flat NGS plot

[tsharma017]

Hi,
Could you help me figure out why our ngsplot is flat?
This is my code
outputname_TSS=${outputdir}/${output_name}.TSS
outputname_TES=${outputdir}/${output_name}.TES

echo "ngs.plot.r -G hg19 -R bed -C $sample_config -O $outputname_genebody -T $output_name -L 5000"
echo "ngs.plot.r -G hg19 -R bed -C $sample_config -O $outputname_TSS -T $output_name -L 3000"
echo "ngs.plot.r -G hg19 -R bed -C $sample_config -O $outputname_TES -T $output_name -L 3000"

ngs.plot.r -G hg19 -R bed -C $sample_config -O $outputname_genebody -T $output_name -L 5000
ngs.plot.r -G hg19 -R bed -C $sample_config -O $outputname_TSS -T $output_name -L 3000
ngs.plot.r -G hg19 -R bed -C $sample_config -O $outputname_TES -T $output_name -L 3000

ngs.plot.r -G hg19 -R bed -C $sample_config -E /projects/academic/remiadel/tej/RT2436_ATAC_Results/bwa/merged_library/diff_Peaks_LNCAP.2_inTSS.bed -O $outputname_genebody -T $output_name -L 5000
~
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~ This is my sample of my .bam file
NB501975:226:HNYGVBGXM:3:22604:20467:2886 99 1 13796 22 76M = 13873 153 CATTTGTCCTGCCCACCTTCTTAGAAGCGAGACGGAGCAGACCCATCTGCTACTGCCCTTTCTATAATAACTGAAG AAAAAEAEEEEEEE6EEEEAEEEEEEEEA//EEEEE6EEEEE6EEEAEAA<AEEEE/A/EEE/EEEEEEEEA/EEE MC:Z:76M MD:Z:72A3 PG:Z:MarkDuplicates RG:Z:LuCaP167_Control_REP1_T1 NM:i:1 AS:i:72 XS:i:72
NB501975:226:HNYGVBGXM:3:22604:20467:2886 147 1 13873 22 76M = 13796 -153 TAGCTGCCCTGGACTATTCACCCCCTAGTCTCAATTTAAGAAGATCCCCATGGTCACAGGGCCCCTGCCTGGGGGC AE/EEE<EEAEEEEAA6EEAEEEEEEEEEEEEEAEEEE/EEEEE/EEEEE/EE/AEEEEEEEEEEEEEEEEAAA6A MC:Z:76M MD:Z:53C22 PG:Z:MarkDuplicates RG:Z:LuCaP167_Control_REP1_T1 NM:i:1 AS:i:71 XS:i:71
NB501975:226:HNYGVBGXM:4:22609:21700:11750 163 1 16431 22 76M = 16533 177 GTCCAGAGCTCTACAGTTTGAAAACCACTATTTTATGAACCAAGTAGAACAAGATATTTGAAATGGAAACTATTCA AAAAA6EE6EAEEEEEAEAEEEE/EEEEEEEEEEAEEEAEAEEEEEEEEEEEEEEEEE<<EE/EA/E//EEEEEEE MC:Z:75M MD:Z:76 PG:Z:MarkDuplicates RG:Z:LuCaP167_Control_REP1_T1 NM:i:0 AS:i:76 XS:i:71
NB501975:226:HNYGVBGXM:4:22609:21700:11750 83 1 16533 22 75M = 16431 -177 ATAAACCCACAGAAAATCCACCCGAGTGCACTGAGCACAGCAGAAATCAGGTGGCCTCAAAGAGCTGCTCCCACC EA<EAEEEAEE/EEEEEE//EEEEEE<AE<<EEA//6A</EA/EEEEE/EE/EAEE/EEEE6EEEE/EEEAAAAA MC:Z:76M MD:Z:1C36G0C35 PG:Z:MarkDuplicates RG:Z:LuCaP167_Control_REP1_T1 NM:i:3 AS:i:63 XS:i:63
NB501975:226:HNYGVBGXM:2:23301:12240:7365 99 1 48155 49 76M = 48159 80 GACCAAACATGTTCACATCGTGTGCGTTCCATTTTCCTAATGGAAAGTGGGGGGAAGTGATTTTCTGTCCTCATAT AAAAAEEEAEEEE//EEE/EEE/E/AEE/EE/AEE/EAEEE/EEE/E/66/EAEEEAEEAE<EE/A6AE//6AEE< XA:Z:19,+89766,76M,1;15,-102482917,76M,1; MC:Z:76M MD:Z:76 PG:Z:MarkDuplicates RG:Z:LuCaP167_Control_REP1_T1 NM:i:0 AS:i:76 XS:i:71
