ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/UnipathsFromTrustedKmers ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/ShortQueryLookup ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/Fastb2Fasta ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/Qualb2Quala ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/ExtractSolexaReads ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/UnipathLocs ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/CorrectUnipaths ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/Vote ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/EvaluateCorrectedPairs ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrustedB1 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MakeNormalEdgeGraph ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/UnipathEval ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/GenomeReadLocs ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/RemoveSuspiciousReads2 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrustedASub ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MakeRcDb ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/GenomeToPaths ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/checkLock ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/EvaluateStrongKmers ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/UnibaseCopyNumberIdeal ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/TrustedFromQuals ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/LookAlignsToGaplessAligns ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrusted4 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrustedA1 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/ReadsToPaths ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkGenomicKmersInReads ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrustedA3 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/RecoverUnipaths ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/RescueKmers ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/BuildUnipathLinkGraphs ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrustedB2 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/PanForGold ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/CleanHyper ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/FindGenomicKmers ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/GcBiasCurve2 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/GetTruerReads ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/UnibasesFromTrustedKAdjs ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/EvalTrusted ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/SimulateReads ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/Singe ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/Unipather ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/FindUnipathLocs ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrustedB3 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/UniquifyAligns2 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/LibraryStatsFromUnibases ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/QueryLookupTable ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/Shaver ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/RePath ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/PrepareAllPathsInput ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/GenomeSizeFromUnibases ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrustedA2 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/FindLinks0 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrusted5 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/Quala2Qualb ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/EvalHyper ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/PrepareGenome ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/FindKmerFrequencies ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/UnipatherBig ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/RunAllPaths ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/BitvectorOp ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/LocalizeReads ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/ViewHyper ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrusted2 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MakeLookupTable ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrusted6 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/PathsToLocs ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/FindLinks ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/DumpHyper ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/FastbStats ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MakeDepend ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/TrueUnipathCoverage ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/StandardScaffold ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/ImperfectLookupTable ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/UnibaseCopyNumber ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/Fasta2Fastb ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/MarkTrusted1 ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/KAdjsFromUnibases ET_EXEC /var/tmp/portage/sci-biology/allpaths-2.0/image//usr/share/allpaths/bin/ProvisionalEdits
