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MARC::blastxCDS

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  1. perl diya.pl -conf conf/genome-annotator-for-ncbi.xml tmp/NZ_ABZT01 -out 007 -set OUTPUTDIR=007 -set MYSEQID=008 -set MYUNIREFD=db/uniref50/uniref50.fasta -set MYRPSD=db/cdd/Cdd -set MYCLUSTERS=db/clusters/PRK_Clusters.bcp -set MYCDD=db/cddid_all.tbl
  2.  
  3. Do It Yourself Annotator (diya) v. 1.0;
  4.         --help for usage
  5.         --license for copyright information
  6.  
  7. The diya home directory is '/home/jasperk/Apps/DIYA-master/'
  8. Using '007/' as output directory
  9. --set: the value of the global variable $OUTPUTDIR will be '007'
  10. --set: the value of the global variable $MYSEQID will be '008'
  11. --set: the value of the global variable $MYUNIREFD will be 'db/uniref50/uniref50.fasta'
  12. --set: the value of the global variable $MYRPSD will be 'db/cdd/Cdd'
  13. --set: the value of the global variable $MYCLUSTERS will be 'db/clusters/PRK_Clusters.bcp'
  14. --set: the value of the global variable $MYCDD will be 'db/cddid_all.tbl'
  15. Using 'conf/genome-annotator-for-ncbi.xml'
  16. Reading 'conf/genome-annotator-for-ncbi.xml'
  17. File count is 1
  18. Next input file is 'tmp/NZ_ABZT01'
  19. <mode> for the pipeline is 'serial'
  20. Current <order> is 'assemble_pseudocontig make-single-fa MARC::glimmer3 extractCDS MARC::blastpCDS MARC::rpsblastCDS'
  21.  
  22. Preparing to run 'assemble_pseudocontig', step count of 1
  23. 'assemble_pseudocontig' is a 'script'
  24. 'assemble_pseudocontig' is a 'script'
  25. Format of 'tmp/NZ_ABZT01' is 'fasta'
  26. No <inputformat> found for step 'assemble_pseudocontig', no conversion needed
  27. No <inputfrom> found for 'assemble_pseudocontig'
  28. 'tmp/NZ_ABZT01' will be used as input file for 'assemble_pseudocontig'
  29. Using '007/' as output directory
  30. '007/NZ_ABZT01' will be used as input file for 'assemble_pseudocontig'
  31. Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'assemble_pseudocontig'
  32. Found <executable> 'diya-assemble_pseudocontig.pl' for 'assemble_pseudocontig' in 'conf/genome-annotator-for-ncbi.xml'
  33. Using '007/' as output directory
  34. Output file name for 'assemble_pseudocontig' is '007/2012_11_16_17_41_11-assemble_pseudocontig.out'
  35. Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'assemble_pseudocontig'
  36. Found <executable> 'diya-assemble_pseudocontig.pl' for 'assemble_pseudocontig' in 'conf/genome-annotator-for-ncbi.xml'
  37. Found <command> '-infile INPUTFILE -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir OUTPUTDIR' for 'assemble_pseudocontig'
  38. Found <command> '-infile INPUTFILE -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir OUTPUTDIR' for 'assemble_pseudocontig'
  39. 'assemble_pseudocontig' command before substitution is '/home/jasperk/Apps/DIYA-master/scripts/diya-assemble_pseudocontig.pl -infile INPUTFILE -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir OUTPUTDIR'
  40. 'INPUTFILE' will be substituted with '007/NZ_ABZT01'
  41. 'OUTPUTFILE' will be substituted with '007/2012_11_16_17_41_11-assemble_pseudocontig.out'
  42. 'assemble_pseudocontig' command after parser-specific substitution is '/home/jasperk/Apps/DIYA-master/scripts/diya-assemble_pseudocontig.pl -infile 007/NZ_ABZT01 -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir OUTPUTDIR'
  43. Using '007/' as output directory
  44. 'OUTPUTDIR' will be substituted with '007/'
  45. 'assemble_pseudocontig' command after global substitution is '/home/jasperk/Apps/DIYA-master/scripts/diya-assemble_pseudocontig.pl -infile 007/NZ_ABZT01 -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid MYSEQID -outdir 007/'
  46. 'MYCDD' will be substituted with 'db/cddid_all.tbl'
  47. 'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
  48. 'MYSEQID' will be substituted with '008'
  49. 'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
  50. 'MYRPSD' will be substituted with 'db/cdd/Cdd'
  51. 'OUTPUTDIR' will be substituted with '007'
  52. 'assemble_pseudocontig' command after variable substitution is '/home/jasperk/Apps/DIYA-master/scripts/diya-assemble_pseudocontig.pl -infile 007/NZ_ABZT01 -scaff MYSCAFF -species MYSPECIES -strain MYSTRAIN -seqid 008 -outdir 007/'
  53. <mode> for the pipeline is 'serial'
  54. <mode> for the pipeline is 'serial'
  55. <mode> for the pipeline is 'serial'
  56. <mode> for the pipeline is 'serial'
  57. <mode> for the pipeline is 'serial'
  58. Scaffold file appears not to exist at MYSCAFF. Carrying on without scaffolding
  59.  
