "positive" 15.0 0.01 10 2.0 "/pylcmsprocessing/Rscript/cliques_matching.cpp" |======================================================================| 100%
No traceback available 2: createNetworkMultifiles(dm[sel_idx, , drop = FALSE], raw_files, opened_raw_files, match_files, size_batch = size_batch, ref_xcms = ref_xcms, cosFilter = cosFilter, bpp = bpp) 1: groupFeatures(dm, val_int_var, raw_files, opened_raw_files, match_files, adducts, main_adducts, ionization_mode = POLARITY, ppm = PPM, dmz = DMZ, size_batch = NUM_CORES, cut_size = NUM_BY_BATCH, cosFilter = 0.6, ref_xcms = PATH_MODEL, path_matching = PATH_MATCHING, bbp = bpp) 3: seq.default(1, length(annot), by = num_line) 2: seq(1, length(annot), by = num_line) 1: buildDataMatrixSimplified(dm, annot, PATH_OUTPUT_SIMPLE) 2022-05-18|12:56:49|DEBUG: stderr:Processing batch 1 Variables: 1-5001 current cliques size is 10000 Error in if (nrow(alle) == 0) next : argument is of length zero Calls: groupFeatures -> createNetworkMultifiles Error in seq.default(1, length(annot), by = num_line) : object 'annot' not found Calls: buildDataMatrixSimplified -> seq -> seq.default Error in seq.default(1, length(annot), by = num_line) : object 'annot' not found Calls: buildDataMatrixFull -> seq -> seq.default