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: ../../../asmPackage/bin/../Linux-x86_64/bin/terminator Java: ../../../asmPackage/bin:. Inputs are 4054230.0 140818799 Computed coverage is 35.0 Using threshold 9 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. 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 0m34.389s user 0m12.321s sys 0m4.116s 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 0m16.330s user 0m19.562s sys 0m2.952s 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 2m11.180s user 1m24.035s sys 0m28.530s 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 1m27.307s user 0m51.289s sys 0m23.344s Processing file genome_output.contigs.fasta Processing file genome_output.scaffold.fasta BEGIN PROCESSING KEYS DONE PROCESSING KEYS PROCESSED 0 RECORDS FOR OUTPUT Processing file genome_output.contigs.fasta