sundar@sundar-desktop:/media/ubuntu/allpaths-2.2/src$ ./RunAllPaths PRE=zainoutputdir DATA_SUBDIR=MyTestData RUN=MyRun REFERENCE_NAME=Staph TARGETS=all SOURCE_DIR=input/input.sample_reads REFERENCE_FASTB=input/input.reference/genome.fastb K=20 EVALUATION=REFERENCE MAXPAR=1 PARALLEL_BATCHES=1 -------------------------------------------------------------------------------- Tue Jul 27 13:39:59 2010 run (pid=9194) RunAllPaths PRE=zainoutputdir DATA_SUBDIR=MyTestData RUN=MyRun \ REFERENCE_NAME=Staph TARGETS=all \ SOURCE_DIR=input/input.sample_reads \ REFERENCE_FASTB=input/input.reference/genome.fastb K=20 \ EVALUATION=REFERENCE MAXPAR=1 PARALLEL_BATCHES=1 -------------------------------------------------------------------------------- running on sundar-desktop MARK_TRUSTED_A_MIN_SUPPORT = 4, MARK_TRUSTED_A_MAX_UNSUPPORTED_TO_TEST = 5, MARK_TRUSTED_B_MIN_SUPPORT = 4, MARK_TRUSTED_B_MAX_UNSUPPORTED_TO_TEST = 5 run dir is zainoutputdir/Staph/MyTestData/MyRun Found existing genome.fastb file in reference directory. Ignoring REFERENCE_FASTB option. targetsToMake = 174 zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/CleanHyper.out zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/EvalHyper.out zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/FindLinks.out zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/LocalizeReads.out zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/RecoverUnipaths.out zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/StandardScaffold.out zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper.extra.fastb zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper.extra.to_align zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper.fasta zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper.fastb zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper.initial zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper.links zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper.lookup zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper.normalEdgeGraph zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper.normalEdgeGraph.fastb zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/hyper.trusted_paths zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/linear_scaffolds.fasta zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/reads.qltout zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/reads.qltout.filtered zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/run/reads.fastb zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/run/reads.paths.k20 zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/run/reads.paths_rc.k20 zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/run/reads.pathsdb.k20 zainoutputdir/Staph/MyTestData/MyRun/ASSEMBLIES/test/showTrusted/index.html zainoutputdir/Staph/MyTestData/MyRun/genome.size zainoutputdir/Staph/MyTestData/MyRun/reads.aligns_to_ref.ilt.qltout zainoutputdir/Staph/MyTestData/MyRun/reads.aligns_to_ref.uniq.ilt.qltout zainoutputdir/Staph/MyTestData/MyRun/reads.fastb zainoutputdir/Staph/MyTestData/MyRun/reads.id_map zainoutputdir/Staph/MyTestData/MyRun/reads.lengths zainoutputdir/Staph/MyTestData/MyRun/reads.pairto zainoutputdir/Staph/MyTestData/MyRun/reads.pairto_index zainoutputdir/Staph/MyTestData/MyRun/reads.pairtob zainoutputdir/Staph/MyTestData/MyRun/reads.paths.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.paths_rc.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.pathsdb.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.ref.locs zainoutputdir/Staph/MyTestData/MyRun/reads.ref.locs_index zainoutputdir/Staph/MyTestData/MyRun/reads.ref.locs_indexr zainoutputdir/Staph/MyTestData/MyRun/reads.trusted_unipaths.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.trusted_unipathsdb.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.unibases.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.unilocs.20.10.1 zainoutputdir/Staph/MyTestData/MyRun/reads.unilocs.20.10.1.indexr zainoutputdir/Staph/MyTestData/MyRun/reads.unipathgraph.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.unipathgraph_fp.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.unipathgraphplus.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.unipaths.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.unipaths.predicted_count.k20 zainoutputdir/Staph/MyTestData/MyRun/reads.unipathsdb.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_ec.fastb zainoutputdir/Staph/MyTestData/MyRun/reads_ec.lane_index zainoutputdir/Staph/MyTestData/MyRun/reads_ec.lane_infos zainoutputdir/Staph/MyTestData/MyRun/reads_ec.pairto zainoutputdir/Staph/MyTestData/MyRun/reads_ec.pairto_index zainoutputdir/Staph/MyTestData/MyRun/reads_ec.pairtob zainoutputdir/Staph/MyTestData/MyRun/reads_newsep.pairto zainoutputdir/Staph/MyTestData/MyRun/reads_newsep.pairto_index zainoutputdir/Staph/MyTestData/MyRun/reads_newsep.pairtob zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.aligns_to_unibases.ilt.qltout zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.fastb zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.id_map zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.lane_index zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.lane_infos zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.lengths zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.pairto zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.pairto_index zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.pairtob zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.paths.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.paths_rc.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_nosusp.pathsdb.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.aligns_to_ref.ilt.qltout zainoutputdir/Staph/MyTestData/MyRun/reads_orig.aligns_to_ref.uniq.ilt.qltout zainoutputdir/Staph/MyTestData/MyRun/reads_orig.fastb zainoutputdir/Staph/MyTestData/MyRun/reads_orig.fastb.trusted_as_strong.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.fastb.trusted_as_strong.k21 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.fastb.trusted_as_strong.k21.EvaluateStrongKmers.out zainoutputdir/Staph/MyTestData/MyRun/reads_orig.freq_table.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.freq_table.k21 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.gc_bias.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.genomic_unibases.k20.UnipathEval.out zainoutputdir/Staph/MyTestData/MyRun/reads_orig.genomic_unibases.k20.fastb zainoutputdir/Staph/MyTestData/MyRun/reads_orig.genomic_unibases.k20.lookup zainoutputdir/Staph/MyTestData/MyRun/reads_orig.genomic_unibases.predicted_count.