no output from ONCOCNV_getCounts.pl

[ramakrishnas]

Hi,

since the shell script is not working I started running the commands individually. I noticed that tjere is no output file from ONCOCNV_getCounts.pl couldn't figure out what the error is. could advice me if this is due to the overlapping regions in the bed file. see below for the complete output on the terminal

Thanks
Ram
perl ~/biotools/ONCOCNV-6.9/src/ONCOCNV_getCounts.pl getControlStats -m Ampli -b bedfiles/ecmp_iWG_IAD166152_1.20181012.designed.bed -c bamfiles/N103_C01_NA12787cellline_S5.bam, bamfiles/N023_A6_LRS_1_092711_S4.bam -o Control.stats.txt
number of targeted regions: 6521
These two regions overlap by more than 75%: chr7 140481362 - 140481481 and 140481350 - 140481469
merged into BRAF_8.19268_1.212400.BRAF_8.19268_1.7277: chr7:140481350-140481481
These two regions overlap by more than 75%: chr7 128851476 - 128851602 and 128851509 - 128851617
merged into CHP2_SMO_5_1.91226.CHP2_SMO_5_1.92038: chr7:128851476-128851617
These two regions overlap by more than 75%: chr22 29091675 - 29091804 and 29091658 - 29091786
merged into SP_130.44364_1.226729.SP_130.44364_1.82460: chr22:29091658-29091804
These two regions overlap by more than 75%: chr19 41737069 - 41737200 and 41737086 - 41737215
merged into AXL_6.17481_1.352.AXL_6.17481_1.36514: chr19:41737069-41737215
These two regions overlap by more than 75%: chr19 11172374 - 11172470 and 11172397 - 11172524
merged into SMARCA4_35.28997_1.47562.SMARCA4_35.28997_1.98537: chr19:11172374-11172524
These two regions overlap by more than 75%: chr19 52716249 - 52716350 and 52716210 - 52716333
merged into SP_108.56083_1.148366.SP_108.56083_1.216597: chr19:52716210-52716350
These two regions overlap by more than 75%: chr19 4047877 - 4048018 and 4047910 - 4048049
merged into ZBTB7A_1.67873.ZBTB7A_1.81922: chr19:4047877-4048049
These two regions overlap by more than 75%: chr8 128752974 - 128753086 and 128753005 - 128753110
merged into MYC_3.179895_1.146699.MYC_3.179895_1.193715: chr8:128752974-128753110
These two regions overlap by more than 75%: chr1 11190805 - 11190931 and 11190789 - 11190899
merged into SP_8.22255_1.172662.SP_8.22255_1.60091: chr1:11190789-11190931
These two regions overlap by more than 75%: chr11 108216397 - 108216514 and 108216380 - 108216495
merged into ATM_4.34438_1.116103.ATM_4.34438_1.83519: chr11:108216380-108216514
These two regions overlap by more than 75%: chr17 56439828 - 56439952 and 56439850 - 56439975
merged into RNF43_5.17250_1.32609.RNF43_5.17250_1.80351: chr17:56439828-56439975
These two regions overlap by more than 75%: chr17 12011122 - 12011207 and 12011142 - 12011263
merged into SP_83.21899_1.100027.SP_83.21899_1.54849: chr17:12011122-12011263
These two regions overlap by more than 75%: chr16 89842097 - 89842208 and 89842117 - 89842235
merged into FANCA_23.53959_1.124713.FANCA_23.53959_1.8864: chr16:89842097-89842235
These two regions overlap by more than 75%: chr16 89807127 - 89807236 and 89807083 - 89807222
merged into FANCA_6.33590_1.121771.FANCA_6.33590_1.28197: chr16:89807083-89807236
These two regions overlap by more than 75%: chr3 37088968 - 37089093 and 37088982 - 37089106
merged into MLH1_16.37834_1.241717.MLH1_16.37834_1.77471: chr3:37088968-37089106
These two regions overlap by more than 75%: chr3 38181918 - 38182044 and 38181902 - 38182018
merged into SP_133.35672_1.195191.SP_133.35672_1.66065: chr3:38181902-38182044
These two regions overlap by more than 75%: chr15 66774080 - 66774199 and 66774093 - 66774211
merged into SP_75.51183_1.106366.SP_75.51183_1.212778: chr15:66774080-66774211
These two regions overlap by more than 75%: chrX 76872074 - 76872145 and 76872015 - 76872133
merged into ATRX_14.12742_1.29312.ATRX_14.12742_1.8946: chrX:76872015-76872145
These two regions overlap by more than 75%: chrX 76845225 - 76845342 and 76845238 - 76845356
merged into ATRX_9.52579_1.32513.ATRX_9.52579_1.37867: chrX:76845225-76845356
These two regions overlap by more than 75%: chrX 47426026 - 47426157 and 47426002 - 47426126
merged into SP_217.19864_1.57866.SP_217.19864_1.83905: chrX:47426002-47426157
These two regions overlap by more than 75%: chr4 84384658 - 84384779 and 84384638 - 84384758
merged into FAM175A_2.126304.FAM175A_2.23466: chr4:84384638-84384779
These two regions overlap by more than 75%: chr4 55972822 - 55972946 and 55972807 - 55972898
merged into SP_164.30020_1.130391.SP_164.30020_1.33497: chr4:55972807-55972946
These two regions overlap by more than 75%: chr9 135785898 - 135786025 and 135785878 - 135786003
merged into OCP1_TSC1_34_1.180877.OCP1_TSC1_34_1.74209: chr9:135785878-135786025
These two regions overlap by more than 75%: chr13 48953705 - 48953770 and 48953628 - 48953758
merged into CHP2_RB1_5_1.194495.OCP1_RB1_24_1.50011: chr13:48953628-48953770
These two regions overlap by more than 75%: chr10 89624190 - 89624321 and 89624219 - 89624354
merged into CHP2_PTEN_1_1.101892.CHP2_PTEN_1_1.138223: chr10:89624190-89624354
These two regions overlap by more than 75%: chr10 43615517 - 43615607 and 43615456 - 43615591
merged into CHP2_RET_4_1.138016.CHP2_RET_4_1.5615: chr10:43615456-43615607
These two regions overlap by more than 75%: chr5 67591990 - 67592115 and 67591973 - 67592088
merged into OCP1_PIK3R1_35_1.179919.OCP1_PIK3R1_35_1.186198: chr5:67591973-67592115

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--Coordinates are read--

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Total target length: 719043