  60. Total size of pseudocontig = 13930
  61. Contigs tiled  = 0
  62. Total length of tiled contigs =
  63. Untiled contigs = 1
  64. Total length of untiled contigs = 13930
  65. Number of excluded contigs =
  66. Total length of excluded contigs = 0
  67.  
  68. Preparing to run 'make-single-fa', step count of 2
  69. 'make-single-fa' is a 'script'
  70. 'make-single-fa' is a 'script'
  71. Format of 'tmp/NZ_ABZT01' is 'fasta'
  72. No <inputformat> found for step 'make-single-fa', no conversion needed
  73. No <inputfrom> found for 'make-single-fa'
  74. 'tmp/NZ_ABZT01' will be used as input file for 'make-single-fa'
  75. Using '007/' as output directory
  76. '007/NZ_ABZT01' will be used as input file for 'make-single-fa'
  77. Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'make-single-fa'
  78. Found <executable> 'make-single-fa.pl' for 'make-single-fa' in 'conf/genome-annotator-for-ncbi.xml'
  79. Using '007/' as output directory
  80. Output file name for 'make-single-fa' is '007/2012_11_16_17_41_12-make-single-fa.out'
  81. Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'make-single-fa'
  82. Found <executable> 'make-single-fa.pl' for 'make-single-fa' in 'conf/genome-annotator-for-ncbi.xml'
  83. Found <command> 'MYSEQID.gbk OUTPUTDIR' for 'make-single-fa'
  84. Found <command> 'MYSEQID.gbk OUTPUTDIR' for 'make-single-fa'
  85. 'make-single-fa' command before substitution is '/home/jasperk/Apps/DIYA-master/scripts/make-single-fa.pl MYSEQID.gbk OUTPUTDIR'
  86. 'INPUTFILE' will be substituted with '007/NZ_ABZT01'
  87. 'OUTPUTFILE' will be substituted with '007/2012_11_16_17_41_12-make-single-fa.out'
  88. 'make-single-fa' command after parser-specific substitution is '/home/jasperk/Apps/DIYA-master/scripts/make-single-fa.pl MYSEQID.gbk OUTPUTDIR'
  89. Using '007/' as output directory
  90. 'OUTPUTDIR' will be substituted with '007/'
  91. 'make-single-fa' command after global substitution is '/home/jasperk/Apps/DIYA-master/scripts/make-single-fa.pl MYSEQID.gbk 007/'
  92. 'MYCDD' will be substituted with 'db/cddid_all.tbl'
  93. 'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
  94. 'MYSEQID' will be substituted with '008'
  95. 'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
  96. 'MYRPSD' will be substituted with 'db/cdd/Cdd'
  97. 'OUTPUTDIR' will be substituted with '007'
  98. 'make-single-fa' command after variable substitution is '/home/jasperk/Apps/DIYA-master/scripts/make-single-fa.pl 008.gbk 007/'
  99. <mode> for the pipeline is 'serial'
  100. <mode> for the pipeline is 'serial'
  101. <mode> for the pipeline is 'serial'
  102. <mode> for the pipeline is 'serial'
  103. <mode> for the pipeline is 'serial'
  104.  
