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  1. darkwing@FOWL:~$ cat firasproject/primary/typescript.txt
  2. Script started on Mon 02 Dec 2013 02:28:09 PM EST
  3. darkwing@FOWL:~/firasproject/primary$ date
  4. Mon Dec 2 14:28:12 EST 2013
  5. darkwing@FOWL:~/firasproject/primary$ ls -a
  6. .
  7. ..
  8. 1000Gphase1randomcaucasianexomebams
  9. 12_parental_dedup_realigned_recal_reduced_reads.bai
  10. 12_parental_dedup_realigned_recal_reduced_reads.bam
  11. 12_TMZ_dedup_realigned_recal_reduced_reads.bai
  12. 12_TMZ_dedup_realigned_recal_reduced_reads.bam
  13. 22_parental_dedup_realigned_recal_reduced_reads.bai
  14. 22_parental_dedup_realigned_recal_reduced_reads.bam
  15. 22_TMZ_dedup_realigned_recal_reduced_reads.bai
  16. 22_TMZ_dedup_realigned_recal_reduced_reads.bam
  17. 39_parental_dedup_realigned_recal_reduced_reads.bai
  18. 39_parental_dedup_realigned_recal_reduced_reads.bam
  19. 39_TMZ_dedup_realigned_recal_reduced_reads.bai
  20. 39_TMZ_dedup_realigned_recal_reduced_reads.bam
  21. 59_parental_dedup_realigned_recal_reduced_reads.bai
  22. 59_parental_dedup_realigned_recal_reduced_reads.bam
  23. 59_TMZ_dedup_realigned_recal_reduced_reads.bai
  24. 59_TMZ_dedup_realigned_recal_reduced_reads.bam
  25. examplecommand
  26. fastafiles
  27. pertinentfaqs
  28. phase1.exome.alignment.index
  29. post_recal_data.table
  30. recal_data.table
  31. recalibration_plots.pdf
  32. rginfo
  33. Sakira_06062013.odt
  34. Sakira_phred33_06112013.odt
  35. screenlog.0
  36. script
  37. .target_intervals.list
  38. teamviewerscript
  39. tmp
  40. typescript
  41. Untitled Document
  42. darkwing@FOWL:~/firasproject/primary$ ls 1000Gphase1randomcaucasianexomebams/
  43. HG00103.mapped.illumina.mosaik.GBR.exome.20110411.bam
  44. HG00103.mapped.illumina.mosaik.GBR.exome.20110411.bam.bai
  45. HG00114.mapped.illumina.mosaik.GBR.exome.20110411.bam
  46. HG00114.mapped.illumina.mosaik.GBR.exome.20110411.bam.bai
  47. HG00158.mapped.illumina.mosaik.GBR.exome.20110411.bam
  48. HG00158.mapped.illumina.mosaik.GBR.exome.20110411.bam.bai
  49. HG00181.mapped.illumina.mosaik.FIN.exome.20110521.bam
  50. HG00181.mapped.illumina.mosaik.FIN.exome.20110521.bam.bai
  51. HG00233.mapped.illumina.mosaik.GBR.exome.20110411.bam
  52. HG00233.mapped.illumina.mosaik.GBR.exome.20110411.bam.bai
  53. HG00238.mapped.illumina.mosaik.GBR.exome.20110411.bam
  54. HG00238.mapped.illumina.mosaik.GBR.exome.20110411.bam.bai
  55. HG00240.mapped.illumina.mosaik.GBR.exome.20110411.bam
  56. HG00252.mapped.illumina.mosaik.GBR.exome.20110411.bam
  57. HG00252.mapped.illumina.mosaik.GBR.exome.20110411.bam.bai
  58. HG00258.mapped.illumina.mosaik.GBR.exome.20110411.bam
  59. HG00258.mapped.illumina.mosaik.GBR.exome.20110411.bam.bai
  60. HG00261.mapped.illumina.mosaik.GBR.exome.20110411.bam
  61. HG00261.mapped.illumina.mosaik.GBR.exome.20110411.bam.bai
  62. HG00276.mapped.illumina.mosaik.FIN.exome.20110411.bam
  63. HG00276.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  64. HG00282.mapped.illumina.mosaik.FIN.exome.20110411.bam
  65. HG00282.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  66. HG00312.mapped.illumina.mosaik.FIN.exome.20110411.bam
  67. HG00312.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  68. HG00313.mapped.illumina.mosaik.FIN.exome.20110411.bam
  69. HG00313.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  70. HG00318.mapped.illumina.mosaik.FIN.exome.20110411.bam
  71. HG00318.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  72. HG00331.mapped.illumina.mosaik.FIN.exome.20110411.bam
  73. HG00331.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  74. HG00334.mapped.illumina.mosaik.FIN.exome.20110411.bam
