[seanb80@n2150 Oly_Plat_Illu]$ /gscratch/srlab/programs/platanus_1.2.4/platanus gap_close -t 50 -o Oly_ -c Oly_Scaffold_scaffold.fa -IP1 /gscratch/srlab/data/OlyData/Illumina/151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.trimmed -IP2 /gscratch/srlab/data/OlyData/Illumina/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.trimmed -IP3 /gscratch/srlab/data/OlyData/Illumina/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.trimmed -IP4 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.trimmed -IP5 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.trimmed -IP6 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.trimmed -IP7 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.trimmed -IP8 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.trimmed -IP9 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.trimmed Platanus version: 1.2.4 /gscratch/srlab/programs/platanus_1.2.4/platanus gap_close -t 50 -o Oly_ -c Oly_Scaffold_scaffold.fa -IP1 /gscratch/srlab/data/OlyData/Illumina/151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/151114_I191_FCH3Y35BCXX_L1_wHAIPI023992-37_2.fq.trimmed -IP2 /gscratch/srlab/data/OlyData/Illumina/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/151114_I191_FCH3Y35BCXX_L2_wHAMPI023991-66_2.fq.trimmed -IP3 /gscratch/srlab/data/OlyData/Illumina/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/151118_I137_FCH3KNJBBXX_L5_wHAXPI023905-96_2.fq.trimmed -IP4 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCABDLAAPEI-62_2.fq.trimmed -IP5 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L3_WHOSTibkDCACDTAAPEI-75_2.fq.trimmed -IP6 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCABDLAAPEI-62_2.fq.trimmed -IP7 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L4_WHOSTibkDCACDTAAPEI-75_2.fq.trimmed -IP8 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L5_WHOSTibkDCAADWAAPEI-74_2.fq.trimmed -IP9 /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_1.fq.trimmed /gscratch/srlab/data/OlyData/Illumina/160103_I137_FCH3V5YBBXX_L6_WHOSTibkDCAADWAAPEI-74_2.fq.trimmed K=32, making hash table... [PAIR_LIBRARY 1] mapping reads... TOTAL_PAIR = 61248273 MAPPED_IN_SAME_CONTIG = 44184 (0.000721392) estimating insert-size... PEAK = 175 LOWER_LIMIT (permissible range to estimate AVE_INS)= 44 UPPER_LIMIT (permissible range to estimate AVE_INS)= 306 AVE_INS = 181 SD_INS = 47 mapping reads that cover small gaps... [PAIR_LIBRARY 2] mapping reads... TOTAL_PAIR = 58749332 MAPPED_IN_SAME_CONTIG = 16856 (0.000286914) estimating insert-size... PEAK = 181 LOWER_LIMIT (permissible range to estimate AVE_INS)= 45 UPPER_LIMIT (permissible range to estimate AVE_INS)= 317 AVE_INS = 185 SD_INS = 60 mapping reads that cover small gaps... [PAIR_LIBRARY 3] mapping reads... TOTAL_PAIR = 40482782 MAPPED_IN_SAME_CONTIG = 132251 (0.00326685) estimating insert-size... PEAK = 262 LOWER_LIMIT (permissible range to estimate AVE_INS)= 66 UPPER_LIMIT (permissible range to estimate AVE_INS)= 459 AVE_INS = 237 SD_INS = 67 mapping reads that cover small gaps... [PAIR_LIBRARY 4] mapping reads... TOTAL_PAIR = 76114318 MAPPED_IN_SAME_CONTIG = 3717 (4.88344e-05) estimating insert-size... PEAK = 237 LOWER_LIMIT (permissible range to estimate AVE_INS)= 59 UPPER_LIMIT (permissible range to estimate AVE_INS)= 415 AVE_INS = 121 SD_INS = 46 mapping reads that cover small gaps... [PAIR_LIBRARY 5] mapping reads... TOTAL_PAIR = 33193824 MAPPED_IN_SAME_CONTIG = 1076 (3.24157e-05) estimating insert-size... PEAK = 138 LOWER_LIMIT (permissible range to estimate AVE_INS)= 35 UPPER_LIMIT (permissible range to estimate AVE_INS)= 242 AVE_INS = 109 SD_INS = 44 mapping reads that cover small gaps... [PAIR_LIBRARY 6] mapping reads... TOTAL_PAIR = 74772608 MAPPED_IN_SAME_CONTIG = 3706 (4.95636e-05) estimating insert-size... PEAK = 109 LOWER_LIMIT (permissible range to estimate AVE_INS)= 27 UPPER_LIMIT (permissible range to estimate AVE_INS)= 191 