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robsyme

bash -x `which nextflow` run .

robsyme
Nov 18th, 2015
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  1. rsyme@magnus-1:~/scratch/03-dijon> bash -x `which nextflow` run .
  2. + test -s /home/rsyme/.alias
  3. + true
  4. + . /etc/bash.bashrc.local
  5. ++ . /opt/modules/default/etc/modules.sh
  6. +++ '[' rsyme = root ']'
  7. +++ case "`/bin/ls -l /proc/$$/exe`" in
  8. ++++ /bin/ls -l /proc/2542/exe
  9. +++ . /opt/modules/default/init/bash
  10. ++++ '[' 3.2.10 = '' ']'
  11. ++++ MODULE_VERSION_STACK=3.2.10
  12. ++++ export MODULE_VERSION_STACK
  13. ++++ MODULESHOME=/opt/modules/3.2.6.7
  14. ++++ export MODULESHOME
  15. ++++ '[' slurm/14.11.8-pawsey-3:pawseytools/1.9:modules/3.2.6.7:eswrap/1.1.0-1.020200.1231.0:switch/1.0-1.0502.51632.2.84.ari:craype-network-aries:craype/2.1.2:cce/8.3.0:cray-libsci/13.0.0:udreg/2.3.2-1.0502.8763.1.11.ari:ugni/5.0-1.0502.9037.7.26.ari:pmi/5.0.4-1
  16. .0000.10161.132.4.ari:dmapp/7.0.1-1.0502.9080.9.32.ari:gni-headers/3.0-1.0502.9038.7.4.ari:xpmem/0.1-2.0502.51169.1.11.ari:job/1.5.5-0.1_2.0502.52111.3.39.ari:csa/3.0.0-1_2.0502.51200.1.108.ari:alps/5.2.1-2.0502.8712.10.32.ari:rca/1.0.0-2.0502.51491.3.92.ari:atp/
  17. 1.7.3:PrgEnv-cray/5.2.25:craype-haswell:cray-mpich/7.0.0 = '' ']'
  18. ++++ '[' /opt/cray/craype/default/modulefiles:/opt/cray/ari/modulefiles:/ivec/cle52/magnus/modulefiles/apps:/ivec/cle52/magnus/modulefiles/bio-apps:/ivec/cle52/magnus/modulefiles/devel:/ivec/cle52/magnus/modulefiles/python:/ivec/cle52/magnus/modulefiles/tools:/op
  19. t/cray/modulefiles:/opt/modulefiles = '' ']'
  20. ++++ export CRAY_SITE_LIST_DIR=/etc/opt/cray/modules
  21. ++++ CRAY_SITE_LIST_DIR=/etc/opt/cray/modules
  22. +++++ grep CRAY_SITE_LIST /etc/opt/cray/modules/site_list_config
  23. ++++ site_list_dir=CRAY_SITE_LIST_DIR=/etc/opt/cray/modules
  24. ++++ export CRAY_SITE_LIST_DIR=/etc/opt/cray/modules
  25. ++++ CRAY_SITE_LIST_DIR=/etc/opt/cray/modules
  26. ++++ sorted_file=
  27. ++++ '[' -f /etc/opt/cray/modules/site_usermodules ']'
  28. +++++ for i in '${MODULESHOME}/init/.usermodules' '${CRAY_SITE_LIST_DIR}/site_usermodules'
  29. +++++ echo /opt/modules/3.2.6.7/init/.usermodules
  30. +++++ strings -n1 - /opt/modules/3.2.6.7/init/.usermodules
  31. +++++ sort
  32. +++++ uniq
  33. +++++ for i in '${MODULESHOME}/init/.usermodules' '${CRAY_SITE_LIST_DIR}/site_usermodules'
  34. +++++ echo /etc/opt/cray/modules/site_usermodules
  35. +++++ strings -n1 - /etc/opt/cray/modules/site_usermodules
  36. +++++ sort
  37. +++++ uniq
  38. ++++ sorted_file='/opt/modules/3.2.6.7/init/.usermodules
  39. acml
  40. alps
  41. apprentice2
  42. atp
  43. blcr
  44. cce
  45. chapel
  46. cray-fftw
  47. cray-libsci
  48. cray-mpich2
  49. craypat
  50. craype
  51. cray-petsc
  52. cray-petsc-complex
  53. cray-shmem
  54. cray-tpsl
  55. cray-trilinos
  56. cudatoolkit
  57. ddt
  58. fftw
  59. ga
  60. gcc
  61. hdf5
  62. hdf5-parallel
  63. intel
  64. iobuf
  65. java
  66. lgdb
  67. libfast
  68. libsci_acc
  69. mpich1
  70. mrnet
  71. netcdf
  72. netcdf-hdf5parallel
  73. netcdf-nofsync
  74. netcdf-nofsync-hdf5parallel
  75. ntk
  76. onesided
  77. papi
  78. parallel-netcdf
  79. pathscale
  80. perftools
  81. petsc
  82. petsc-complex
  83. pgi
  84. pmi
  85. PrgEnv-cray
  86. PrgEnv-gnu
  87. PrgEnv-intel
  88. PrgEnv-pathscale
  89. PrgEnv-pgi
  90. stat
  91. totalview
  92. tpsl
  93. trilinos
  94. xt-asyncpe
  95. xt-craypat
  96. xt-lgdb
  97. xt-libsci
  98. xt-mpich2
  99. xt-mpt
  100. xt-papi
  101. xt-shmem
  102. xt-totalview
  103. /etc/opt/cray/modules/site_usermodules'
  104. +++++ sed 's/ /:/g'
  105. +++++ echo /opt/modules/3.2.6.7/init/.usermodules acml alps apprentice2 atp blcr cce chapel cray-fftw cray-libsci cray-mpich2 craypat craype cray-petsc cray-petsc-complex cray-shmem cray-tpsl cray-trilinos cudatoolkit ddt fftw ga gcc hdf5 hdf5-parallel intel iobu
  106. f java lgdb libfast libsci_acc mpich1 mrnet netcdf netcdf-hdf5parallel netcdf-nofsync netcdf-nofsync-hdf5parallel ntk onesided papi parallel-netcdf pathscale perftools petsc petsc-complex pgi pmi PrgEnv-cray PrgEnv-gnu PrgEnv-intel PrgEnv-pathscale PrgEnv-pgi sta
  107. t totalview tpsl trilinos xt-asyncpe xt-craypat xt-lgdb xt-libsci xt-mpich2 xt-mpt xt-papi xt-shmem xt-totalview /etc/opt/cray/modules/site_usermodules
  108. +++++ sed 's/\/opt\/modules\/3\.2\.6\.7\/init\/\.usermodules://'
  109. ++++ export USERMODULES=acml:alps:apprentice2:atp:blcr:cce:chapel:cray-fftw:cray-libsci:cray-mpich2:craypat:craype:cray-petsc:cray-petsc-complex:cray-shmem:cray-tpsl:cray-trilinos:cudatoolkit:ddt:fftw:ga:gcc:hdf5:hdf5-parallel:intel:iobuf:java:lgdb:libfast:libsci
  110. _acc:mpich1:mrnet:netcdf:netcdf-hdf5parallel:netcdf-nofsync:netcdf-nofsync-hdf5parallel:ntk:onesided:papi:parallel-netcdf:pathscale:perftools:petsc:petsc-complex:pgi:pmi:PrgEnv-cray:PrgEnv-gnu:PrgEnv-intel:PrgEnv-pathscale:PrgEnv-pgi:stat:totalview:tpsl:trilinos:
  111. xt-asyncpe:xt-craypat:xt-lgdb:xt-libsci:xt-mpich2:xt-mpt:xt-papi:xt-shmem:xt-totalview:/etc/opt/cray/modules/site_usermodules
  112. ++++ USERMODULES=acml:alps:apprentice2:atp:blcr:cce:chapel:cray-fftw:cray-libsci:cray-mpich2:craypat:craype:cray-petsc:cray-petsc-complex:cray-shmem:cray-tpsl:cray-trilinos:cudatoolkit:ddt:fftw:ga:gcc:hdf5:hdf5-parallel:intel:iobuf:java:lgdb:libfast:libsci_acc:mp