  75. HG00334.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  76. HG00346.mapped.illumina.mosaik.FIN.exome.20110411.bam
  77. HG00346.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  78. HG00353.mapped.illumina.mosaik.FIN.exome.20110411.bam
  79. HG00353.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  80. HG00371.mapped.illumina.mosaik.FIN.exome.20110411.bam
  81. HG00371.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  82. HG00377.mapped.illumina.mosaik.FIN.exome.20110411.bam
  83. HG00377.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  84. HG00379.mapped.illumina.mosaik.FIN.exome.20110411.bam
  85. HG00379.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  86. HG00380.mapped.illumina.mosaik.FIN.exome.20110411.bam
  87. HG00380.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  88. HG00383.mapped.illumina.mosaik.FIN.exome.20110411.bam
  89. HG00383.mapped.illumina.mosaik.FIN.exome.20110411.bam.bai
  90. HG01334.mapped.illumina.mosaik.GBR.exome.20110411.bam
  91. HG01334.mapped.illumina.mosaik.GBR.exome.20110411.bam.bai
  92. NA06984.mapped.illumina.mosaik.CEU.exome.20110521.bam
  93. NA06984.mapped.illumina.mosaik.CEU.exome.20110521.bam.bai
  94. NA06989.mapped.illumina.mosaik.CEU.exome.20110411.bam
  95. NA06989.mapped.illumina.mosaik.CEU.exome.20110411.bam.bai
  96. NA11840.mapped.illumina.mosaik.CEU.exome.20110411.bam
  97. NA11840.mapped.illumina.mosaik.CEU.exome.20110411.bam.bai
  98. NA12283.mapped.illumina.mosaik.CEU.exome.20110411.bam
  99. NA12283.mapped.illumina.mosaik.CEU.exome.20110411.bam.bai
  100. NA12340.mapped.illumina.mosaik.CEU.exome.20110521.bam
  101. NA12340.mapped.illumina.mosaik.CEU.exome.20110521.bam.bai
  102. NA12717.mapped.illumina.mosaik.CEU.exome.20110411.bam
  103. NA12717.mapped.illumina.mosaik.CEU.exome.20110411.bam.bai
  104. NA12750.mapped.illumina.mosaik.CEU.exome.20110411.bam
  105. NA12750.mapped.illumina.mosaik.CEU.exome.20110411.bam.bai
  106. NA12760.mapped.illumina.mosaik.CEU.exome.20110411.bam
  107. NA12760.mapped.illumina.mosaik.CEU.exome.20110411.bam.bai
  108. NA12761.mapped.illumina.mosaik.CEU.exome.20110411.bam
  109. NA12761.mapped.illumina.mosaik.CEU.exome.20110411.bam.bai
  110. NA12777.mapped.illumina.mosaik.CEU.exome.20110521.bam
  111. NA12777.mapped.illumina.mosaik.CEU.exome.20110521.bam.bai
  112. NA12830.mapped.illumina.mosaik.CEU.exome.20110411.bam
  113. NA12830.mapped.illumina.mosaik.CEU.exome.20110411.bam.bai
  114. NA12889.mapped.illumina.mosaik.CEU.exome.20110411.bam
  115. NA12889.mapped.illumina.mosaik.CEU.exome.20110411.bam.bai
  116. NA12891.mapped.illumina.mosaik.CEU.exome.20110411.bam
  117. NA12891.mapped.illumina.mosaik.CEU.exome.20110411.bam.bai
  118. NA20543.mapped.illumina.mosaik.TSI.exome.20110521.bam
  119. NA20543.mapped.illumina.mosaik.TSI.exome.20110521.bam.bai
  120. NA20581.mapped.illumina.mosaik.TSI.exome.20110521.bam
  121. NA20581.mapped.illumina.mosaik.TSI.exome.20110521.bam.bai
  122. NA20769.mapped.illumina.mosaik.TSI.exome.20110411.bam
  123. NA20769.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  124. NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bam
  125. NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  126. NA20774.mapped.illumina.mosaik.TSI.exome.20110411.bam
  127. NA20774.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  128. NA20775.mapped.illumina.mosaik.TSI.exome.20110411.bam
  129. NA20775.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  130. NA20778.mapped.illumina.mosaik.TSI.exome.20110411.bam
  131. NA20778.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  132. NA20785.mapped.illumina.mosaik.TSI.exome.20110411.bam