NB501975:226:HNYGVBGXM:2:23301:12240:7365 147 1 48159 49 76M = 48155 -80 AAACATGTTCACATCGTGTGCGTTCCATTTTCCTAATGGAAAGTGGGGGGAAGGGATTTTCTGTCCTCATATAGAG A/</EEEA///E<E/A/EAEA/A<<AEEEE/EAEAEEEEEE/EAEEEEEEEEE/EE/EEEEEE/EEEEEEEAAAAA XA:Z:19,-89770,76M,2;15,+102482913,76M,2; MC:Z:76M MD:Z:53T22 PG:Z:MarkDuplicates RG:Z:LuCaP167_Control_REP1_T1 NM:i:1 AS:i:71 XS:i:66
NB501975:226:HNYGVBGXM:1:11106:24315:15796 163 1 56630 25 75M = 56648 93 AACCAACACTTCTTATTCTGCTGCTATTCTAGAGAAAATCATTTTCCTCATTTCTGAACAAGAGAAAATGAAATA AAAA/EEEEEEEEEEEEEEEAEEEEEEE/EEEEE/EE/EEEEEAEEA6EEEAE</EE/<AEEEE/<E/EAAAEEE XA:Z:15,-102474479,75M,2;19,+98205,75M,2; MC:Z:75M MD:Z:25G49 PG:Z:MarkDuplicates RG:Z:LuCaP167_Control_REP1_T1 NM:i:1 AS:i:70 XS:i:65
NB501975:226:HNYGVBGXM:1:11106:24315:15796 83 1 56648 25 75M = 56630 -93 TGCTGCTATTCTAGAGAAAATCATTTTCCTCATTTCTGAACAAGAGAAAATGAAATACAGCTCTAAACAAATGCC A<AE/EA/EEEEEEEE/EAEEEEEEEAEEEA/EEEEEEEEEEEEEE/EE/EEAAEAEEEE/EEAEEEA/EAAAAA XA:Z:19,-98223,75M,1;15,+102474461,75M,1; MC:Z:75M MD:Z:7G67 PG:Z:MarkDuplicates RG:Z:LuCaP167_Control_REP1_T1 NM:i:1 AS:i:70 XS:i:70
NB501975:226:HNYGVBGXM:4:22502:11753:10042 163 1 58218 25 76M = 58374 230 ATTCTGAAATGGAACTGTTCCAGGTTGAAGAAATAAGAAAGGGAATTGGGAAGAGCAATGCCCAGTGAAAAAGAAG AAAAAEEEEEEEEEEEEEEEEEAEEEEEEEEE6E/AA/EEEEAE//EAEEEEE/EEEEEEEEEEE/A//AAEEA<E XA:Z:19,+99794,76M,0;15,-102472889,76M,0; MC:Z:74M MD:Z:76 PG:Z:MarkDuplicates RG:Z:LuCaP167_Control_REP1_T1 NM:i:0 AS:i:76 XS:i:76
NB501975:226:HNYGVBGXM:4:22502:11753:10042 83 1 58374 25 74M = 58218 -230 GTTAGAGTGATCCTGTCAAACATATATGCTTCTAGATTTTTTTAAAGACTGTTTCTACTAAGAAAGCATAGACC EE<EAAEAAEEEEEE/EEEEEEAE/AAEEEEAEEEEAEAAEE6EEEEEEEEAEEE6EE/EEEEE6EEEEAAAAA XA:Z:15,+102472735,74M,1;19,-99950,74M,1; MC:Z:76M MD:Z:74 PG:Z:MarkDuplicates RG:Z:LuCaP16

And this is a sample of my .bed file
1 169853073 169893959 SCYL3 -
1 169795039 169854080 C1orf112 +
1 27612063 27635185 FGR -
1 196651877 196747504 CFH +
1 24357004 24413725 STPG1 -
1 24415801 24472976 NIPAL3 +
1 33007985 33036883 AK2 -
1 23019447 23083689 KDM1A +
1 54784550 54801198 TTC22 -
1 112523513 112619141 ST7L -
1 169722639 169734079 SELE -
1 6634169 6701816 DNAJC11 -
1 171090904 171117819 FMO3 +
1 23506437 23531233 E2F2 -
1 209583713 209613939 CAMK1G +
1 1702378 1724357 CDK11A -
1 1751231 1778790 NADK -
1 114716915 114757984 CSDE1 -
1 18630845 18748866 PAX7 +
1 11026522 11047239 MASP2 -
1 27725978 27763122 FAM76A +
1 209756052 209782310 TRAF3IP3 +
1 231338292 231355023 SPRTN +
1 171781659 171797716 EEF1AKNMT +
1 41027201 41242116 SCMH1 -
1 171248498 171285978 FMO1 +
Any help will be really appreciated.

Thanks,

Tshar017