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  1. variant_effect_predictor.pl -i test.vcf -o output.vcf --force_overwrite --database -format vcf -vcf
  2. 2015-06-03 17:05:04 - Starting...
  3. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 460, <GEN0> line 2.
  4. Use of uninitialized value in length at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 2.
  5. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 496, <GEN0> line 2.
  6. Use of uninitialized value in split at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 585, <GEN0> line 2.
  7. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 594, <GEN0> line 2.
  8. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 2.
  9. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 2.
  10. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 2.
  11. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2730, <GEN0> line 2.
  12. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2731, <GEN0> line 2.
  13.  
  14. WARNING: Start  or end -1 coordinate invalid on line 3
  15. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 460, <GEN0> line 3.
  16. Use of uninitialized value in length at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 3.
  17. Argument "Depths" isn't numeric in addition (+) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 3.
  18. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 496, <GEN0> line 3.
  19. Use of uninitialized value in split at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 585, <GEN0> line 3.
  20. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 594, <GEN0> line 3.
  21. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 3.
  22. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 3.
  23.  
  24. WARNING: Start Depths or end -1 coordinate invalid on line 5
  25. Argument "and" isn't numeric in addition (+) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 3.
  26.  
  27. WARNING: Start and or end 1 coordinate invalid on line 6
  28. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 460, <GEN0> line 4.
  29. Use of uninitialized value in length at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 4.
  30. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 496, <GEN0> line 4.
  31. Use of uninitialized value in split at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 585, <GEN0> line 4.
  32. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 594, <GEN0> line 4.
  33. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 4.
  34. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 4.
  35. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 4.
  36. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2730, <GEN0> line 4.
  37. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2731, <GEN0> line 4.
  38.  
  39. WARNING: Start  or end -1 coordinate invalid on line 8
  40. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 460, <GEN0> line 4.
  41. Use of uninitialized value in length at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 4.
  42. Argument "Depth">" isn't numeric in addition (+) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 4.
  43. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 496, <GEN0> line 4.
  44. Use of uninitialized value in split at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 585, <GEN0> line 4.
  45. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 594, <GEN0> line 4.
  46. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 4.
  47. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 4.
  48. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 4.
  49.  
  50. WARNING: Start Depth"> or end -1 coordinate invalid on line 9
  51. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 460, <GEN0> line 5.
  52. Use of uninitialized value in length at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 5.
  53. Argument "POS" isn't numeric in addition (+) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 5.
  54. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 496, <GEN0> line 5.
  55. Use of uninitialized value in split at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 585, <GEN0> line 5.
  56. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 594, <GEN0> line 5.
  57. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  58. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  59.  
  60. WARNING: Start POS or end -1 coordinate invalid on line 11
  61. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 460, <GEN0> line 5.
  62. Argument "ALT" isn't numeric in addition (+) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 5.
  63. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 496, <GEN0> line 5.
  64. Use of uninitialized value in split at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 585, <GEN0> line 5.
  65. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 594, <GEN0> line 5.
  66. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  67.  
  68. WARNING: Start ALT or end 4 coordinate invalid on line 12
  69. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 460, <GEN0> line 5.
  70. Use of uninitialized value in length at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 5.
  71. Argument "INFO" isn't numeric in addition (+) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 5.
  72. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 496, <GEN0> line 5.
  73. Use of uninitialized value in split at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 585, <GEN0> line 5.
  74. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 594, <GEN0> line 5.
  75. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  76. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  77.  
  78. WARNING: Start INFO or end inf coordinate invalid on line 13
  79. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 460, <GEN0> line 5.
  80. Use of uninitialized value in length at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 5.
  81. Argument "TUMO" isn't numeric in addition (+) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 5.
  82. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 496, <GEN0> line 5.
  83. Use of uninitialized value in split at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 585, <GEN0> line 5.
  84. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 594, <GEN0> line 5.
  85. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  86. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  87. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  88.  
  89. WARNING: Start TUMO or end -1 coordinate invalid on line 14
  90. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 460, <GEN0> line 5.
  91. Use of uninitialized value in length at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 5.
  92. Argument "NO" isn't numeric in addition (+) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 5.
  93. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 496, <GEN0> line 5.
  94. Use of uninitialized value in split at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 585, <GEN0> line 5.
  95. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 594, <GEN0> line 5.
  96. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  97. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  98. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  99.  
  100. WARNING: Start NO or end -1 coordinate invalid on line 15
  101. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 460, <GEN0> line 5.
  102. Use of uninitialized value in length at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 493, <GEN0> line 5.
  103. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 496, <GEN0> line 5.
  104. Use of uninitialized value in split at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 585, <GEN0> line 5.
  105. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 594, <GEN0> line 5.
  106. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  107. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  108. Use of uninitialized value in string eq at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 638, <GEN0> line 5.
  109. Use of uninitialized value in pattern match (m//) at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2730, <GEN0> line 5.
  110. Use of uninitialized value in concatenation (.) or string at /share/apps/src/ensembl_79-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 2731, <GEN0> line 5.
  111.  
  112. WARNING: Start  or end -1 coordinate invalid on line 16
  113. 2015-06-03 17:05:04 - Read 7 variants into buffer
  114. 2015-06-03 17:05:04 - Reading transcript data from cache and/or database
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