  133. NA20785.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  134. NA20796.mapped.illumina.mosaik.TSI.exome.20110411.bam
  135. NA20796.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  136. NA20800.mapped.illumina.mosaik.TSI.exome.20110411.bam
  137. NA20800.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  138. NA20801.mapped.illumina.mosaik.TSI.exome.20110411.bam
  139. NA20801.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  140. NA20812.mapped.illumina.mosaik.TSI.exome.20110411.bam
  141. NA20812.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  142. NA20826.mapped.illumina.mosaik.TSI.exome.20110411.bam
  143. NA20826.mapped.illumina.mosaik.TSI.exome.20110411.bam.bai
  144. darkwing@FOWL:~/firasproject/primary$ cd 1000Gphase1randomcaucasianexomebams/
  145. darkwing@FOWL:~/firasproject/primary/1000Gphase1randomcaucasianexomebams$ for i in *.bam.bai; do mv $i `basename $i .bam.bai`.bai; done
  146. darkwing@FOWL:~/firasproject/primary/1000Gphase1randomcaucasianexomebams$ ls
  147. HG00103.mapped.illumina.mosaik.GBR.exome.20110411.bai
  148. HG00103.mapped.illumina.mosaik.GBR.exome.20110411.bam
  149. HG00114.mapped.illumina.mosaik.GBR.exome.20110411.bai
  150. HG00114.mapped.illumina.mosaik.GBR.exome.20110411.bam
  151. HG00158.mapped.illumina.mosaik.GBR.exome.20110411.bai
  152. HG00158.mapped.illumina.mosaik.GBR.exome.20110411.bam
  153. HG00181.mapped.illumina.mosaik.FIN.exome.20110521.bai
  154. HG00181.mapped.illumina.mosaik.FIN.exome.20110521.bam
  155. HG00233.mapped.illumina.mosaik.GBR.exome.20110411.bai
  156. HG00233.mapped.illumina.mosaik.GBR.exome.20110411.bam
  157. HG00238.mapped.illumina.mosaik.GBR.exome.20110411.bai
  158. HG00238.mapped.illumina.mosaik.GBR.exome.20110411.bam
  159. HG00240.mapped.illumina.mosaik.GBR.exome.20110411.bam
  160. HG00252.mapped.illumina.mosaik.GBR.exome.20110411.bai
  161. HG00252.mapped.illumina.mosaik.GBR.exome.20110411.bam
  162. HG00258.mapped.illumina.mosaik.GBR.exome.20110411.bai
  163. HG00258.mapped.illumina.mosaik.GBR.exome.20110411.bam
  164. HG00261.mapped.illumina.mosaik.GBR.exome.20110411.bai
  165. HG00261.mapped.illumina.mosaik.GBR.exome.20110411.bam
  166. HG00276.mapped.illumina.mosaik.FIN.exome.20110411.bai
  167. HG00276.mapped.illumina.mosaik.FIN.exome.20110411.bam
  168. HG00282.mapped.illumina.mosaik.FIN.exome.20110411.bai
  169. HG00282.mapped.illumina.mosaik.FIN.exome.20110411.bam
  170. HG00312.mapped.illumina.mosaik.FIN.exome.20110411.bai
  171. HG00312.mapped.illumina.mosaik.FIN.exome.20110411.bam
  172. HG00313.mapped.illumina.mosaik.FIN.exome.20110411.bai
  173. HG00313.mapped.illumina.mosaik.FIN.exome.20110411.bam
  174. HG00318.mapped.illumina.mosaik.FIN.exome.20110411.bai
  175. HG00318.mapped.illumina.mosaik.FIN.exome.20110411.bam
  176. HG00331.mapped.illumina.mosaik.FIN.exome.20110411.bai
  177. HG00331.mapped.illumina.mosaik.FIN.exome.20110411.bam
  178. HG00334.mapped.illumina.mosaik.FIN.exome.20110411.bai
  179. HG00334.mapped.illumina.mosaik.FIN.exome.20110411.bam
  180. HG00346.mapped.illumina.mosaik.FIN.exome.20110411.bai
  181. HG00346.mapped.illumina.mosaik.FIN.exome.20110411.bam
  182. HG00353.mapped.illumina.mosaik.FIN.exome.20110411.bai
  183. HG00353.mapped.illumina.mosaik.FIN.exome.20110411.bam
  184. HG00371.mapped.illumina.mosaik.FIN.exome.20110411.bai
  185. HG00371.mapped.illumina.mosaik.FIN.exome.20110411.bam
  186. HG00377.mapped.illumina.mosaik.FIN.exome.20110411.bai
  187. HG00377.mapped.illumina.mosaik.FIN.exome.20110411.bam
  188. HG00379.mapped.illumina.mosaik.FIN.exome.20110411.bai
  189. HG00379.mapped.illumina.mosaik.FIN.exome.20110411.bam
  190. HG00380.mapped.illumina.mosaik.FIN.exome.20110411.bai
