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 2753470.0 83359599 Computed coverage is 30.0 Using threshold 7 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. Prefixes for files I will read are [short_X, frag_X] Checking for short_..fastq Checking for frag_..fastq Processing file frag_1.fastq prefix frag_ FOR FASTA OUTPUT Processed 0 reads Processed 1000000 reads Processed 2000000 reads Checking for short_..fastq Checking for frag_..fastq Processing file frag_2.fastq prefix frag_ FOR FASTA OUTPUT Processed 0 reads Processed 1000000 reads Processed 2000000 reads Checking for short_..fastq Processing file short_1.fastq prefix short_ FOR FASTA OUTPUT Processed 0 reads Processed 1000000 reads Processed 2000000 reads Processed 3000000 reads Processed 4000000 reads Processed 5000000 reads Processed 6000000 reads Checking for short_..fastq Processing file short_2.fastq prefix short_ FOR FASTA OUTPUT Processed 0 reads Processed 1000000 reads Processed 2000000 reads Processed 3000000 reads Processed 4000000 reads Processed 5000000 reads Processed 6000000 reads Library file built Launching bowtie aligner: /fs/szattic-asmg5/sergek/GAGE/asmPackage/bin/get_singles.pl -reads ./mapping -assembly ./ -suffix utg.fasta --threads 2 Bowtie finished For file /fs/szattic-asmg5/sergek/GAGE/staph/recipe/test/short_1.bout prefix is short_ Read 0 mapping records from /fs/szattic-asmg5/sergek/GAGE/staph/recipe/test/short_1.bout For file /fs/szattic-asmg5/sergek/GAGE/staph/recipe/test/short_2.bout prefix is short_ Read 0 mapping records from /fs/szattic-asmg5/sergek/GAGE/staph/recipe/test/short_2.bout For file /fs/szattic-asmg5/sergek/GAGE/staph/recipe/test/frag_1.bout prefix is frag_ Read 0 mapping records from /fs/szattic-asmg5/sergek/GAGE/staph/recipe/test/frag_1.bout For file /fs/szattic-asmg5/sergek/GAGE/staph/recipe/test/frag_2.bout prefix is frag_ Read 0 mapping records from /fs/szattic-asmg5/sergek/GAGE/staph/recipe/test/frag_2.bout Processed in 0 contig records real 5m20.748s user 4m2.808s sys 1m27.081s Contig Bank doesn't exist; creating Read Bank doesn't exist; creating frag Bank doesn't exist; creating lib Bank doesn't exist; creating parsing fasta file Read 0 reads Read 1000000 reads Read 2000000 reads Read 3000000 reads Read 4000000 reads Closing frag stream/bank Closing read stream/bank Handling contigs Contig stream closed. real 5m47.668s user 1m49.001s sys 1m43.488s Running bambus 3) running clk... ...success 4) running Bundler... ...success 5) running MarkRepeats... ...success  97 repeats found 6) running OrientContigs... ...success 7) running bank2fasta... ...success  637 contigs 8) running printScaff... ...success! real 4m58.767s user 1m36.552s sys 1m43.978s 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