  113. ich1:mrnet:netcdf:netcdf-hdf5parallel:netcdf-nofsync:netcdf-nofsync-hdf5parallel:ntk:onesided:papi:parallel-netcdf:pathscale:perftools:petsc:petsc-complex:pgi:pmi:PrgEnv-cray:PrgEnv-gnu:PrgEnv-intel:PrgEnv-pathscale:PrgEnv-pgi:stat:totalview:tpsl:trilinos:xt-asyn
  114. cpe:xt-craypat:xt-lgdb:xt-libsci:xt-mpich2:xt-mpt:xt-papi:xt-shmem:xt-totalview:/etc/opt/cray/modules/site_usermodules
  115. ++++ sorted_file=
  116. ++++ '[' -f /etc/opt/cray/modules/site_targetmodules ']'
  117. +++++ for i in '${MODULESHOME}/init/.targetmodules' '${CRAY_SITE_LIST_DIR}/site_targetmodules'
  118. +++++ echo /opt/modules/3.2.6.7/init/.targetmodules
  119. +++++ strings -n1 - /opt/modules/3.2.6.7/init/.targetmodules
  120. +++++ sort
  121. +++++ uniq
  122. +++++ for i in '${MODULESHOME}/init/.targetmodules' '${CRAY_SITE_LIST_DIR}/site_targetmodules'
  123. +++++ echo /etc/opt/cray/modules/site_targetmodules
  124. +++++ strings -n1 - /etc/opt/cray/modules/site_targetmodules
  125. +++++ sort
  126. +++++ uniq
  127. ++++ sorted_file='/opt/modules/3.2.6.7/init/.targetmodules
  128. craype-abudhabi
  129. craype-abudhabi-cu
  130. craype-accel-nvidia20
  131. craype-accel-nvidia30
  132. craype-accel-nvidia35
  133. craype-barcelona
  134. craype-hugepages128K
  135. craype-hugepages128M
  136. craype-hugepages16M
  137. craype-hugepages256M
  138. craype-hugepages2M
  139. craype-hugepages512K
  140. craype-hugepages512M
  141. craype-hugepages64M
  142. craype-hugepages8M
  143. craype-interlagos
  144. craype-interlagos-cu
  145. craype-istanbul
  146. craype-ivybridge
  147. craype-knc
  148. craype-mc12
  149. craype-mc8
  150. craype-network-aries
  151. craype-network-gemini
  152. craype-network-seastar
  153. craype-sandybridge
  154. craype-shanghai
  155. craype-target-compute_node
  156. craype-target-local_host
  157. craype-target-native
  158. craype-target-petest
  159. craype-xeon
  160. xtpe-barcelona
  161. xtpe-interlagos
  162. xtpe-interlagos-cu
  163. xtpe-istanbul
  164. xtpe-mc12
  165. xtpe-mc8
  166. xtpe-network-gemini
  167. xtpe-network-seastar
  168. xtpe-shanghai
  169. xtpe-target-native
  170. xtpe-xeon
  171. /etc/opt/cray/modules/site_targetmodules'
  172. +++++ sed 's/ /:/g'
  173. +++++ sed 's/\/opt\/modules\/3\.2\.6\.7\/init\/\.targetmodules://'
  174. +++++ echo /opt/modules/3.2.6.7/init/.targetmodules craype-abudhabi craype-abudhabi-cu craype-accel-nvidia20 craype-accel-nvidia30 craype-accel-nvidia35 craype-barcelona craype-hugepages128K craype-hugepages128M craype-hugepages16M craype-hugepages256M craype-hug
  175. epages2M craype-hugepages512K craype-hugepages512M craype-hugepages64M craype-hugepages8M craype-interlagos craype-interlagos-cu craype-istanbul craype-ivybridge craype-knc craype-mc12 craype-mc8 craype-network-aries craype-network-gemini craype-network-seastar c
  176. raype-sandybridge craype-shanghai craype-target-compute_node craype-target-local_host craype-target-native craype-target-petest craype-xeon xtpe-barcelona xtpe-interlagos xtpe-interlagos-cu xtpe-istanbul xtpe-mc12 xtpe-mc8 xtpe-network-gemini xtpe-network-seastar
  177. xtpe-shanghai xtpe-target-native xtpe-xeon /etc/opt/cray/modules/site_targetmodules
  178. ++++ export TARGETMODULES=craype-abudhabi:craype-abudhabi-cu:craype-accel-nvidia20:craype-accel-nvidia30:craype-accel-nvidia35:craype-barcelona:craype-hugepages128K:craype-hugepages128M:craype-hugepages16M:craype-hugepages256M:craype-hugepages2M:craype-hugepages5
  179. 12K:craype-hugepages512M:craype-hugepages64M:craype-hugepages8M:craype-interlagos:craype-interlagos-cu:craype-istanbul:craype-ivybridge:craype-knc:craype-mc12:craype-mc8:craype-network-aries:craype-network-gemini:craype-network-seastar:craype-sandybridge:craype-s
  180. hanghai:craype-target-compute_node:craype-target-local_host:craype-target-native:craype-target-petest:craype-xeon:xtpe-barcelona:xtpe-interlagos:xtpe-interlagos-cu:xtpe-istanbul:xtpe-mc12:xtpe-mc8:xtpe-network-gemini:xtpe-network-seastar:xtpe-shanghai:xtpe-target
  181. -native:xtpe-xeon:/etc/opt/cray/modules/site_targetmodules
  182. ++++ TARGETMODULES=craype-abudhabi:craype-abudhabi-cu:craype-accel-nvidia20:craype-accel-nvidia30:craype-accel-nvidia35:craype-barcelona:craype-hugepages128K:craype-hugepages128M:craype-hugepages16M:craype-hugepages256M:craype-hugepages2M:craype-hugepages512K:cra
  183. ype-hugepages512M:craype-hugepages64M:craype-hugepages8M:craype-interlagos:craype-interlagos-cu:craype-istanbul:craype-ivybridge:craype-knc:craype-mc12:craype-mc8:craype-network-aries:craype-network-gemini:craype-network-seastar:craype-sandybridge:craype-shanghai
  184. :craype-target-compute_node:craype-target-local_host:craype-target-native:craype-target-petest:craype-xeon:xtpe-barcelona:xtpe-interlagos:xtpe-interlagos-cu:xtpe-istanbul:xtpe-mc12:xtpe-mc8:xtpe-network-gemini:xtpe-network-seastar:xtpe-shanghai:xtpe-target-native
  185. :xtpe-xeon:/etc/opt/cray/modules/site_targetmodules
  186. ++++ sorted_file=
  187. ++++ '[' -f /etc/opt/cray/modules/site_librarymodules ']'
  188. +++++ for i in '${MODULESHOME}/init/.librarymodules' '${CRAY_SITE_LIST_DIR}/site_librarymodules'
  189. +++++ echo /opt/modules/3.2.6.7/init/.librarymodules
  190. +++++ strings -n1 - /opt/modules/3.2.6.7/init/.librarymodules
  191. +++++ sort
  192. +++++ uniq
  193. +++++ for i in '${MODULESHOME}/init/.librarymodules' '${CRAY_SITE_LIST_DIR}/site_librarymodules'
  194. +++++ echo /etc/opt/cray/modules/site_librarymodules
  195. +++++ strings -n1 - /etc/opt/cray/modules/site_librarymodules
  196. +++++ sort
  197. +++++ uniq
  198. ++++ sorted_file='/opt/modules/3.2.6.7/init/.librarymodules