  105. Preparing to run 'MARC::glimmer3', step count of 3
  106. 'MARC::glimmer3' is a 'parser'
  107. Loaded module 'diya::MARC::glimmer3'
  108. 'MARC::glimmer3' is a 'parser'
  109. No <inputformat> for 'MARC::glimmer3'
  110. Format of 'tmp/NZ_ABZT01' is 'fasta'
  111. No <inputformat> found for step 'MARC::glimmer3', no conversion needed
  112. No <inputfrom> found for 'MARC::glimmer3'
  113. 'tmp/NZ_ABZT01' will be used as input file for 'MARC::glimmer3'
  114. Using '007/' as output directory
  115. '007/NZ_ABZT01' will be used as input file for 'MARC::glimmer3'
  116. Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'MARC::glimmer3'
  117. Found <executable> 'g3-from-scratch2.csh' for 'MARC::glimmer3' in 'conf/genome-annotator-for-ncbi.xml'
  118. Using '007/' as output directory
  119. Output file name for 'MARC::glimmer3' is '007/2012_11_16_17_41_12-MARC::glimmer3.out'
  120. Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'MARC::glimmer3'
  121. Found <executable> 'g3-from-scratch2.csh' for 'MARC::glimmer3' in 'conf/genome-annotator-for-ncbi.xml'
  122. Found <command> 'MYSEQID.fa MYSEQID OUTPUTDIR' for 'MARC::glimmer3'
  123. Found <command> 'MYSEQID.fa MYSEQID OUTPUTDIR' for 'MARC::glimmer3'
  124. 'MARC::glimmer3' command before substitution is '/home/jasperk/Apps/DIYA-master/scripts/g3-from-scratch2.csh MYSEQID.fa MYSEQID OUTPUTDIR'
  125. 'INPUTFILE' will be substituted with '007/NZ_ABZT01'
  126. 'OUTPUTFILE' will be substituted with '007/2012_11_16_17_41_12-MARC::glimmer3.out'
  127. 'MARC::glimmer3' command after parser-specific substitution is '/home/jasperk/Apps/DIYA-master/scripts/g3-from-scratch2.csh MYSEQID.fa MYSEQID OUTPUTDIR'
  128. Using '007/' as output directory
  129. 'OUTPUTDIR' will be substituted with '007/'
  130. 'MARC::glimmer3' command after global substitution is '/home/jasperk/Apps/DIYA-master/scripts/g3-from-scratch2.csh MYSEQID.fa MYSEQID 007/'
  131. 'MYCDD' will be substituted with 'db/cddid_all.tbl'
  132. 'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
  133. 'MYSEQID' will be substituted with '008'
  134. 'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
  135. 'MYRPSD' will be substituted with 'db/cdd/Cdd'
  136. 'OUTPUTDIR' will be substituted with '007'
  137. 'MARC::glimmer3' command after variable substitution is '/home/jasperk/Apps/DIYA-master/scripts/g3-from-scratch2.csh 008.fa 008 007/'
  138. <mode> for the pipeline is 'serial'
  139. <mode> for the pipeline is 'serial'
  140. <mode> for the pipeline is 'serial'
  141. Starting at Fri Nov 16 17:41:12 2012
  142.  
  143. Sequence file = 007//008.fa
  144. Excluded regions file = none
  145. Circular genome = true
  146. Initial minimum gene length = 90 bp
  147. Determine optimal min gene length to maximize number of genes
  148. Maximum overlap bases = 30
  149. Start codons = atg,gtg,ttg
  150. Stop codons = taa,tag,tga
  151. Sequence length = 13930
  152. Final minimum gene length = 286
  153. Number of genes = 10
  154. Total bases = 4965
  155. Starting at Fri Nov 16 17:41:12 2012
  156.  
  157. Sequence file = 007//008.fa
  158. Number of sequences = 1
  159. ICM model file = 007//008.icm
  160. Excluded regions file = none
  161. List of orfs file = none
  162. Input is NOT separate orfs
  163. Independent (non-coding) scores are used
  164. Circular genome = false
  165. Truncated orfs = false
  166. Minimum gene length = 110 bp
  167. Maximum overlap bases = 50
  168. Threshold score = 30
  169. Use first start codon = false
  170. Start codons = atg,gtg,ttg
  171. Start probs = 0.600,0.300,0.100
  172. Stop codons = taa,tag,tga
  173. GC percentage = 40.9%
  174. Ignore score on orfs longer than 572
  175. Analyzing Sequence #1
  176. Start Find_Orfs
  177. Start Score_Orfs
  178. Start Process_Events
  179. Start Trace_Back
  180. <mode> for the pipeline is 'serial'
  181. <mode> for the pipeline is 'serial'
  182. Step 1 of 4:  Finding long orfs for training
  183. Step 2 of 4:  Extracting training sequences
  184. Step 3 of 4:  Building ICM
  185. Step 4 of 4:  Running Glimmer3
  186. /usr/bin/tigr-glimmer glimmer3 -l -o50 -g110 -t30 007//008.fa 007//008.icm 007//008
  187. Finished with g3-from-scratch
  188.  