  191. HG00380.mapped.illumina.mosaik.FIN.exome.20110411.bam
  192. HG00383.mapped.illumina.mosaik.FIN.exome.20110411.bai
  193. HG00383.mapped.illumina.mosaik.FIN.exome.20110411.bam
  194. HG01334.mapped.illumina.mosaik.GBR.exome.20110411.bai
  195. HG01334.mapped.illumina.mosaik.GBR.exome.20110411.bam
  196. NA06984.mapped.illumina.mosaik.CEU.exome.20110521.bai
  197. NA06984.mapped.illumina.mosaik.CEU.exome.20110521.bam
  198. NA06989.mapped.illumina.mosaik.CEU.exome.20110411.bai
  199. NA06989.mapped.illumina.mosaik.CEU.exome.20110411.bam
  200. NA11840.mapped.illumina.mosaik.CEU.exome.20110411.bai
  201. NA11840.mapped.illumina.mosaik.CEU.exome.20110411.bam
  202. NA12283.mapped.illumina.mosaik.CEU.exome.20110411.bai
  203. NA12283.mapped.illumina.mosaik.CEU.exome.20110411.bam
  204. NA12340.mapped.illumina.mosaik.CEU.exome.20110521.bai
  205. NA12340.mapped.illumina.mosaik.CEU.exome.20110521.bam
  206. NA12717.mapped.illumina.mosaik.CEU.exome.20110411.bai
  207. NA12717.mapped.illumina.mosaik.CEU.exome.20110411.bam
  208. NA12750.mapped.illumina.mosaik.CEU.exome.20110411.bai
  209. NA12750.mapped.illumina.mosaik.CEU.exome.20110411.bam
  210. NA12760.mapped.illumina.mosaik.CEU.exome.20110411.bai
  211. NA12760.mapped.illumina.mosaik.CEU.exome.20110411.bam
  212. NA12761.mapped.illumina.mosaik.CEU.exome.20110411.bai
  213. NA12761.mapped.illumina.mosaik.CEU.exome.20110411.bam
  214. NA12777.mapped.illumina.mosaik.CEU.exome.20110521.bai
  215. NA12777.mapped.illumina.mosaik.CEU.exome.20110521.bam
  216. NA12830.mapped.illumina.mosaik.CEU.exome.20110411.bai
  217. NA12830.mapped.illumina.mosaik.CEU.exome.20110411.bam
  218. NA12889.mapped.illumina.mosaik.CEU.exome.20110411.bai
  219. NA12889.mapped.illumina.mosaik.CEU.exome.20110411.bam
  220. NA12891.mapped.illumina.mosaik.CEU.exome.20110411.bai
  221. NA12891.mapped.illumina.mosaik.CEU.exome.20110411.bam
  222. NA20543.mapped.illumina.mosaik.TSI.exome.20110521.bai
  223. NA20543.mapped.illumina.mosaik.TSI.exome.20110521.bam
  224. NA20581.mapped.illumina.mosaik.TSI.exome.20110521.bai
  225. NA20581.mapped.illumina.mosaik.TSI.exome.20110521.bam
  226. NA20769.mapped.illumina.mosaik.TSI.exome.20110411.bai
  227. NA20769.mapped.illumina.mosaik.TSI.exome.20110411.bam
  228. NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bai
  229. NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bam
  230. NA20774.mapped.illumina.mosaik.TSI.exome.20110411.bai
  231. NA20774.mapped.illumina.mosaik.TSI.exome.20110411.bam
  232. NA20775.mapped.illumina.mosaik.TSI.exome.20110411.bai
  233. NA20775.mapped.illumina.mosaik.TSI.exome.20110411.bam
  234. NA20778.mapped.illumina.mosaik.TSI.exome.20110411.bai
  235. NA20778.mapped.illumina.mosaik.TSI.exome.20110411.bam
  236. NA20785.mapped.illumina.mosaik.TSI.exome.20110411.bai
  237. NA20785.mapped.illumina.mosaik.TSI.exome.20110411.bam
  238. NA20796.mapped.illumina.mosaik.TSI.exome.20110411.bai
  239. NA20796.mapped.illumina.mosaik.TSI.exome.20110411.bam
  240. NA20800.mapped.illumina.mosaik.TSI.exome.20110411.bai
  241. NA20800.mapped.illumina.mosaik.TSI.exome.20110411.bam
  242. NA20801.mapped.illumina.mosaik.TSI.exome.20110411.bai
  243. NA20801.mapped.illumina.mosaik.TSI.exome.20110411.bam
  244. NA20812.mapped.illumina.mosaik.TSI.exome.20110411.bai
  245. NA20812.mapped.illumina.mosaik.TSI.exome.20110411.bam
  246. NA20826.mapped.illumina.mosaik.TSI.exome.20110411.bai
  247. NA20826.mapped.illumina.mosaik.TSI.exome.20110411.bam
  248. darkwing@FOWL:~/firasproject/primary/1000Gphase1randomcaucasianexomebams$ # All the 1000G BAMs now have the same basename
  249. darkwing@FOWL:~/firasproject/primary/1000Gphase1randomcaucasianexomebams$ cd ..