  199. acml
  200. alps
  201. apprentice2
  202. atp
  203. cray-fftw
  204. cray-libsci
  205. cray-mpich2
  206. cray-petsc
  207. cray-petsc-complex
  208. cray-shmem
  209. cray-tpsl
  210. cray-trilinos
  211. cudatoolkit
  212. fftw
  213. ga
  214. hdf5
  215. hdf5-parallel
  216. iobuf
  217. lgdb
  218. libfast
  219. libsci_acc
  220. mpich1
  221. mpich2
  222. mrnet
  223. netcdf
  224. netcdf-hdf5parallel
  225. netcdf-nofsync
  226. netcdf-nofsync-hdf5parallel
  227. ntk
  228. onesided
  229. papi
  230. parallel-netcdf
  231. petsc
  232. petsc-complex
  233. pmi
  234. shmem
  235. tpsl
  236. trilinos
  237. xt-atp
  238. xt-lgdb
  239. xt-libsci
  240. xt-mpt
  241. xt-papi
  242. /etc/opt/cray/modules/site_librarymodules'
  243. +++++ echo /opt/modules/3.2.6.7/init/.librarymodules acml alps apprentice2 atp cray-fftw cray-libsci cray-mpich2 cray-petsc cray-petsc-complex cray-shmem cray-tpsl cray-trilinos cudatoolkit fftw ga hdf5 hdf5-parallel iobuf lgdb libfast libsci_acc mpich1 mpich2 mr
  244. net netcdf netcdf-hdf5parallel netcdf-nofsync netcdf-nofsync-hdf5parallel ntk onesided papi parallel-netcdf petsc petsc-complex pmi shmem tpsl trilinos xt-atp xt-lgdb xt-libsci xt-mpt xt-papi /etc/opt/cray/modules/site_librarymodules
  245. +++++ sed 's/ /:/g'
  246. +++++ sed 's/\/opt\/modules\/3\.2\.6\.7\/init\/\.librarymodules://'
  247. ++++ export LIBRARYMODULES=acml:alps:apprentice2:atp:cray-fftw:cray-libsci:cray-mpich2:cray-petsc:cray-petsc-complex:cray-shmem:cray-tpsl:cray-trilinos:cudatoolkit:fftw:ga:hdf5:hdf5-parallel:iobuf:lgdb:libfast:libsci_acc:mpich1:mpich2:mrnet:netcdf:netcdf-hdf5para
  248. llel:netcdf-nofsync:netcdf-nofsync-hdf5parallel:ntk:onesided:papi:parallel-netcdf:petsc:petsc-complex:pmi:shmem:tpsl:trilinos:xt-atp:xt-lgdb:xt-libsci:xt-mpt:xt-papi:/etc/opt/cray/modules/site_librarymodules
  249. ++++ LIBRARYMODULES=acml:alps:apprentice2:atp:cray-fftw:cray-libsci:cray-mpich2:cray-petsc:cray-petsc-complex:cray-shmem:cray-tpsl:cray-trilinos:cudatoolkit:fftw:ga:hdf5:hdf5-parallel:iobuf:lgdb:libfast:libsci_acc:mpich1:mpich2:mrnet:netcdf:netcdf-hdf5parallel:ne
  250. tcdf-nofsync:netcdf-nofsync-hdf5parallel:ntk:onesided:papi:parallel-netcdf:petsc:petsc-complex:pmi:shmem:tpsl:trilinos:xt-atp:xt-lgdb:xt-libsci:xt-mpt:xt-papi:/etc/opt/cray/modules/site_librarymodules
  251. ++++ sorted_file=
  252. +++++ for i in '${MODULESHOME}/init/.prgenvmodules'
  253. +++++ echo /opt/modules/3.2.6.7/init/.prgenvmodules
  254. +++++ strings -n1 - /opt/modules/3.2.6.7/init/.prgenvmodules
  255. +++++ sort
  256. +++++ uniq
  257. ++++ sorted_file='/opt/modules/3.2.6.7/init/.prgenvmodules
  258. PrgEnv-cray
  259. PrgEnv-gnu
  260. PrgEnv-intel
  261. PrgEnv-pathscale
  262. PrgEnv-pgi'
  263. +++++ echo /opt/modules/3.2.6.7/init/.prgenvmodules PrgEnv-cray PrgEnv-gnu PrgEnv-intel PrgEnv-pathscale PrgEnv-pgi
  264. +++++ sed 's/ /:/g'
  265. +++++ sed 's/\/opt\/modules\/3\.2\.6\.7\/init\/\.prgenvmodules://'
  266. ++++ export PRGENVMODULES=PrgEnv-cray:PrgEnv-gnu:PrgEnv-intel:PrgEnv-pathscale:PrgEnv-pgi
  267. ++++ PRGENVMODULES=PrgEnv-cray:PrgEnv-gnu:PrgEnv-intel:PrgEnv-pathscale:PrgEnv-pgi
  268. ++++ sorted_file=
  269. ++++ '[' -f /etc/opt/cray/modules/site_toolmodules ']'
  270. +++++ for i in '${MODULESHOME}/init/.toolmodules' '${CRAY_SITE_LIST_DIR}/site_toolmodules'
  271. +++++ echo /opt/modules/3.2.6.7/init/.toolmodules
  272. +++++ strings -n1 - /opt/modules/3.2.6.7/init/.toolmodules
  273. +++++ sort
  274. +++++ uniq
  275. +++++ for i in '${MODULESHOME}/init/.toolmodules' '${CRAY_SITE_LIST_DIR}/site_toolmodules'
  276. +++++ echo /etc/opt/cray/modules/site_toolmodules
  277. +++++ strings -n1 - /etc/opt/cray/modules/site_toolmodules
  278. +++++ sort
  279. +++++ uniq
  280. ++++ sorted_file='/opt/modules/3.2.6.7/init/.toolmodules
  281. apprentice
  282. apprentice2
  283. atp
  284. chapel
  285. craypat
  286. ddt
  287. gdb
  288. iobuf
  289. mrnet
  290. papi
  291. perftools
  292. stat
  293. totalview
  294. xt-craypat
  295. xt-lgdb
  296. xt-papi
  297. xt-totalview
  298. /etc/opt/cray/modules/site_toolmodules'
  299. +++++ echo /opt/modules/3.2.6.7/init/.toolmodules apprentice apprentice2 atp chapel craypat ddt gdb iobuf mrnet papi perftools stat totalview xt-craypat xt-lgdb xt-papi xt-totalview /etc/opt/cray/modules/site_toolmodules
  300. +++++ sed 's/ /:/g'
  301. +++++ sed 's/\/opt\/modules\/3\.2\.6\.7\/init\/\.toolmodules://'
  302. ++++ export TOOLMODULES=apprentice:apprentice2:atp:chapel:craypat:ddt:gdb:iobuf:mrnet:papi:perftools:stat:totalview:xt-craypat:xt-lgdb:xt-papi:xt-totalview:/etc/opt/cray/modules/site_toolmodules
  303. ++++ TOOLMODULES=apprentice:apprentice2:atp:chapel:craypat:ddt:gdb:iobuf:mrnet:papi:perftools:stat:totalview:xt-craypat:xt-lgdb:xt-papi:xt-totalview:/etc/opt/cray/modules/site_toolmodules
  304. +++ module add modules/3.2.6.7
  305. ++++ /opt/modules/3.2.6.7/bin/modulecmd bash add modules/3.2.6.7
  306. +++ eval
  307. ++ '[' -z true ']'
  308. ++ '[' rsyme = root ']'
  309. ++ '[' -z true ']'
  310. ++ '[' -z true ']'
  311. ++ export IVEC_CLUSTER=magnus
  312. ++ IVEC_CLUSTER=magnus
  313. ++ export IVEC_OS=cle52
  314. ++ IVEC_OS=cle52
  315. ++ '[' -z true ']'
  316. + PATH=/opt/cray/atp/1.7.3/bin:/opt/cray/rca/1.0.0-2.0502.51491.3.92.ari/bin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/sbin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/bin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/sbin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.