  189. Created 'diya::MARC::glimmer3' object
  190. Parsing 007/008.predict
  191. Using '007/' as output directory
  192. Sequence is 007/008.gbk
  193. 007/2012_11_16_17_41_12-MARC::glimmer3.outFound output file '007/2012_11_16_17_41_12-MARC::glimmer3.out' for 'MARC::glimmer3'
  194. Preparing to run 'extractCDS', step count of 4
  195. 'extractCDS' is a 'script'
  196. 'extractCDS' is a 'script'
  197. Format of 'tmp/NZ_ABZT01' is 'fasta'
  198. No <inputformat> found for step 'extractCDS', no conversion needed
  199. Found <inputfrom> 'MARC::glimmer3' for 'extractCDS'
  200. Output file from 'MARC::glimmer3' will be used as input file for 'extractCDS'
  201. Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'extractCDS'
  202. Found <executable> 'extractCDS.pl' for 'extractCDS' in 'conf/genome-annotator-for-ncbi.xml'
  203. Using '007/' as output directory
  204. Output file name for 'extractCDS' is '007/2012_11_16_17_41_12-extractCDS.out'
  205. Found <home> '/home/jasperk/Apps/DIYA-master/scripts/' for 'extractCDS'
  206. Found <executable> 'extractCDS.pl' for 'extractCDS' in 'conf/genome-annotator-for-ncbi.xml'
  207. Found <command> 'INPUTFILE OUTPUTFILE OUTPUTDIR' for 'extractCDS'
  208. Found <command> 'INPUTFILE OUTPUTFILE OUTPUTDIR' for 'extractCDS'
  209. 'extractCDS' command before substitution is '/home/jasperk/Apps/DIYA-master/scripts/extractCDS.pl INPUTFILE OUTPUTFILE OUTPUTDIR'
  210. 'INPUTFILE' will be substituted with '007/2012_11_16_17_41_12-MARC::glimmer3.out'
  211. 'OUTPUTFILE' will be substituted with '007/2012_11_16_17_41_12-extractCDS.out'
  212. 'extractCDS' command after parser-specific substitution is '/home/jasperk/Apps/DIYA-master/scripts/extractCDS.pl 007/2012_11_16_17_41_12-MARC::glimmer3.out 007/2012_11_16_17_41_12-extractCDS.out OUTPUTDIR'
  213. Using '007/' as output directory
  214. 'OUTPUTDIR' will be substituted with '007/'
  215. 'extractCDS' command after global substitution is '/home/jasperk/Apps/DIYA-master/scripts/extractCDS.pl 007/2012_11_16_17_41_12-MARC::glimmer3.out 007/2012_11_16_17_41_12-extractCDS.out 007/'
  216. 'MYCDD' will be substituted with 'db/cddid_all.tbl'
  217. 'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
  218. 'MYSEQID' will be substituted with '008'
  219. 'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
  220. 'MYRPSD' will be substituted with 'db/cdd/Cdd'
  221. 'OUTPUTDIR' will be substituted with '007'
  222. 'extractCDS' command after variable substitution is '/home/jasperk/Apps/DIYA-master/scripts/extractCDS.pl 007/2012_11_16_17_41_12-MARC::glimmer3.out 007/2012_11_16_17_41_12-extractCDS.out 007/'
  223. <mode> for the pipeline is 'serial'
  224. <mode> for the pipeline is 'serial'
  225. <mode> for the pipeline is 'serial'
  226. <mode> for the pipeline is 'serial'
  227. <mode> for the pipeline is 'serial'
  228.  
