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  • ewilbanks
    Member
    • Mar 2009
    • 83
    #1

    minimus2 assembly merge

    Hi folks,

    I'm using minimus2 to merge two different assemblies - a long read (LRseq - moleculo data) assembly done w/ celera and an idba_ud assembled illumina dataset. I've tried varying the required overlap from 250 to 1kb and I'm getting output in some of the log files that confuses me. Does anyone know why even if -D OVERLAP=250 (as in command below) it would say that the minimum overlap allowed was 5? Shouldn't this value be 250? or am I misunderstanding this parameter? The whole log file for this run is attached in case that helps clarify things. Thanks in advance!

    Lizzy

    minimus2 asmMeta.hyb1-contig-250-500 -D REFCOUNT=2030 -D OVERLAP=250

    ...... relevant section from runAmos.log.....
    Read bank is asmMeta.hyb1-contig-250-500.bnk
    Alignment error rate is 0.06
    Minimum overlap bases is 5
    Output will be written to the bank
    Input is being read from the bank
    Processed 1031 layouts
    ................................................................





    --------------------------------------
    whole log output
    ----------------------------------------


    !!! 2013-09-27 10:19:14 Started by [email protected] on Fri Sep 27 10:19:14 2013

    !!! 2013-09-27 10:19:15 Doing step 10: Building AMOS bank & Dumping reads
    !!! 2013-09-27 10:19:15 Running: rm -fr asmMeta.hyb1-contig-250-500.bnk
    !!! 2013-09-27 10:19:15 Done! Elapsed time:0d 0h 0m 0s

    !!! 2013-09-27 10:19:15 Doing step 11
    !!! 2013-09-27 10:19:15 Running: /home/ewilbanks/software/amos-3.1.0/bin/bank-transact -c -z -b asmMeta.hyb1-contig-250-500.bnk -m asmMeta.hyb1-contig-250-500.afg
    START DATE: Fri Sep 27 10:19:15 2013
    Bank is: asmMeta.hyb1-contig-250-500.bnk
    0% 100%
    AFG ..................................................
    Messages read: 125110
    Objects added: 125110
    Objects deleted: 0
    Objects replaced: 0
    END DATE: Fri Sep 27 10:19:36 2013
    !!! 2013-09-27 10:19:37 Done! Elapsed time:0d 0h 0m 22s

    !!! 2013-09-27 10:19:37 Doing step 12
    !!! 2013-09-27 10:19:37 Running: /home/ewilbanks/software/amos-3.1.0/bin/dumpreads asmMeta.hyb1-contig-250-500.bnk -M 2030 > asmMeta.hyb1-contig-250-500.ref.seq
    Objects seen: 62554
    Objects written: 2030
    !!! 2013-09-27 10:19:42 Done! Elapsed time:0d 0h 0m 5s

    !!! 2013-09-27 10:19:42 Doing step 13
    !!! 2013-09-27 10:19:42 Running: /home/ewilbanks/software/amos-3.1.0/bin/dumpreads asmMeta.hyb1-contig-250-500.bnk -m 2030 > asmMeta.hyb1-contig-250-500.qry.seq
    Objects seen: 62554
    Objects written: 60524
    !!! 2013-09-27 10:20:03 Done! Elapsed time:0d 0h 0m 21s

    !!! 2013-09-27 10:20:03 Doing step 20: Getting overlaps
    !!! 2013-09-27 10:20:03 Running: /home/ewilbanks/bin/nucmer -maxmatch -c 250 asmMeta.hyb1-contig-250-500.ref.seq asmMeta.hyb1-contig-250-500.qry.seq -p asmMeta.hyb1-contig-250-500
    1: PREPARING DATA
    2,3: RUNNING mummer AND CREATING CLUSTERS
    # reading input file "asmMeta.hyb1-contig-250-500.ntref" of length 33402029
    # construct suffix tree for sequence of length 33402029
    # (maximum reference length is 536870908)
    # (maximum query length is 4294967295)
    # process 334020 characters per dot
    #....................................................................................................
    # CONSTRUCTIONTIME /home/ewilbanks/software/MUMmer3.23/mummer asmMeta.hyb1-contig-250-500.ntref 14.76
    # reading input file "/share/eisen-z2/ewilbanks/Moleculo/celera.assemble/full_sergey2/asmMeta/9-terminator/minimus2merge/asmMeta.hyb1-contig-250-500.qry.seq" of length 148717247
    # matching query-file "/share/eisen-z2/ewilbanks/Moleculo/celera.assemble/full_sergey2/asmMeta/9-terminator/minimus2merge/asmMeta.hyb1-contig-250-500.qry.seq"
    # against subject-file "asmMeta.hyb1-contig-250-500.ntref"
    # COMPLETETIME /home/ewilbanks/software/MUMmer3.23/mummer asmMeta.hyb1-contig-250-500.ntref 180.23
    # SPACE /home/ewilbanks/software/MUMmer3.23/mummer asmMeta.hyb1-contig-250-500.ntref 176.61
    4: FINISHING DATA
    !!! 2013-09-27 10:24:26 Done! Elapsed time:0d 0h 4m 23s