  317. ari/bin:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/bin:/opt/cray/xpmem/0.1-2.0502.51169.1.11.ari/bin:/opt/cray/dmapp/7.0.1-1.0502.9080.9.32.ari/bin:/opt/cray/pmi/5.0.4-1.0000.10161.132.4.ari/bin:/opt/cray/ugni/5.0-1.0502.9037.7.26.ari/bin:/opt/cray/udreg/2.3.2
  318. -1.0502.8763.1.11.ari/bin:/opt/cray/cce/8.3.0/cray-binutils/x86_64-unknown-linux-gnu/bin:/opt/cray/cce/8.3.0/craylibs/x86-64/bin:/opt/cray/cce/8.3.0/cftn/bin:/opt/cray/cce/8.3.0/CC/bin:/opt/cray/craype/2.1.2/bin:/opt/cray/switch/1.0-1.0502.51632.2.84.ari/bin:/opt
  319. /cray/eslogin/eswrap/1.1.0-1.020200.1231.0/bin:/opt/modules/3.2.6.7/bin:/ivec/tools/pawseytools/1.9/bin:/opt/slurm/munge/bin:/opt/slurm/14.11.8-pawsey-3/bin:/home/rsyme/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/
  320. lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src/git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/top
  321. hat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current:/group/bppp002/rsyme/bin:/home/rsyme/.local/bin
  322. + PATH=/opt/cray/atp/1.7.3/bin:/opt/cray/rca/1.0.0-2.0502.51491.3.92.ari/bin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/sbin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/bin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/sbin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.
  323. ari/bin:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/bin:/opt/cray/xpmem/0.1-2.0502.51169.1.11.ari/bin:/opt/cray/dmapp/7.0.1-1.0502.9080.9.32.ari/bin:/opt/cray/pmi/5.0.4-1.0000.10161.132.4.ari/bin:/opt/cray/ugni/5.0-1.0502.9037.7.26.ari/bin:/opt/cray/udreg/2.3.2
  324. -1.0502.8763.1.11.ari/bin:/opt/cray/cce/8.3.0/cray-binutils/x86_64-unknown-linux-gnu/bin:/opt/cray/cce/8.3.0/craylibs/x86-64/bin:/opt/cray/cce/8.3.0/cftn/bin:/opt/cray/cce/8.3.0/CC/bin:/opt/cray/craype/2.1.2/bin:/opt/cray/switch/1.0-1.0502.51632.2.84.ari/bin:/opt
  325. /cray/eslogin/eswrap/1.1.0-1.020200.1231.0/bin:/opt/modules/3.2.6.7/bin:/ivec/tools/pawseytools/1.9/bin:/opt/slurm/munge/bin:/opt/slurm/14.11.8-pawsey-3/bin:/home/rsyme/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/
  326. lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src/git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/top
  327. hat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current:/group/bppp002/rsyme/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin
  328. + for prog in trim_galore fastqc git-annex bowtie2 tophat samtools trinity bbmap
  329. + PATH=/opt/cray/atp/1.7.3/bin:/opt/cray/rca/1.0.0-2.0502.51491.3.92.ari/bin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/sbin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/bin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/sbin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.
  330. ari/bin:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/bin:/opt/cray/xpmem/0.1-2.0502.51169.1.11.ari/bin:/opt/cray/dmapp/7.0.1-1.0502.9080.9.32.ari/bin:/opt/cray/pmi/5.0.4-1.0000.10161.132.4.ari/bin:/opt/cray/ugni/5.0-1.0502.9037.7.26.ari/bin:/opt/cray/udreg/2.3.2
  331. -1.0502.8763.1.11.ari/bin:/opt/cray/cce/8.3.0/cray-binutils/x86_64-unknown-linux-gnu/bin:/opt/cray/cce/8.3.0/craylibs/x86-64/bin:/opt/cray/cce/8.3.0/cftn/bin:/opt/cray/cce/8.3.0/CC/bin:/opt/cray/craype/2.1.2/bin:/opt/cray/switch/1.0-1.0502.51632.2.84.ari/bin:/opt
  332. /cray/eslogin/eswrap/1.1.0-1.020200.1231.0/bin:/opt/modules/3.2.6.7/bin:/ivec/tools/pawseytools/1.9/bin:/opt/slurm/munge/bin:/opt/slurm/14.11.8-pawsey-3/bin:/home/rsyme/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/
  333. lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src/git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/top
  334. hat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current:/group/bppp002/rsyme/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current
  335. + for prog in trim_galore fastqc git-annex bowtie2 tophat samtools trinity bbmap
  336. + PATH=/opt/cray/atp/1.7.3/bin:/opt/cray/rca/1.0.0-2.0502.51491.3.92.ari/bin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/sbin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/bin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/sbin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.
  337. ari/bin:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/bin:/opt/cray/xpmem/0.1-2.0502.51169.1.11.ari/bin:/opt/cray/dmapp/7.0.1-1.0502.9080.9.32.ari/bin:/opt/cray/pmi/5.0.4-1.0000.10161.132.4.ari/bin:/opt/cray/ugni/5.0-1.0502.9037.7.26.ari/bin:/opt/cray/udreg/2.3.2
  338. -1.0502.8763.1.11.ari/bin:/opt/cray/cce/8.3.0/cray-binutils/x86_64-unknown-linux-gnu/bin:/opt/cray/cce/8.3.0/craylibs/x86-64/bin:/opt/cray/cce/8.3.0/cftn/bin:/opt/cray/cce/8.3.0/CC/bin:/opt/cray/craype/2.1.2/bin:/opt/cray/switch/1.0-1.0502.51632.2.84.ari/bin:/opt
  339. /cray/eslogin/eswrap/1.1.0-1.020200.1231.0/bin:/opt/modules/3.2.6.7/bin:/ivec/tools/pawseytools/1.9/bin:/opt/slurm/munge/bin:/opt/slurm/14.11.8-pawsey-3/bin:/home/rsyme/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/
  340. lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src/git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/top
  341. hat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current:/group/bppp002/rsyme/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current
  342. + for prog in trim_galore fastqc git-annex bowtie2 tophat samtools trinity bbmap
  343. + PATH=/opt/cray/atp/1.7.3/bin:/opt/cray/rca/1.0.0-2.0502.51491.3.92.ari/bin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/sbin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/bin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/sbin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.
  344. ari/bin:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/bin:/opt/cray/xpmem/0.1-2.0502.51169.1.11.ari/bin:/opt/cray/dmapp/7.0.1-1.0502.9080.9.32.ari/bin:/opt/cray/pmi/5.0.4-1.0000.10161.132.4.ari/bin:/opt/cray/ugni/5.0-1.0502.9037.7.26.ari/bin:/opt/cray/udreg/2.3.2
  345. -1.0502.8763.1.11.ari/bin:/opt/cray/cce/8.3.0/cray-binutils/x86_64-unknown-linux-gnu/bin:/opt/cray/cce/8.3.0/craylibs/x86-64/bin:/opt/cray/cce/8.3.0/cftn/bin:/opt/cray/cce/8.3.0/CC/bin:/opt/cray/craype/2.1.2/bin:/opt/cray/switch/1.0-1.0502.51632.2.84.ari/bin:/opt
  346. /cray/eslogin/eswrap/1.1.0-1.020200.1231.0/bin:/opt/modules/3.2.6.7/bin:/ivec/tools/pawseytools/1.9/bin:/opt/slurm/munge/bin:/opt/slurm/14.11.8-pawsey-3/bin:/home/rsyme/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/
  347. lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src/git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/top
  348. hat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current:/group/bppp002/rsyme/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src
  349. /git-annex/current
  350. + for prog in trim_galore fastqc git-annex bowtie2 tophat samtools trinity bbmap
  351. + PATH=/opt/cray/atp/1.7.3/bin:/opt/cray/rca/1.0.0-2.0502.51491.3.92.ari/bin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/sbin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/bin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/sbin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.
