Bug 304563

Summary:	sci-biology/allpaths installs ELF files in /usr/share
Product:	Gentoo Linux	Reporter:	Diego Elio Pettenò (RETIRED) <flameeyes>
Component:	New packages	Assignee:	Andrey Kislyuk (RETIRED) <weaver>
Status:	RESOLVED FIXED
Severity:	normal	CC:	sci-biology, ssundar86
Priority:	High
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---

Description Diego Elio Pettenò (RETIRED) gentoo-dev

2010-02-11 14:56:32 UTC

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

Comment 1 sundar 2010-07-27 08:25:16 UTC

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

Comment 2 sundar 2010-07-27 08:27:48 UTC

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

Comment 3 Justin Lecher (RETIRED) gentoo-dev

2010-07-27 08:33:03 UTC

What do you want to tell us with that?

Comment 4 Andrey Kislyuk (RETIRED) gentoo-dev

2011-01-25 17:31:59 UTC

Fixed in sci-biology/allpathslg