  229. Preparing to run 'MARC::blastpCDS', step count of 5
  230. 'MARC::blastpCDS' is a 'parser'
  231. Loaded module 'diya::MARC::blastpCDS'
  232. 'MARC::blastpCDS' is a 'parser'
  233. No <inputformat> for 'MARC::blastpCDS'
  234. Format of 'tmp/NZ_ABZT01' is 'fasta'
  235. No <inputformat> found for step 'MARC::blastpCDS', no conversion needed
  236. Found <inputfrom> 'extractCDS' for 'MARC::blastpCDS'
  237. Output file from 'extractCDS' will be used as input file for 'MARC::blastpCDS'
  238. Found <home> '/usr/bin/' for 'MARC::blastpCDS'
  239. Found <executable> 'blastall' for 'MARC::blastpCDS' in 'conf/genome-annotator-for-ncbi.xml'
  240. Using '007/' as output directory
  241. Output file name for 'MARC::blastpCDS' is '007/2012_11_16_17_41_12-MARC::blastpCDS.out'
  242. Found <home> '/usr/bin/' for 'MARC::blastpCDS'
  243. Found <executable> 'blastall' for 'MARC::blastpCDS' in 'conf/genome-annotator-for-ncbi.xml'
  244. Found <command> '-i INPUTFILE -p blastx -d MYUNIREFD -o OUTPUTFILE -e .001 -v 1 -b 1 -a 8' for 'MARC::blastpCDS'
  245. Found <command> '-i INPUTFILE -p blastx -d MYUNIREFD -o OUTPUTFILE -e .001 -v 1 -b 1 -a 8' for 'MARC::blastpCDS'
  246. 'MARC::blastpCDS' command before substitution is '/usr/bin/blastall -i INPUTFILE -p blastx -d MYUNIREFD -o OUTPUTFILE -e .001 -v 1 -b 1 -a 8'
  247. 'INPUTFILE' will be substituted with '007/2012_11_16_17_41_12-extractCDS.out'
  248. 'OUTPUTFILE' will be substituted with '007/2012_11_16_17_41_12-MARC::blastpCDS.out'
  249. 'MARC::blastpCDS' command after parser-specific substitution is '/usr/bin/blastall -i 007/2012_11_16_17_41_12-extractCDS.out -p blastx -d MYUNIREFD -o 007/2012_11_16_17_41_12-MARC::blastpCDS.out -e .001 -v 1 -b 1 -a 8'
  250. Using '007/' as output directory
  251. 'OUTPUTDIR' will be substituted with '007/'
  252. 'MARC::blastpCDS' command after global substitution is '/usr/bin/blastall -i 007/2012_11_16_17_41_12-extractCDS.out -p blastx -d MYUNIREFD -o 007/2012_11_16_17_41_12-MARC::blastpCDS.out -e .001 -v 1 -b 1 -a 8'
  253. 'MYCDD' will be substituted with 'db/cddid_all.tbl'
  254. 'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
  255. 'MYSEQID' will be substituted with '008'
  256. 'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
  257. 'MYRPSD' will be substituted with 'db/cdd/Cdd'
  258. 'OUTPUTDIR' will be substituted with '007'
  259. 'MARC::blastpCDS' command after variable substitution is '/usr/bin/blastall -i 007/2012_11_16_17_41_12-extractCDS.out -p blastx -d db/uniref50/uniref50.fasta -o 007/2012_11_16_17_41_12-MARC::blastpCDS.out -e .001 -v 1 -b 1 -a 8'
  260. <mode> for the pipeline is 'serial'
  261. <mode> for the pipeline is 'serial'
  262. <mode> for the pipeline is 'serial'
  263. <mode> for the pipeline is 'serial'
  264. <mode> for the pipeline is 'serial'
  265.  