  250. darkwing@FOWL:~/firasproject/primary$ # Let's run a test session to demonstrate the GATK error, let's use two input samples - one a 1000G BAM and one a sample BAM
  251. darkwing@FOWL:~/firasproject/primary$ java -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $GATK/resources/ftp.broadinstitute.org/bundle/2.5/b37/essential/human_g1k_v37.fasta -I 12_parental_dedup_realigned_recal_reduced_reads.bam -I 1000Gphase1randomcaucasianexomebams/HG00103.mapped.illumina.mosaik.GBR.exome.20110411.bam -o test.vcf
  252. INFO 14:37:01,861 HelpFormatter - --------------------------------------------------------------------------------
  253. INFO 14:37:01,864 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29
  254. INFO 14:37:01,864 HelpFormatter - Copyright (c) 2010 The Broad Institute
  255. INFO 14:37:01,864 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
  256. INFO 14:37:01,870 HelpFormatter - Program Args: -T HaplotypeCaller -R /Software/GenomeAnalysisTK-2.7-2-g6bda569/resources/ftp.broadinstitute.org/bundle/2.5/b37/essential/human_g1k_v37.fasta -I 12_parental_dedup_realigned_recal_reduced_reads.bam -I 1000Gphase1randomcaucasianexomebams/HG00103.mapped.illumina.mosaik.GBR.exome.20110411.bam -o test.vcf
  257. INFO 14:37:01,870 HelpFormatter - Date/Time: 2013/12/02 14:37:01
  258. INFO 14:37:01,870 HelpFormatter - --------------------------------------------------------------------------------
  259. INFO 14:37:01,870 HelpFormatter - --------------------------------------------------------------------------------
  260. INFO 14:37:01,990 GenomeAnalysisEngine - Strictness is SILENT
  261. INFO 14:37:02,136 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
  262. INFO 14:37:02,146 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
  263. INFO 14:37:02,174 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
  264. INFO 14:37:02,185 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
  265. INFO 14:37:02,371 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
  266. INFO 14:37:02,998 GenomeAnalysisEngine - Done preparing for traversal
  267. INFO 14:37:02,999 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
  268. INFO 14:37:03,000 ProgressMeter - Location processed.active regions runtime per.1M.active regions completed total.runtime remaining
  269. INFO 14:37:03,175 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
  270. INFO 14:37:33,003 ProgressMeter - 1:1589033 0.00e+00 30.0 s 49.6 w 0.1% 16.3 h 16.3 h
  271. ^Cdarkwing@FOWL:~/firasproject/primary$ rm test.vcf
  272. darkwing@FOWL:~/firasproject/primary$ java -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $GATK/resources/ftp.broadinstitute.org/bundle/2.5/b37/essential/human_g1k_v37.fasta -I 12_parental_dedup_realigned_recal_reduced_reads.bam -I 1000Gphase1randomcaucasianexomebams/NA207 -o test.vcfNA20769.mapped.illumina.mosaik.TSI.exome.20110411.bai
  273. NA20769.mapped.illumina.mosaik.TSI.exome.20110411.bam
  274. NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bai
  275. NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bam
  276. NA20774.mapped.illumina.mosaik.TSI.exome.20110411.bai
  277. NA20774.mapped.illumina.mosaik.TSI.exome.20110411.bam
  278. NA20775.mapped.illumina.mosaik.TSI.exome.20110411.bai
  279. NA20775.mapped.illumina.mosaik.TSI.exome.20110411.bam
  280. NA20778.mapped.illumina.mosaik.TSI.exome.20110411.bai
  281. NA20778.mapped.illumina.mosaik.TSI.exome.20110411.bam
  282. NA20785.mapped.illumina.mosaik.TSI.exome.20110411.bai
  283. NA20785.mapped.illumina.mosaik.TSI.exome.20110411.bam
  284. NA20796.mapped.illumina.mosaik.TSI.exome.20110411.bai
  285. NA20796.mapped.illumina.mosaik.TSI.exome.20110411.bam
  286. darkwing@FOWL:~/firasproject/primary$ java -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $GATK/resources/ftp.broadinstitute.org/bundle/2.5/b37/essential/human_g1k_v37.fasta -I 12_parental_dedup_realigned_recal_reduced_reads.bam -I 1000Gphase1randomcaucasianexomebams/NA207 -o test.vcf
  287. NA20769.mapped.illumina.mosaik.TSI.exome.20110411.bai
  288. NA20769.mapped.illumina.mosaik.TSI.exome.20110411.bam
  289. NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bai
  290. NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bam
  291. NA20774.mapped.illumina.mosaik.TSI.exome.20110411.bai
  292. NA20774.mapped.illumina.mosaik.TSI.exome.20110411.bam
  293. NA20775.mapped.illumina.mosaik.TSI.exome.20110411.bai
  294. NA20775.mapped.illumina.mosaik.TSI.exome.20110411.bam
