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 doOverlapBasedTrimming=0 ovlOverlapper=ovl bogBadMateDepth=1000 unitigger=bog stopAfter=unitigger *.frg) > runCA.log 2>&1 real 7m40.469s user 14m37.833s sys 1m3.242s Inputs are 2753470.0 83359599 Computed coverage is 30.0 Using threshold 7 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 doOverlapBasedTrimming=0 ovlOverlapper=ovl bogBadMateDepth=7 unitigger=bog stopAfter=utgcns *.frg) > runCA.log 2>&1 real 1m57.209s user 4m48.559s sys 0m11.453s 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 0m35.623s user 0m6.037s sys 0m5.850s Prefixes for files I will read are [short_X, frag_X] 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 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 Checking for short_..fastq Checking for frag_..fastq Checking for short_..fastq Checking for frag_..fastq Checking for short_..fastq Checking for frag_..fastq 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 ../original -assembly ./ -suffix utg.fasta --threads 2 Bowtie finished For file /fs/szattic-asmg5/sergek/GAGE/staph/test/short_1.bout prefix is short_ Read 0 mapping records from /fs/szattic-asmg5/sergek/GAGE/staph/test/short_1.bout For file /fs/szattic-asmg5/sergek/GAGE/staph/test/short_2.bout prefix is short_ Read 0 mapping records from /fs/szattic-asmg5/sergek/GAGE/staph/test/short_2.bout For file /fs/szattic-asmg5/sergek/GAGE/staph/test/frag_1.bout prefix is frag_ Read 0 mapping records from /fs/szattic-asmg5/sergek/GAGE/staph/test/frag_1.bout For file /fs/szattic-asmg5/sergek/GAGE/staph/test/frag_2.bout prefix is frag_ Read 0 mapping records from /fs/szattic-asmg5/sergek/GAGE/staph/test/frag_2.bout Processed in 0 contig records real 6m16.688s user 4m17.795s sys 1m45.851s 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 8m12.749s user 2m10.977s sys 2m21.558s 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 4m11.028s user 1m43.336s sys 1m38.050s