  352. ari/bin:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/bin:/opt/cray/xpmem/0.1-2.0502.51169.1.11.ari/bin:/opt/cray/dmapp/7.0.1-1.0502.9080.9.32.ari/bin:/opt/cray/pmi/5.0.4-1.0000.10161.132.4.ari/bin:/opt/cray/ugni/5.0-1.0502.9037.7.26.ari/bin:/opt/cray/udreg/2.3.2
  353. -1.0502.8763.1.11.ari/bin:/opt/cray/cce/8.3.0/cray-binutils/x86_64-unknown-linux-gnu/bin:/opt/cray/cce/8.3.0/craylibs/x86-64/bin:/opt/cray/cce/8.3.0/cftn/bin:/opt/cray/cce/8.3.0/CC/bin:/opt/cray/craype/2.1.2/bin:/opt/cray/switch/1.0-1.0502.51632.2.84.ari/bin:/opt
  354. /cray/eslogin/eswrap/1.1.0-1.020200.1231.0/bin:/opt/modules/3.2.6.7/bin:/ivec/tools/pawseytools/1.9/bin:/opt/slurm/munge/bin:/opt/slurm/14.11.8-pawsey-3/bin:/home/rsyme/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/
  355. lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src/git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/top
  356. hat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current:/group/bppp002/rsyme/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src
  357. /git-annex/current:/home/rsyme/src/bowtie2/current
  358. + for prog in trim_galore fastqc git-annex bowtie2 tophat samtools trinity bbmap
  359. + PATH=/opt/cray/atp/1.7.3/bin:/opt/cray/rca/1.0.0-2.0502.51491.3.92.ari/bin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/sbin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/bin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/sbin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.
  360. ari/bin:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/bin:/opt/cray/xpmem/0.1-2.0502.51169.1.11.ari/bin:/opt/cray/dmapp/7.0.1-1.0502.9080.9.32.ari/bin:/opt/cray/pmi/5.0.4-1.0000.10161.132.4.ari/bin:/opt/cray/ugni/5.0-1.0502.9037.7.26.ari/bin:/opt/cray/udreg/2.3.2
  361. -1.0502.8763.1.11.ari/bin:/opt/cray/cce/8.3.0/cray-binutils/x86_64-unknown-linux-gnu/bin:/opt/cray/cce/8.3.0/craylibs/x86-64/bin:/opt/cray/cce/8.3.0/cftn/bin:/opt/cray/cce/8.3.0/CC/bin:/opt/cray/craype/2.1.2/bin:/opt/cray/switch/1.0-1.0502.51632.2.84.ari/bin:/opt
  362. /cray/eslogin/eswrap/1.1.0-1.020200.1231.0/bin:/opt/modules/3.2.6.7/bin:/ivec/tools/pawseytools/1.9/bin:/opt/slurm/munge/bin:/opt/slurm/14.11.8-pawsey-3/bin:/home/rsyme/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/
  363. lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src/git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/top
  364. hat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current:/group/bppp002/rsyme/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src
  365. /git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/tophat/current
  366. + for prog in trim_galore fastqc git-annex bowtie2 tophat samtools trinity bbmap
  367. + PATH=/opt/cray/atp/1.7.3/bin:/opt/cray/rca/1.0.0-2.0502.51491.3.92.ari/bin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/sbin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/bin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/sbin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.
  368. ari/bin:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/bin:/opt/cray/xpmem/0.1-2.0502.51169.1.11.ari/bin:/opt/cray/dmapp/7.0.1-1.0502.9080.9.32.ari/bin:/opt/cray/pmi/5.0.4-1.0000.10161.132.4.ari/bin:/opt/cray/ugni/5.0-1.0502.9037.7.26.ari/bin:/opt/cray/udreg/2.3.2
  369. -1.0502.8763.1.11.ari/bin:/opt/cray/cce/8.3.0/cray-binutils/x86_64-unknown-linux-gnu/bin:/opt/cray/cce/8.3.0/craylibs/x86-64/bin:/opt/cray/cce/8.3.0/cftn/bin:/opt/cray/cce/8.3.0/CC/bin:/opt/cray/craype/2.1.2/bin:/opt/cray/switch/1.0-1.0502.51632.2.84.ari/bin:/opt
  370. /cray/eslogin/eswrap/1.1.0-1.020200.1231.0/bin:/opt/modules/3.2.6.7/bin:/ivec/tools/pawseytools/1.9/bin:/opt/slurm/munge/bin:/opt/slurm/14.11.8-pawsey-3/bin:/home/rsyme/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/
  371. lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src/git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/top
  372. hat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current:/group/bppp002/rsyme/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src
  373. /git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/tophat/current:/home/rsyme/src/samtools/current
  374. + for prog in trim_galore fastqc git-annex bowtie2 tophat samtools trinity bbmap
  375. + PATH=/opt/cray/atp/1.7.3/bin:/opt/cray/rca/1.0.0-2.0502.51491.3.92.ari/bin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/sbin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/bin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/sbin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.
  376. ari/bin:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/bin:/opt/cray/xpmem/0.1-2.0502.51169.1.11.ari/bin:/opt/cray/dmapp/7.0.1-1.0502.9080.9.32.ari/bin:/opt/cray/pmi/5.0.4-1.0000.10161.132.4.ari/bin:/opt/cray/ugni/5.0-1.0502.9037.7.26.ari/bin:/opt/cray/udreg/2.3.2
  377. -1.0502.8763.1.11.ari/bin:/opt/cray/cce/8.3.0/cray-binutils/x86_64-unknown-linux-gnu/bin:/opt/cray/cce/8.3.0/craylibs/x86-64/bin:/opt/cray/cce/8.3.0/cftn/bin:/opt/cray/cce/8.3.0/CC/bin:/opt/cray/craype/2.1.2/bin:/opt/cray/switch/1.0-1.0502.51632.2.84.ari/bin:/opt
  378. /cray/eslogin/eswrap/1.1.0-1.020200.1231.0/bin:/opt/modules/3.2.6.7/bin:/ivec/tools/pawseytools/1.9/bin:/opt/slurm/munge/bin:/opt/slurm/14.11.8-pawsey-3/bin:/home/rsyme/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/
  379. lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src/git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/top
  380. hat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current:/group/bppp002/rsyme/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src
  381. /git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/tophat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current
  382. + for prog in trim_galore fastqc git-annex bowtie2 tophat samtools trinity bbmap
  383. + PATH=/opt/cray/atp/1.7.3/bin:/opt/cray/rca/1.0.0-2.0502.51491.3.92.ari/bin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/sbin:/opt/cray/alps/5.2.1-2.0502.8712.10.32.ari/bin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/sbin:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.