  295. NA20778.mapped.illumina.mosaik.TSI.exome.20110411.bai
  296. NA20778.mapped.illumina.mosaik.TSI.exome.20110411.bam
  297. NA20785.mapped.illumina.mosaik.TSI.exome.20110411.bai
  298. NA20785.mapped.illumina.mosaik.TSI.exome.20110411.bam
  299. NA20796.mapped.illumina.mosaik.TSI.exome.20110411.bai
  300. NA20796.mapped.illumina.mosaik.TSI.exome.20110411.bam
  301. darkwing@FOWL:~/firasproject/primary$ java -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $GATK/resources/ftp.broadinstitute.org/bundle/2.5/b37/essential/human_g1k_v37.fasta -I 12_parental_dedup_realigned_recal_reduced_reads.bam -I 1000Gphase1randomcaucasianexomebams/NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bam -o test.vcf
  302. INFO 14:40:02,858 HelpFormatter - --------------------------------------------------------------------------------
  303. INFO 14:40:02,861 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29
  304. INFO 14:40:02,861 HelpFormatter - Copyright (c) 2010 The Broad Institute
  305. INFO 14:40:02,861 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
  306. INFO 14:40:02,866 HelpFormatter - Program Args: -T HaplotypeCaller -R /Software/GenomeAnalysisTK-2.7-2-g6bda569/resources/ftp.broadinstitute.org/bundle/2.5/b37/essential/human_g1k_v37.fasta -I 12_parental_dedup_realigned_recal_reduced_reads.bam -I 1000Gphase1randomcaucasianexomebams/NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bam -o test.vcf
  307. INFO 14:40:02,867 HelpFormatter - Date/Time: 2013/12/02 14:40:02
  308. INFO 14:40:02,867 HelpFormatter - --------------------------------------------------------------------------------
  309. INFO 14:40:02,867 HelpFormatter - --------------------------------------------------------------------------------
  310. INFO 14:40:02,985 GenomeAnalysisEngine - Strictness is SILENT
  311. INFO 14:40:03,131 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
  312. INFO 14:40:03,140 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
  313. INFO 14:40:03,172 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
  314. INFO 14:40:03,186 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
  315. INFO 14:40:03,376 GenomeAnalysisEngine - Preparing for traversal over 2 BAM files
  316. INFO 14:40:04,029 GenomeAnalysisEngine - Done preparing for traversal
  317. INFO 14:40:04,030 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
  318. INFO 14:40:04,031 ProgressMeter - Location processed.active regions runtime per.1M.active regions completed total.runtime remaining
  319. INFO 14:40:04,168 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units
  320. INFO 14:40:34,034 ProgressMeter - 1:1558091 0.00e+00 30.0 s 49.6 w 0.1% 16.6 h 16.6 h
  321. ^Cdarkwing@FOWL:~/firasproject/primary$ rm test.vcf
  322. darkwing@FOWL:~/firasproject/primary$ # It appears that GATK doesn't complain when input files are supplied as direct parameters rather than in a list file
  323. darkwing@FOWL:~/firasproject/primary$ # Let's test if creating a list file has any effect
  324. darkwing@FOWL:~/firasproject/primary$ # Let's generate a list of input BAMs for the parent cohort
  325. darkwing@FOWL:~/firasproject/primary$ find $PWD -maxdepth 1 -type f -name "*parent*bam" >> inputbamlistforrawparentvcf.list
  326. darkwing@FOWL:~/firasproject/primary$ cat inputbamlistforrawparentvcf.list
  327. /home/darkwing/firasproject/primary/22_parental_dedup_realigned_recal_reduced_reads.bam
  328. /home/darkwing/firasproject/primary/59_parental_dedup_realigned_recal_reduced_reads.bam
  329. /home/darkwing/firasproject/primary/39_parental_dedup_realigned_recal_reduced_reads.bam
  330. /home/darkwing/firasproject/primary/12_parental_dedup_realigned_recal_reduced_reads.bam
  331. darkwing@FOWL:~/firasproject/primary$ # Now let's append the 1000G BAMs to this list
  332. darkwing@FOWL:~/firasproject/primary$ find $PWD/1000* -maxdepth 1 -type f -name "*bam" >> inputbamlistforrawparentvcf.list
  333. darkwing@FOWL:~/firasproject/primary$ cat inputbamlistforrawparentvcf.list
  334. /home/darkwing/firasproject/primary/22_parental_dedup_realigned_recal_reduced_reads.bam
  335. /home/darkwing/firasproject/primary/59_parental_dedup_realigned_recal_reduced_reads.bam
  336. /home/darkwing/firasproject/primary/39_parental_dedup_realigned_recal_reduced_reads.bam
  337. /home/darkwing/firasproject/primary/12_parental_dedup_realigned_recal_reduced_reads.bam
  338. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20770.mapped.illumina.mosaik.TSI.exome.20110411.bam