  266. Created 'diya::MARC::blastpCDS' object
  267. 007/2012_11_16_17_41_12-MARC::blastpCDS.outFound output file '007/2012_11_16_17_41_12-MARC::blastpCDS.out' for 'MARC::blastpCDS'
  268. Indexing '007/2012_11_16_17_41_12-MARC::blastpCDS.out'
  269. 007/2012_11_16_17_41_12-MARC::glimmer3.outFound output file '007/2012_11_16_17_41_12-MARC::glimmer3.out' for 'MARC::glimmer3'
  270. Genbank output file is '007/2012_11_16_17_41_12-MARC::blastpCDS.out.gbk'
  271. Preparing to run 'MARC::rpsblastCDS', step count of 6
  272. 'MARC::rpsblastCDS' is a 'parser'
  273. Loaded module 'diya::MARC::rpsblastCDS'
  274. 'MARC::rpsblastCDS' is a 'parser'
  275. No <inputformat> for 'MARC::rpsblastCDS'
  276. Format of 'tmp/NZ_ABZT01' is 'fasta'
  277. No <inputformat> found for step 'MARC::rpsblastCDS', no conversion needed
  278. Found <inputfrom> 'extractCDS' for 'MARC::rpsblastCDS'
  279. Output file from 'extractCDS' will be used as input file for 'MARC::rpsblastCDS'
  280. Found <home> '/usr/bin/' for 'MARC::rpsblastCDS'
  281. Found <executable> 'rpsblast' for 'MARC::rpsblastCDS' in 'conf/genome-annotator-for-ncbi.xml'
  282. Using '007/' as output directory
  283. Output file name for 'MARC::rpsblastCDS' is '007/2012_11_16_17_42_34-MARC::rpsblastCDS.out'
  284. Found <home> '/usr/bin/' for 'MARC::rpsblastCDS'
  285. Found <executable> 'rpsblast' for 'MARC::rpsblastCDS' in 'conf/genome-annotator-for-ncbi.xml'
  286. Found <command> '-d MYRPSD -i INPUTFILE -o OUTPUTFILE -e .001 -I T -p F -v 1 -b 1 -a 8' for 'MARC::rpsblastCDS'
  287. Found <command> '-d MYRPSD -i INPUTFILE -o OUTPUTFILE -e .001 -I T -p F -v 1 -b 1 -a 8' for 'MARC::rpsblastCDS'
  288. 'MARC::rpsblastCDS' command before substitution is '/usr/bin/rpsblast -d MYRPSD -i INPUTFILE -o OUTPUTFILE -e .001 -I T -p F -v 1 -b 1 -a 8'
  289. 'INPUTFILE' will be substituted with '007/2012_11_16_17_41_12-extractCDS.out'
  290. 'OUTPUTFILE' will be substituted with '007/2012_11_16_17_42_34-MARC::rpsblastCDS.out'
  291. 'MARC::rpsblastCDS' command after parser-specific substitution is '/usr/bin/rpsblast -d MYRPSD -i 007/2012_11_16_17_41_12-extractCDS.out -o 007/2012_11_16_17_42_34-MARC::rpsblastCDS.out -e .001 -I T -p F -v 1 -b 1 -a 8'
  292. Using '007/' as output directory
  293. 'OUTPUTDIR' will be substituted with '007/'
  294. 'MARC::rpsblastCDS' command after global substitution is '/usr/bin/rpsblast -d MYRPSD -i 007/2012_11_16_17_41_12-extractCDS.out -o 007/2012_11_16_17_42_34-MARC::rpsblastCDS.out -e .001 -I T -p F -v 1 -b 1 -a 8'
  295. 'MYCDD' will be substituted with 'db/cddid_all.tbl'
  296. 'MYUNIREFD' will be substituted with 'db/uniref50/uniref50.fasta'
  297. 'MYSEQID' will be substituted with '008'
  298. 'MYCLUSTERS' will be substituted with 'db/clusters/PRK_Clusters.bcp'
  299. 'MYRPSD' will be substituted with 'db/cdd/Cdd'
  300. 'OUTPUTDIR' will be substituted with '007'
  301. 'MARC::rpsblastCDS' command after variable substitution is '/usr/bin/rpsblast -d db/cdd/Cdd -i 007/2012_11_16_17_41_12-extractCDS.out -o 007/2012_11_16_17_42_34-MARC::rpsblastCDS.out -e .001 -I T -p F -v 1 -b 1 -a 8'
  302. <mode> for the pipeline is 'serial'
  303. <mode> for the pipeline is 'serial'
  304. <mode> for the pipeline is 'serial'
  305. <mode> for the pipeline is 'serial'
  306. <mode> for the pipeline is 'serial'
  307.  
  308. Created 'diya::MARC::rpsblastCDS' object
  309. Cluster map from 'db/clusters/PRK_Clusters.bcp' loaded
  310. CDD map from 'db/cddid_all.tbl' loaded
  311. 007/2012_11_16_17_42_34-MARC::rpsblastCDS.outFound output file '007/2012_11_16_17_42_34-MARC::rpsblastCDS.out' for 'MARC::rpsblastCDS'
  312. Indexing '007/2012_11_16_17_42_34-MARC::rpsblastCDS.out'
  313. No output file name for parser 'MARC::blastxCDS' found at /usr/local/share/perl/5.14.2/diya.pm line 1542.
RAW Paste Data
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