  384. ari/bin:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/bin:/opt/cray/xpmem/0.1-2.0502.51169.1.11.ari/bin:/opt/cray/dmapp/7.0.1-1.0502.9080.9.32.ari/bin:/opt/cray/pmi/5.0.4-1.0000.10161.132.4.ari/bin:/opt/cray/ugni/5.0-1.0502.9037.7.26.ari/bin:/opt/cray/udreg/2.3.2
  385. -1.0502.8763.1.11.ari/bin:/opt/cray/cce/8.3.0/cray-binutils/x86_64-unknown-linux-gnu/bin:/opt/cray/cce/8.3.0/craylibs/x86-64/bin:/opt/cray/cce/8.3.0/cftn/bin:/opt/cray/cce/8.3.0/CC/bin:/opt/cray/craype/2.1.2/bin:/opt/cray/switch/1.0-1.0502.51632.2.84.ari/bin:/opt
  386. /cray/eslogin/eswrap/1.1.0-1.020200.1231.0/bin:/opt/modules/3.2.6.7/bin:/ivec/tools/pawseytools/1.9/bin:/opt/slurm/munge/bin:/opt/slurm/14.11.8-pawsey-3/bin:/home/rsyme/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib/mit/bin:/usr/
  387. lib/mit/sbin:/sbin:/usr/sbin:.:/usr/lib/qt3/bin:/opt/cray/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src/git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/top
  388. hat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current:/group/bppp002/rsyme/bin:/home/rsyme/.local/bin:/home/rsyme/src/byobu/bin:/home/rsyme/src/trim_galore/current:/home/rsyme/src/fastqc/current:/home/rsyme/src
  389. /git-annex/current:/home/rsyme/src/bowtie2/current:/home/rsyme/src/tophat/current:/home/rsyme/src/samtools/current:/home/rsyme/src/trinity/current:/home/rsyme/src/bbmap/current
  390. + export PATH
  391. + [[ -n screen ]]
  392. + [[ screen != \d\u\m\b ]]
  393. ++ tput setaf 2
  394. tput: unknown terminal "screen"
  395. ++ tput bold
  396. tput: unknown terminal "screen"
  397. + GREEN=
  398. ++ tput setaf 3
  399. tput: unknown terminal "screen"
  400. + YELLOW=
  401. ++ tput setaf 1
  402. tput: unknown terminal "screen"
  403. + RED=
  404. ++ tput sgr0
  405. tput: unknown terminal "screen"
  406. + NORMAL=
  407. + '[' /home/rsyme/bin/nextflow = bash ']'
  408. + '[' /home/rsyme/bin/nextflow = /bin/bash ']'
  409. + NXF_HOME=/home/rsyme/.nextflow
  410. + NXF_VER=0.16.2
  411. + NXF_ORG=nextflow-io
  412. + NXF_ASSETS=/home/rsyme/.nextflow/assets
  413. + NXF_CLI='/home/rsyme/bin/nextflow run .'
  414. + export NXF_CLI
  415. + export NXF_ORG
  416. + export NXF_HOME
  417. + bg=
  418. + jvmopts=()
  419. + declare -a jvmopts
  420. + args=("$@")
  421. + declare -a args
  422. + cli=(clone config drop help history info ls pull run view node console)
  423. + declare -a cli
  424. + cmd=
  425. + [[ 2 != 0 ]]
  426. + case $1 in
  427. + [[ -n run ]]
  428. + [[ run != -* ]]
  429. + [[ ! -n '' ]]
  430. + [[ clone config drop help history info ls pull run view node console =~ run ]]
  431. + cmd=run
  432. + shift
  433. + [[ 1 != 0 ]]
  434. + case $1 in
  435. + [[ -n . ]]
  436. + [[ . != -* ]]
  437. + [[ ! -n run ]]
  438. + shift
  439. + [[ 0 != 0 ]]
  440. + CAPSULE_LOG=
  441. + CAPSULE_RESET=
  442. + CAPSULE_CACHE_DIR=/home/rsyme/.nextflow/capsule
  443. + NXF_PACK=one
  444. + NXF_MODE=
  445. + NXF_JAR=nextflow-0.16.2-one.jar
  446. + NXF_BIN=/home/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar
  447. + NXF_BASE=http://www.nextflow.io/releases
  448. ++ dirname /home/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar
  449. + NXF_PATH=/home/rsyme/.nextflow/framework/0.16.2
  450. + NXF_URL=http://www.nextflow.io/releases/v0.16.2/nextflow-0.16.2-one.jar
  451. + NXF_GRAB=
  452. + NXF_CLASSPATH=
  453. + NXF_LAUNCHER=/home/rsyme/.nextflow/tmp/launcher/nextflow-one_0.16.2
  454. + NXF_MPIRUN=
  455. + [[ '' == ignite ]]
  456. + [[ one = \a\l\l ]]
  457. + '[' '!' -x '' ']'
  458. + '[' -d /usr/lib64/jvm/java ']'
  459. + '[' -x /usr/lib64/jvm/java/jre/sh/java ']'
  460. + JAVA_CMD=/usr/lib64/jvm/java/bin/java
  461. + '[' '!' -d /home/rsyme/.nextflow/tmp/launcher/nextflow-one_0.16.2 ']'
  462. + '[' '!' -f /home/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar ']'
  463. + check=.+:.+:.+
  464. + [[ '' =~ .+:.+:.+ ]]
  465. + [[ -n '' ]]
  466. + [[ -n '' ]]
  467. + [[ run == \c\o\n\s\o\l\e ]]
  468. + [[ run == \n\o\d\e ]]
  469. ++ tty -s
  470. ++ tput cols
  471. ++ true
  472. + COLUMNS=
  473. + JAVA_OPTS='-noverify -Dcapsule.trampoline -Dcapsule.java.cmd=/usr/lib64/jvm/java/bin/java'
  474. + [[ run == console ]]
  475. + JAVA_OPTS+=' -Djava.awt.headless=true'
  476. + [[ -n '' ]]
  477. + [[ -n /usr/lib64/jvm/java ]]
  478. + JAVA_OPTS+=' -Dcapsule.java.home=/usr/lib64/jvm/java'
  479. + [[ -n '' ]]
  480. + [[ -n '' ]]
  481. + [[ run != \r\u\n ]]
  482. + [[ -n '' ]]
  483. + [[ -n '' ]]
  484. + [[ -n '' ]]
  485. + [[ -n '' ]]
  486. + [[ -n '' ]]
  487. + [[ -n '' ]]
  488. + export JAVA_CMD
  489. + export CAPSULE_CACHE_DIR
  490. + hash md5sum
  491. + MD5=md5sum
  492. + '[' '!' md5sum ']'
  493. + '[' '' ']'
  494. ++ env_md5
  495. ++ cat
  496. ++ md5sum
  497. ++ cut -f1 '-d '
  498. + LAUNCH_FILE=/home/rsyme/.nextflow/tmp/launcher/nextflow-one_0.16.2/classpath-a77aacaa0375250dddee5656a26c91dc
  499. + '[' -s /home/rsyme/.nextflow/tmp/launcher/nextflow-one_0.16.2/classpath-a77aacaa0375250dddee5656a26c91dc ']'
  500. + '[' /home/rsyme/.nextflow/tmp/launcher/nextflow-one_0.16.2/classpath-a77aacaa0375250dddee5656a26c91dc -nt /home/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar ']'
  501. + launcher=($(cat "$LAUNCH_FILE"))
  502. ++ cat /home/rsyme/.nextflow/tmp/launcher/nextflow-one_0.16.2/classpath-a77aacaa0375250dddee5656a26c91dc
  503. + launch_nextflow
  504. + local 'cmdline="/usr/lib64/jvm/java/bin/java" "-Xoptionsfile=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64/compressedrefs/options.default" "-Xlockword:mode=default,noLockword=java/lang/String,noLockword=java/util/MapEntry,noLockword=java/util/HashMap$Entry,
  505. noLockword=org/apache/harmony/luni/util/ModifiedMap$Entry,noLockword=java/util/Hashtable$Entry,noLockword=java/lang/invoke/MethodType,noLockword=java/lang/invoke/MethodHandle,noLockword=java/lang/invoke/CollectHandle,noLockword=java/lang/invoke/ConstructorHandle,
  506. noLockword=java/lang/invoke/ConvertHandle,noLockword=java/lang/invoke/ArgumentConversionHandle,noLockword=java/lang/invoke/AsTypeHandle,noLockword=java/lang/invoke/ExplicitCastHandle,noLockword=java/lang/invoke/FilterReturnHandle,noLockword=java/lang/invoke/Direc
  507. tHandle,noLockword=java/lang/invoke/ReceiverBoundHandle,noLockword=java/lang/invoke/DynamicInvokerHandle,noLockword=java/lang/invoke/FieldHandle,noLockword=java/lang/invoke/FieldGetterHandle,noLockword=java/lang/invoke/FieldSetterHandle,noLockword=java/lang/invok
  508. e/StaticFieldGetterHandle,noLockword=java/lang/invoke/StaticFieldSetterHandle,noLockword=java/lang/invoke/IndirectHandle,noLockword=java/lang/invoke/InterfaceHandle,noLockword=java/lang/invoke/VirtualHandle,noLockword=java/lang/invoke/InvokeExactHandle,noLockword