  339. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA06989.mapped.illumina.mosaik.CEU.exome.20110411.bam
  340. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG01334.mapped.illumina.mosaik.GBR.exome.20110411.bam
  341. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA12283.mapped.illumina.mosaik.CEU.exome.20110411.bam
  342. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20581.mapped.illumina.mosaik.TSI.exome.20110521.bam
  343. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00158.mapped.illumina.mosaik.GBR.exome.20110411.bam
  344. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00318.mapped.illumina.mosaik.FIN.exome.20110411.bam
  345. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA11840.mapped.illumina.mosaik.CEU.exome.20110411.bam
  346. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA06984.mapped.illumina.mosaik.CEU.exome.20110521.bam
  347. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20778.mapped.illumina.mosaik.TSI.exome.20110411.bam
  348. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00380.mapped.illumina.mosaik.FIN.exome.20110411.bam
  349. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA12760.mapped.illumina.mosaik.CEU.exome.20110411.bam
  350. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00114.mapped.illumina.mosaik.GBR.exome.20110411.bam
  351. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00181.mapped.illumina.mosaik.FIN.exome.20110521.bam
  352. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00252.mapped.illumina.mosaik.GBR.exome.20110411.bam
  353. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00258.mapped.illumina.mosaik.GBR.exome.20110411.bam
  354. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00353.mapped.illumina.mosaik.FIN.exome.20110411.bam
  355. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00346.mapped.illumina.mosaik.FIN.exome.20110411.bam
  356. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA12891.mapped.illumina.mosaik.CEU.exome.20110411.bam
  357. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00261.mapped.illumina.mosaik.GBR.exome.20110411.bam
  358. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20812.mapped.illumina.mosaik.TSI.exome.20110411.bam
  359. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00371.mapped.illumina.mosaik.FIN.exome.20110411.bam
  360. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA12750.mapped.illumina.mosaik.CEU.exome.20110411.bam
  361. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA12830.mapped.illumina.mosaik.CEU.exome.20110411.bam
  362. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00379.mapped.illumina.mosaik.FIN.exome.20110411.bam
  363. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00233.mapped.illumina.mosaik.GBR.exome.20110411.bam
  364. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA12889.mapped.illumina.mosaik.CEU.exome.20110411.bam
  365. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00282.mapped.illumina.mosaik.FIN.exome.20110411.bam
  366. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20801.mapped.illumina.mosaik.TSI.exome.20110411.bam
  367. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00331.mapped.illumina.mosaik.FIN.exome.20110411.bam
  368. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20775.mapped.illumina.mosaik.TSI.exome.20110411.bam
  369. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00313.mapped.illumina.mosaik.FIN.exome.20110411.bam
  370. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00383.mapped.illumina.mosaik.FIN.exome.20110411.bam
  371. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20774.mapped.illumina.mosaik.TSI.exome.20110411.bam
  372. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00377.mapped.illumina.mosaik.FIN.exome.20110411.bam
  373. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00103.mapped.illumina.mosaik.GBR.exome.20110411.bam
  374. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20796.mapped.illumina.mosaik.TSI.exome.20110411.bam
  375. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20800.mapped.illumina.mosaik.TSI.exome.20110411.bam
  376. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20785.mapped.illumina.mosaik.TSI.exome.20110411.bam
  377. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00240.mapped.illumina.mosaik.GBR.exome.20110411.bam
  378. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA12777.mapped.illumina.mosaik.CEU.exome.20110521.bam
