Configuration summary: AMOS: /fs/sz-user-supported/Linux-x86_64/packages/AMOS-3.0.1/bin/ CA: /fs/szdevel/core-cbcb-software/Linux-x86_64/packages/wgs-6.1//Linux-amd64/bin/ Terminator: /fs/szattic-asmg5/sergek/GAGE/asmPackage/bin/../Linux-x86_64/bin/terminator Java: /fs/szattic-asmg5/sergek/GAGE/asmPackage/bin:. Running time (/fs/szdevel/core-cbcb-software/Linux-x86_64/packages/wgs-6.1//Linux-amd64/bin/runCA -s /scratch1/sergek/GAGE/rhodo/parallel.spec -d . -p genome ovlOverlapper=ovl doOverlapTrimming=0 bogBadMateDepth=1000 unitigger=bog stopAfter=unitigger *.frg) > runCA.log 2>&1 real 26m27.690s user 99m34.442s sys 4m54.384s Inputs are 4054230.0 140818799 Computed coverage is 35.0 Using threshold 9 Running final cmd time (/fs/szdevel/core-cbcb-software/Linux-x86_64/packages/wgs-6.1//Linux-amd64/bin/runCA -s /scratch1/sergek/GAGE/rhodo/parallel.spec -d . -p genome ovlOverlapper=ovl doOverlapTrimming=0 bogBadMateDepth=9 unitigger=bog stopAfter=utgcns *.frg) > runCA.log 2>&1 real 6m58.388s user 15m52.266s sys 0m42.967s MultiAlignStore::dumpMASRfile()-- Writing './/genome.tigStore/seqDB.v003.utg' unpartitioned. MultiAlignStore::dumpMASRfile()-- Writing './/genome.tigStore/seqDB.v003.ctg' unpartitioned. Writing assembly file Assembly file complete. Writing IID to UID mapping files. IID to UID mapping files complete. All output successfully written. real 2m56.629s user 0m18.645s sys 0m20.501s Scanning store to find libraries used. Added 0 reads to maintain mate relationships. Dumping 0 fragments from unknown library (version 1 has these) Dumping 1408188 fragments from library IID 1 Dumping 1313878 fragments from library IID 2 real 0m32.405s user 0m12.405s sys 0m3.655s time /fs/sz-user-supported/Linux-x86_64/packages/AMOS-3.0.1/bin//toAmos_new -f asm.frgs -a .//genome.asm -U -b genome.bnk Including extra mates from genome.mates The lib name is short real 0m22.128s user 0m25.029s sys 0m6.658s Contig Bank doesn't exist; creating Read Bank doesn't exist; creating frag Bank doesn't exist; creating lib Bank doesn't exist; creating scf Bank doesn't exist; creating link Bank doesn't exist; creating edge Bank doesn't exist; creating Closing frag stream/bank Closing read stream/bank Handling contigs Contig stream closed. Scaffold, link, and edge streams closed real 3m54.627s user 1m32.531s sys 1m21.875s Running bambus 3) running clk... ...success 4) running Bundler... ...success 5) running MarkRepeats... ...success  420 repeats found 6) running OrientContigs... ...success 7) running bank2fasta... ...success  1175 contigs 8) running printScaff... ...success! real 2m46.751s user 0m59.547s sys 1m9.635s