  509. =java/lang/invoke/InvokeGenericHandle,noLockword=java/lang/invoke/VarargsCollectorHandle,noLockword=java/lang/invoke/ThunkTuple" "-Xjcl:jclse7b_26" "-Xverify:none" "-Dsun.java.command=/home/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar" "-Dcapsule.app=
  510. nextflow_0.16.2" "-Dsun.java.launcher=SUN_STANDARD" "-Dsun.boot.library.path=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64/compressedrefs:/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64" "-Djava.home=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre" "-Duser.dir=/hom
  511. e/rsyme/bin" "-Djava.awt.headless=true" "-Dsun.java.launcher.pid=24509" "-Djava.ext.dirs=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/ext" "-Djava.class.path=/home/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar" "-Djava.runtime.version=pxa6470sr6fp1-2014
  512. 0108_01 (SR6 FP1)" "-Dcom.ibm.oti.vm.bootstrap.library.path=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64/compressedrefs:/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64" "-Djava.library.path=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64/compressedrefs:/
  513. usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/lib64:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/lib64:/usr/lib" "-Dcapsule.jar=/home/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar" "-classpath" "/home/rs
  514. yme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar:/home/rsyme/.nextflow/capsule/deps/io/nextflow/nextflow/0.16.2/nextflow-0.16.2.jar:/home/rsyme/.nextflow/capsule/deps/org/apache/ivy/ivy/2.3.0/ivy-2.3.0.jar:/home/rsyme/.nextflow/capsule/deps/io/nextflow/nxf-
  515. commons/0.16.2/nxf-commons-0.16.2.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/groovy/groovy/2.4.5/groovy-2.4.5.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/groovy/groovy-nio/2.4.5/groovy-nio-2.4.5.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus
  516. /groovy/groovy-json/2.4.5/groovy-json-2.4.5.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/groovy/groovy-templates/2.4.5/groovy-templates-2.4.5.jar:/home/rsyme/.nextflow/capsule/deps/org/slf4j/jcl-over-slf4j/1.7.12/jcl-over-slf4j-1.7.12.jar:/home/rsyme/.next
  517. flow/capsule/deps/org/slf4j/jul-to-slf4j/1.7.12/jul-to-slf4j-1.7.12.jar:/home/rsyme/.nextflow/capsule/deps/org/slf4j/log4j-over-slf4j/1.7.12/log4j-over-slf4j-1.7.12.jar:/home/rsyme/.nextflow/capsule/deps/ch/qos/logback/logback-classic/1.1.3/logback-classic-1.1.3.
  518. jar:/home/rsyme/.nextflow/capsule/deps/ch/qos/logback/logback-core/1.1.3/logback-core-1.1.3.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/gpars/gpars/1.2.1/gpars-1.2.1.jar:/home/rsyme/.nextflow/capsule/deps/ch/grengine/grengine/1.0.3/grengine-1.0.3.jar:/hom
  519. e/rsyme/.nextflow/capsule/deps/commons-lang/commons-lang/2.6/commons-lang-2.6.jar:/home/rsyme/.nextflow/capsule/deps/com/beust/jcommander/1.35/jcommander-1.35.jar:/home/rsyme/.nextflow/capsule/deps/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar:/home/rsym
  520. e/.nextflow/capsule/deps/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar:/home/rsyme/.nextflow/capsule/deps/org/iq80/leveldb/leveldb/0.7/leveldb-0.7.jar:/home/rsyme/.nextflow/capsule/deps/org/eclipse/jgit/org.eclipse.jgit/4.0.1.201506240215-r/org.eclipse.jg
  521. it-4.0.1.201506240215-r.jar:/home/rsyme/.nextflow/capsule/deps/io/nextflow/nxf-s3fs/0.2.8g/nxf-s3fs-0.2.8g.jar:/home/rsyme/.nextflow/capsule/deps/com/google/guava/guava/16.0.1/guava-16.0.1.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/groovy/groovy-xml/2.4.
  522. 5/groovy-xml-2.4.5.jar:/home/rsyme/.nextflow/capsule/deps/org/slf4j/slf4j-api/1.7.12/slf4j-api-1.7.12.jar:/home/rsyme/.nextflow/capsule/deps/org/multiverse/multiverse-core/0.7.0/multiverse-core-0.7.0.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/jsr166-mirr
  523. or/jsr166y/1.7.0/jsr166y-1.7.0.jar:/home/rsyme/.nextflow/capsule/deps/org/objenesis/objenesis/2.1/objenesis-2.1.jar:/home/rsyme/.nextflow/capsule/deps/org/iq80/leveldb/leveldb-api/0.7/leveldb-api-0.7.jar:/home/rsyme/.nextflow/capsule/deps/com/jcraft/jsch/0.1.51/j
  524. sch-0.1.51.jar:/home/rsyme/.nextflow/capsule/deps/com/googlecode/javaewah/JavaEWAH/0.7.9/JavaEWAH-0.7.9.jar:/home/rsyme/.nextflow/capsule/deps/com/amazonaws/aws-java-sdk/1.5.6/aws-java-sdk-1.5.6.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/jackson/jackson-
  525. core-asl/1.8.9/jackson-core-asl-1.8.9.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/jackson/jackson-mapper-asl/1.8.9/jackson-mapper-asl-1.8.9.jar:/home/rsyme/.nextflow/capsule/deps/org/apache/httpcomponents/httpclient/4.2/httpclient-4.2.jar:/home/rsyme/.nex
  526. tflow/capsule/deps/commons-codec/commons-codec/1.6/commons-codec-1.6.jar:/home/rsyme/.nextflow/capsule/deps/org/apache/httpcomponents/httpcore/4.2/httpcore-4.2.jar:/home/rsyme/.nextflow/capsule/deps/io/nextflow/nxf-extrae/0.16.2/nxf-extrae-0.16.2.jar" "nextflow.c
  527. li.Launcher" '
  528. + for x in '"${args[@]}"'
  529. + cmdline+=''\''run'\'' '
  530. + for x in '"${args[@]}"'
  531. + cmdline+=''\''.'\'' '
  532. + [[ -n '' ]]
  533. + [[ -n '' ]]
  534. + exec bash -c 'exec "/usr/lib64/jvm/java/bin/java" "-Xoptionsfile=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64/compressedrefs/options.default" "-Xlockword:mode=default,noLockword=java/lang/String,noLockword=java/util/MapEntry,noLockword=java/util/HashMap$En
  535. try,noLockword=org/apache/harmony/luni/util/ModifiedMap$Entry,noLockword=java/util/Hashtable$Entry,noLockword=java/lang/invoke/MethodType,noLockword=java/lang/invoke/MethodHandle,noLockword=java/lang/invoke/CollectHandle,noLockword=java/lang/invoke/ConstructorHan
  536. dle,noLockword=java/lang/invoke/ConvertHandle,noLockword=java/lang/invoke/ArgumentConversionHandle,noLockword=java/lang/invoke/AsTypeHandle,noLockword=java/lang/invoke/ExplicitCastHandle,noLockword=java/lang/invoke/FilterReturnHandle,noLockword=java/lang/invoke/D
  537. irectHandle,noLockword=java/lang/invoke/ReceiverBoundHandle,noLockword=java/lang/invoke/DynamicInvokerHandle,noLockword=java/lang/invoke/FieldHandle,noLockword=java/lang/invoke/FieldGetterHandle,noLockword=java/lang/invoke/FieldSetterHandle,noLockword=java/lang/i
  538. nvoke/StaticFieldGetterHandle,noLockword=java/lang/invoke/StaticFieldSetterHandle,noLockword=java/lang/invoke/IndirectHandle,noLockword=java/lang/invoke/InterfaceHandle,noLockword=java/lang/invoke/VirtualHandle,noLockword=java/lang/invoke/InvokeExactHandle,noLock
  539. word=java/lang/invoke/InvokeGenericHandle,noLockword=java/lang/invoke/VarargsCollectorHandle,noLockword=java/lang/invoke/ThunkTuple" "-Xjcl:jclse7b_26" "-Xverify:none" "-Dsun.java.command=/home/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar" "-Dcapsule.
