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 ./parallel.spec -d . -p genome doOverlapBasedTrimming=0 ovlOverlapper=ovl bogBadMateDepth=1000 stopAfter=unitigger unitigger=bog *.frg) > runCA.log 2>&1 real 972m19.166s user 8476m16.636s sys 301m21.321s Inputs are 8.81678E7 3426844399 Computed coverage is 39.0 Using threshold 10 Running final cmd (time /fs/szdevel/core-cbcb-software/Linux-x86_64/packages/wgs-6.1//Linux-amd64/bin/runCA -s ./parallel.spec -d . -p genome doOverlapBasedTrimming=0 ovlOverlapper=ovl bogBadMateDepth=10 stopAfter=utgcns unitigger=bog *.frg) > runCA.log 2>&1 real 141m34.759s user 286m52.963s sys 9m56.229s 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 161m38.027s user 6m18.106s sys 6m9.550s Scanning store to find libraries used. Added 0 reads to maintain mate relationships. Dumping 0 fragments from unknown library (version 1 has these) Dumping 34268444 fragments from library IID 1 Dumping 187398 fragments from library IID 2 Dumping 11255320 fragments from library IID 3 real 5m52.771s user 3m49.863s sys 0m54.447s 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 lj The lib name is sj real 8m27.565s user 12m2.700s sys 1m23.436s 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 54m39.029s user 26m19.450s sys 18m24.631s Running bambus 3) running clk... ...success 4) running Bundler... ...success 5) running MarkRepeats... ...success  29076 repeats found 6) running OrientContigs... ...success 7) running bank2fasta... ...success  133914 contigs 8) running printScaff... ...success! real 36m18.186s user 16m17.171s sys 12m22.946s