  379. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00238.mapped.illumina.mosaik.GBR.exome.20110411.bam
  380. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20769.mapped.illumina.mosaik.TSI.exome.20110411.bam
  381. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA12717.mapped.illumina.mosaik.CEU.exome.20110411.bam
  382. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20826.mapped.illumina.mosaik.TSI.exome.20110411.bam
  383. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00276.mapped.illumina.mosaik.FIN.exome.20110411.bam
  384. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA12761.mapped.illumina.mosaik.CEU.exome.20110411.bam
  385. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00312.mapped.illumina.mosaik.FIN.exome.20110411.bam
  386. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA12340.mapped.illumina.mosaik.CEU.exome.20110521.bam
  387. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/HG00334.mapped.illumina.mosaik.FIN.exome.20110411.bam
  388. /home/darkwing/firasproject/primary/1000Gphase1randomcaucasianexomebams/NA20543.mapped.illumina.mosaik.TSI.exome.20110521.bam
  389. darkwing@FOWL:~/firasproject/primary$ # Now let's run GATK using this file as an input list
  390. darkwing@FOWL:~/firasproject/primary$ java -jar $GATK/GenomeAnalysisTK.jar -T HaplotypeCaller -R $GATK/resources/ftp.broadinstitute.org/bundle/2.5/b37/essential/human_g1k_v37.fasta -I inputbamlistforrawparentvcf.list -o test.vcfINFO 14:45:43,057 HelpFormatter - --------------------------------------------------------------------------------
  391. INFO 14:45:43,060 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29
  392. INFO 14:45:43,060 HelpFormatter - Copyright (c) 2010 The Broad Institute
  393. INFO 14:45:43,060 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
  394. INFO 14:45:43,066 HelpFormatter - Program Args: -T HaplotypeCaller -R /Software/GenomeAnalysisTK-2.7-2-g6bda569/resources/ftp.broadinstitute.org/bundle/2.5/b37/essential/human_g1k_v37.fasta -I inputbamlistforrawparentvcf.list -o test.vcf
  395. INFO 14:45:43,066 HelpFormatter - Date/Time: 2013/12/02 14:45:43
  396. INFO 14:45:43,066 HelpFormatter - --------------------------------------------------------------------------------
  397. INFO 14:45:43,066 HelpFormatter - --------------------------------------------------------------------------------
  398. INFO 14:45:43,182 GenomeAnalysisEngine - Strictness is SILENT
  399. INFO 14:45:43,321 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250
  400. INFO 14:45:43,330 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
  401. INFO 14:45:43,599 SAMDataSource$SAMReaders - Init 50 BAMs in last 0.27 s, 50 of 55 in 0.27 s / 0.00 m (187.74 tasks/s). 5 remaining with est. completion in 0.03 s / 0.00 m
  402. INFO 14:45:43,617 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.29
  403. INFO 14:45:43,673 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
  404. INFO 14:45:43,862 GenomeAnalysisEngine - Preparing for traversal over 55 BAM files
  405. INFO 14:45:44,613 GATKRunReport - Uploaded run statistics report to AWS S3
  406. ##### ERROR ------------------------------------------------------------------------------------------
  407. ##### ERROR A USER ERROR has occurred (version 2.7-2-g6bda569):
  408. ##### ERROR
  409. ##### ERROR This means that one or more arguments or inputs in your command are incorrect.
  410. ##### ERROR The error message below tells you what is the problem.
  411. ##### ERROR
  412. ##### ERROR If the problem is an invalid argument, please check the online documentation guide
  413. ##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
  414. ##### ERROR
  415. ##### ERROR Visit our website and forum for extensive documentation and answers to
  416. ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
  417. ##### ERROR
  418. ##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
  419. ##### ERROR
  420. ##### ERROR MESSAGE: Invalid command line: Cannot process the provided BAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported.
  421. ##### ERROR ------------------------------------------------------------------------------------------
  422. darkwing@FOWL:~/firasproject/primary$ # GATK complains that the BAMs are not indexed, however that's not the case
  423. darkwing@FOWL:~/firasproject/primary$ exit
  424.  
  425. Script done on Mon 02 Dec 2013 02:47:17 PM EST
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