  540. app=nextflow_0.16.2" "-Dsun.java.launcher=SUN_STANDARD" "-Dsun.boot.library.path=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64/compressedrefs:/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64" "-Djava.home=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre" "-Duser.dir=
  541. /home/rsyme/bin" "-Djava.awt.headless=true" "-Dsun.java.launcher.pid=24509" "-Djava.ext.dirs=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/ext" "-Djava.class.path=/home/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar" "-Djava.runtime.version=pxa6470sr6fp1-
  542. 20140108_01 (SR6 FP1)" "-Dcom.ibm.oti.vm.bootstrap.library.path=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64/compressedrefs:/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64" "-Djava.library.path=/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64/compressedre
  543. fs:/usr/lib64/jvm/java-1.7.0-ibm-1.7.0/jre/lib/amd64:/opt/cray/csa/3.0.0-1_2.0502.51200.1.108.ari/lib64:/opt/cray/job/1.5.5-0.1_2.0502.52111.3.39.ari/lib64:/usr/lib" "-Dcapsule.jar=/home/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar" "-classpath" "/hom
  544. e/rsyme/.nextflow/framework/0.16.2/nextflow-0.16.2-one.jar:/home/rsyme/.nextflow/capsule/deps/io/nextflow/nextflow/0.16.2/nextflow-0.16.2.jar:/home/rsyme/.nextflow/capsule/deps/org/apache/ivy/ivy/2.3.0/ivy-2.3.0.jar:/home/rsyme/.nextflow/capsule/deps/io/nextflow/
  545. nxf-commons/0.16.2/nxf-commons-0.16.2.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/groovy/groovy/2.4.5/groovy-2.4.5.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/groovy/groovy-nio/2.4.5/groovy-nio-2.4.5.jar:/home/rsyme/.nextflow/capsule/deps/org/code
  546. haus/groovy/groovy-json/2.4.5/groovy-json-2.4.5.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/groovy/groovy-templates/2.4.5/groovy-templates-2.4.5.jar:/home/rsyme/.nextflow/capsule/deps/org/slf4j/jcl-over-slf4j/1.7.12/jcl-over-slf4j-1.7.12.jar:/home/rsyme/.
  547. nextflow/capsule/deps/org/slf4j/jul-to-slf4j/1.7.12/jul-to-slf4j-1.7.12.jar:/home/rsyme/.nextflow/capsule/deps/org/slf4j/log4j-over-slf4j/1.7.12/log4j-over-slf4j-1.7.12.jar:/home/rsyme/.nextflow/capsule/deps/ch/qos/logback/logback-classic/1.1.3/logback-classic-1.
  548. 1.3.jar:/home/rsyme/.nextflow/capsule/deps/ch/qos/logback/logback-core/1.1.3/logback-core-1.1.3.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/gpars/gpars/1.2.1/gpars-1.2.1.jar:/home/rsyme/.nextflow/capsule/deps/ch/grengine/grengine/1.0.3/grengine-1.0.3.jar:
  549. /home/rsyme/.nextflow/capsule/deps/commons-lang/commons-lang/2.6/commons-lang-2.6.jar:/home/rsyme/.nextflow/capsule/deps/com/beust/jcommander/1.35/jcommander-1.35.jar:/home/rsyme/.nextflow/capsule/deps/com/google/code/findbugs/jsr305/1.3.9/jsr305-1.3.9.jar:/home/
  550. rsyme/.nextflow/capsule/deps/com/esotericsoftware/kryo/kryo/2.24.0/kryo-2.24.0.jar:/home/rsyme/.nextflow/capsule/deps/org/iq80/leveldb/leveldb/0.7/leveldb-0.7.jar:/home/rsyme/.nextflow/capsule/deps/org/eclipse/jgit/org.eclipse.jgit/4.0.1.201506240215-r/org.eclips
  551. e.jgit-4.0.1.201506240215-r.jar:/home/rsyme/.nextflow/capsule/deps/io/nextflow/nxf-s3fs/0.2.8g/nxf-s3fs-0.2.8g.jar:/home/rsyme/.nextflow/capsule/deps/com/google/guava/guava/16.0.1/guava-16.0.1.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/groovy/groovy-xml/
  552. 2.4.5/groovy-xml-2.4.5.jar:/home/rsyme/.nextflow/capsule/deps/org/slf4j/slf4j-api/1.7.12/slf4j-api-1.7.12.jar:/home/rsyme/.nextflow/capsule/deps/org/multiverse/multiverse-core/0.7.0/multiverse-core-0.7.0.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/jsr166-
  553. mirror/jsr166y/1.7.0/jsr166y-1.7.0.jar:/home/rsyme/.nextflow/capsule/deps/org/objenesis/objenesis/2.1/objenesis-2.1.jar:/home/rsyme/.nextflow/capsule/deps/org/iq80/leveldb/leveldb-api/0.7/leveldb-api-0.7.jar:/home/rsyme/.nextflow/capsule/deps/com/jcraft/jsch/0.1.
  554. 51/jsch-0.1.51.jar:/home/rsyme/.nextflow/capsule/deps/com/googlecode/javaewah/JavaEWAH/0.7.9/JavaEWAH-0.7.9.jar:/home/rsyme/.nextflow/capsule/deps/com/amazonaws/aws-java-sdk/1.5.6/aws-java-sdk-1.5.6.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/jackson/jack
  555. son-core-asl/1.8.9/jackson-core-asl-1.8.9.jar:/home/rsyme/.nextflow/capsule/deps/org/codehaus/jackson/jackson-mapper-asl/1.8.9/jackson-mapper-asl-1.8.9.jar:/home/rsyme/.nextflow/capsule/deps/org/apache/httpcomponents/httpclient/4.2/httpclient-4.2.jar:/home/rsyme/
  556. .nextflow/capsule/deps/commons-codec/commons-codec/1.6/commons-codec-1.6.jar:/home/rsyme/.nextflow/capsule/deps/org/apache/httpcomponents/httpcore/4.2/httpcore-4.2.jar:/home/rsyme/.nextflow/capsule/deps/io/nextflow/nxf-extrae/0.16.2/nxf-extrae-0.16.2.jar" "nextfl
  557. ow.cli.Launcher" '\''run'\'' '\''.'\'' '
  558. N E X T F L O W ~ version 0.16.2
  559. Launching ./main.nf
  560. ERROR ~ Not such file: /home/rsyme/bin/main.nf
  561.  
  562. -- Check '.nextflow.log' file for details
  563. rsyme@magnus-1:~/scratch/03-dijon>
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