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.genomic_unipaths.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.genomic_unipathsdb_big.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.lane_index zainoutputdir/Staph/MyTestData/MyRun/reads_orig.lane_infos zainoutputdir/Staph/MyTestData/MyRun/reads_orig.lanes zainoutputdir/Staph/MyTestData/MyRun/reads_orig.lengths zainoutputdir/Staph/MyTestData/MyRun/reads_orig.pairto zainoutputdir/Staph/MyTestData/MyRun/reads_orig.pairto_index zainoutputdir/Staph/MyTestData/MyRun/reads_orig.pairtob zainoutputdir/Staph/MyTestData/MyRun/reads_orig.props zainoutputdir/Staph/MyTestData/MyRun/reads_orig.qualb zainoutputdir/Staph/MyTestData/MyRun/reads_orig.strong_kmers.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.strong_kmers.k21 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_adjGraph.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_adjGraph.panned.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_adjGraph.panned.shaved.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_as_strong.k21 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_as_strong.panned.k21 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_as_strong.panned.shaved.k21 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_as_strong.panned.shaved.k21.EvaluateStrongKmers.out zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_kmers.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_kmers.k21 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_kmers_A.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_kmers_A.k21 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_kmers_occs.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_kmers_occs_A.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_unibases.corrected.k20.UnipathEval.out zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_unibases.corrected.k20.fastb zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_unibases.corrected.k20.lookup zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_unibases.corrected.predicted_count.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_unibases.k20.fastb zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_unibases.panned.k20.fastb zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_unibases.panned.shaved.k20.fastb zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_unipathGraph.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_unipathGraph.panned.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.trusted_unipaths.predicted_count.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.unsure_kmers_A.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.unsure_kmers_cols_A.k20 zainoutputdir/Staph/MyTestData/MyRun/reads_orig.unsure_kmers_occs_A.k20 zainoutputdir/Staph/MyTestData/genome.fastb zainoutputdir/Staph/MyTestData/genome.freq_table.k20 zainoutputdir/Staph/MyTestData/genome.freq_table.k21 zainoutputdir/Staph/MyTestData/genome.lookup zainoutputdir/Staph/MyTestData/genome.paths.k20 zainoutputdir/Staph/MyTestData/genome.paths_rc.k20 zainoutputdir/Staph/MyTestData/genome.pathsdb_big.k20 zainoutputdir/Staph/MyTestData/genome.unibases.k20 zainoutputdir/Staph/MyTestData/genome.unibases.k20.lookup zainoutputdir/Staph/MyTestData/genome.unipaths.k20 zainoutputdir/Staph/MyTestData/genome.unipaths.placements.k20 zainoutputdir/Staph/MyTestData/genome.unipaths.true_count.k20 zainoutputdir/Staph/MyTestData/genome.unipathsdb_big.k20 zainoutputdir/Staph/MyTestData/ploidy zainoutputdir/Staph/MyTestData/reads_orig.aligns_to_ref.gapless_aligns zainoutputdir/Staph/MyTestData/reads_orig.aligns_to_ref.ilt.qltout zainoutputdir/Staph/MyTestData/reads_orig.aligns_to_ref.uniq.gapless_aligns zainoutputdir/Staph/MyTestData/reads_orig.aligns_to_ref.uniq.ilt.qltout zainoutputdir/Staph/MyTestData/reads_orig.confirmedWithRef.bitvector zainoutputdir/Staph/MyTestData/reads_orig.editedWithRef.fastb zainoutputdir/Staph/MyTestData/reads_orig.fastb zainoutputdir/Staph/MyTestData/reads_orig.freq_table.k20 zainoutputdir/Staph/MyTestData/reads_orig.freq_table.k21 zainoutputdir/Staph/MyTestData/reads_orig.kmerCopyNums.k20 zainoutputdir/Staph/MyTestData/reads_orig.kmerCopyNums.k21 zainoutputdir/Staph/MyTestData/reads_orig.kmerGenomic.k20 zainoutputdir/Staph/MyTestData/reads_orig.kmerGenomic.k21 zainoutputdir/Staph/MyTestData/reads_orig.lane_index zainoutputdir/Staph/MyTestData/reads_orig.lane_infos zainoutputdir/Staph/MyTestData/reads_orig.lanes zainoutputdir/Staph/MyTestData/reads_orig.lengths zainoutputdir/Staph/MyTestData/reads_orig.missingGenomic.k20 zainoutputdir/Staph/MyTestData/reads_orig.missingGenomic.k21 zainoutputdir/Staph/MyTestData/reads_orig.pairto zainoutputdir/Staph/MyTestData/reads_orig.pairto_index zainoutputdir/Staph/MyTestData/reads_orig.pairtob zainoutputdir/Staph/MyTestData/reads_orig.props zainoutputdir/Staph/MyTestData/reads_orig.qualb zainoutputdir/Staph/genome.fastb zainoutputdir/Staph/genome.lookup zainoutputdir/Staph/genome.paths.k20 zainoutputdir/Staph/genome.paths_rc.k20 zainoutputdir/Staph/genome.pathsdb_big.k20 zainoutputdir/Staph/genome.unibases.k20 zainoutputdir/Staph/genome.unibases.k20.lookup zainoutputdir/Staph/genome.unipaths.k20 zainoutputdir/Staph/genome.unipaths.placements.k20 zainoutputdir/Staph/genome.unipaths.true_count.k20 zainoutputdir/Staph/genome.unipathsdb_big.k20 forceTargets = 0 Copy of makefile in: zainoutputdir/Staph/make_mgr/MyTestData/MyRun/test/2010-07-27T13:39:59.make [cp] cp $(REF)/genome.fastb $(DATA)/genome.fastb [cp] Finished command cp [FGK] [FGK] === Build genome kmer frequency table === [FGK] [FGK] Calling FindGenomicKmers to create 1 file(s): [FGK] [FGK] $(DATA)/genome.freq_table.k20 [FGK] [FGK] from 1 file(s): [FGK] [FGK] $(DATA)/genome.fastb [FGK] [FGK] FindGenomicKmers PRE=zainoutputdir DATA=Staph/MyTestData K=20 REBUILD=True /bin/sh: FindGenomicKmers: not found make: *** [zainoutputdir/Staph/MyTestData/genome.freq_table.k20] Error 127
What do you want to tell us with that?
Fixed in sci-biology/allpathslg