AVE_INS = 99 SD_INS = 34 mapping reads that cover small gaps... [PAIR_LIBRARY 7] mapping reads... TOTAL_PAIR = 31504848 MAPPED_IN_SAME_CONTIG = 1086 (3.44709e-05) estimating insert-size... PEAK = 138 LOWER_LIMIT (permissible range to estimate AVE_INS)= 35 UPPER_LIMIT (permissible range to estimate AVE_INS)= 242 AVE_INS = 107 SD_INS = 43 mapping reads that cover small gaps... [PAIR_LIBRARY 8] mapping reads... TOTAL_PAIR = 81999890 MAPPED_IN_SAME_CONTIG = 5187 (6.32562e-05) estimating insert-size... PEAK = 107 LOWER_LIMIT (permissible range to estimate AVE_INS)= 27 UPPER_LIMIT (permissible range to estimate AVE_INS)= 187 AVE_INS = 100 SD_INS = 32 mapping reads that cover small gaps... [PAIR_LIBRARY 9] mapping reads... TOTAL_PAIR = 80404249 MAPPED_IN_SAME_CONTIG = 5233 (6.50836e-05) estimating insert-size... PEAK = 100 LOWER_LIMIT (permissible range to estimate AVE_INS)= 25 UPPER_LIMIT (permissible range to estimate AVE_INS)= 175 AVE_INS = 98 SD_INS = 30 mapping reads that cover small gaps... making hash table of gaps... making consensus sequences to close small gaps... NUM_GAP=1037 NUM_CLOSED_GAP=10 [PAIR_LIBRARY 1] saving reads covering gaps... loading reads covering gaps... assembling localized reads... NUM_GAPS = 1027 NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 25 NUM_CLOSED_GAPS_USING_DE_BRUIJN = 10 NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 14 [PAIR_LIBRARY 2] saving reads covering gaps... loading reads covering gaps... assembling localized reads... NUM_GAPS = 1003 NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 23 NUM_CLOSED_GAPS_USING_DE_BRUIJN = 2 NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 1 [PAIR_LIBRARY 3] saving reads covering gaps... loading reads covering gaps... assembling localized reads... NUM_GAPS = 1000 NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 23 NUM_CLOSED_GAPS_USING_DE_BRUIJN = 6 NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 4 [PAIR_LIBRARY 4] saving reads covering gaps... loading reads covering gaps... assembling localized reads... NUM_GAPS = 990 NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 23 NUM_CLOSED_GAPS_USING_DE_BRUIJN = 0 NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 0 [PAIR_LIBRARY 5] saving reads covering gaps... loading reads covering gaps... assembling localized reads... NUM_GAPS = 990 NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 18 NUM_CLOSED_GAPS_USING_DE_BRUIJN = 0 NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 0 [PAIR_LIBRARY 6] saving reads covering gaps... loading reads covering gaps... assembling localized reads... NUM_GAPS = 990 NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 21 NUM_CLOSED_GAPS_USING_DE_BRUIJN = 0 NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 0 [PAIR_LIBRARY 7] saving reads covering gaps... loading reads covering gaps... assembling localized reads... NUM_GAPS = 990 NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 18 NUM_CLOSED_GAPS_USING_DE_BRUIJN = 0 NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 0 [PAIR_LIBRARY 8] saving reads covering gaps... loading reads covering gaps... assembling localized reads... NUM_GAPS = 990 NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 23 NUM_CLOSED_GAPS_USING_DE_BRUIJN = 1 NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 0 [PAIR_LIBRARY 9] saving reads covering gaps... loading reads covering gaps... assembling localized reads... NUM_GAPS = 989 NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 23 NUM_CLOSED_GAPS_USING_DE_BRUIJN = 0 NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 0 [ALL LIBRARY] assembling localized reads... NUM_GAPS = 989 NUM_NOT_CLOSED_GAPS (too many reads are mapped comapering to coverage)= 37 NUM_CLOSED_GAPS_USING_DE_BRUIJN = 7 NUM_CLOSED_GAPS_USING_OVERLAP_LAYOUT_CONSENSUS = 7 TOTAL_NUM_CLOSED_GAPS = 62 gap_close completed!! #### PROCESS INFORMATION #### VmPeak: 14.569 GByte VmHWM: 3.247 GByte