    !!! 2013-09-27 10:24:26 Doing step 21
    !!! 2013-09-27 10:24:26 Running: /home/ewilbanks/bin/show-coords -H -c -l -o -r -I 94 asmMeta.hyb1-contig-250-500.delta | /home/ewilbanks/software/amos-3.1.0/bin/nucmerAnnotate | egrep 'BEGIN|END|CONTAIN|IDENTITY' > asmMeta.hyb1-contig-250-500.coords
    !!! 2013-09-27 10:24:27 Done! Elapsed time:0d 0h 0m 1s

    !!! 2013-09-27 10:24:27 Doing step 22
    !!! 2013-09-27 10:24:27 Running: /home/ewilbanks/software/amos-3.1.0/bin/nucmer2ovl -ignore 20 -tab asmMeta.hyb1-contig-250-500.coords | /home/ewilbanks/software/amos-3.1.0/bin/sort2 > asmMeta.hyb1-contig-250-500.ovl
    !!! 2013-09-27 10:24:27 Done! Elapsed time:0d 0h 0m 0s

    !!! 2013-09-27 10:24:27 Doing step 23: Converting overlaps
    !!! 2013-09-27 10:24:27 Running: /home/ewilbanks/software/amos-3.1.0/bin/ovl2OVL asmMeta.hyb1-contig-250-500.ovl > asmMeta.hyb1-contig-250-500.OVL
    !!! 2013-09-27 10:24:27 Done! Elapsed time:0d 0h 0m 0s

    !!! 2013-09-27 10:24:27 Doing step 24: Loading overlaps to the bank
    !!! 2013-09-27 10:24:27 Running: rm -f asmMeta.hyb1-contig-250-500.bnk/OVL.*
    !!! 2013-09-27 10:24:27 Done! Elapsed time:0d 0h 0m 0s

    !!! 2013-09-27 10:24:27 Doing step 25
    !!! 2013-09-27 10:24:27 Running: /home/ewilbanks/software/amos-3.1.0/bin/bank-transact -z -b asmMeta.hyb1-contig-250-500.bnk -m asmMeta.hyb1-contig-250-500.OVL
    START DATE: Fri Sep 27 10:24:27 2013
    Bank is: asmMeta.hyb1-contig-250-500.bnk
    0% 100%
    AFG ..................................................
    Messages read: 6242
    Objects added: 6242
    Objects deleted: 0
    Objects replaced: 0
    END DATE: Fri Sep 27 10:24:27 2013
    !!! 2013-09-27 10:24:27 Done! Elapsed time:0d 0h 0m 0s

    !!! 2013-09-27 10:24:27 Doing step 30: Running contigger
    !!! 2013-09-27 10:24:27 Running: rm -f asmMeta.hyb1-contig-250-500.bnk/LAY.*
    !!! 2013-09-27 10:24:27 Done! Elapsed time:0d 0h 0m 0s

    !!! 2013-09-27 10:24:27 Doing step 31
    !!! 2013-09-27 10:24:27 Running: /home/ewilbanks/software/amos-3.1.0/bin/tigger -b asmMeta.hyb1-contig-250-500.bnk
    Pulling reads from bank asmMeta.hyb1-contig-250-500.bnk
    Pulled 62554 reads from bank
    Pulling overlaps from bank asmMeta.hyb1-contig-250-500.bnk
    Pulled 6242 overlaps from bank
    total contained reads hidden 2264
    number of contigs 59469
    this pass containment size is 2264
    2264 containment reads added back on this pass
    sub-total contained reads unhidden 2264
    total contained reads unhidden 2264
    Writing layouts to bank asmMeta.hyb1-contig-250-500.bnk
    !!! 2013-09-27 10:24:28 Done! Elapsed time:0d 0h 0m 1s

    !!! 2013-09-27 10:24:28 Doing step 40: Running consensus
    !!! 2013-09-27 10:24:28 Running: rm -f asmMeta.hyb1-contig-250-500.bnk/CTG.*
    !!! 2013-09-27 10:24:28 Done! Elapsed time:0d 0h 0m 0s

    !!! 2013-09-27 10:24:28 Doing step 41
    !!! 2013-09-27 10:24:28 Running: /home/ewilbanks/software/amos-3.1.0/bin/make-consensus -B -e 0.06 -b asmMeta.hyb1-contig-250-500.bnk -w 15
    Starting on Fri Sep 27 10:24:28 2013

    Read bank is asmMeta.hyb1-contig-250-500.bnk
    Alignment error rate is 0.06
    Minimum overlap bases is 5
    Output will be written to the bank
    Input is being read from the bank
    Processed 1031 layouts
    !!! 2013-09-27 10:25:59 Done! Elapsed time:0d 0h 1m 31s

    !!! 2013-09-27 10:25:59 Doing step 50: Outputting contigs
    !!! 2013-09-27 10:25:59 Running: /home/ewilbanks/software/amos-3.1.0/bin/bank2contig asmMeta.hyb1-contig-250-500.bnk > asmMeta.hyb1-contig-250-500.contig
    Processing asmMeta.hyb1-contig-250-500.bnk at Fri Sep 27 10:25:59 2013
    End: Fri Sep 27 10:26:02 2013
    !!! 2013-09-27 10:26:11 Done! Elapsed time:0d 0h 0m 12s

    !!! 2013-09-27 10:26:11 Doing step 60: Converting to FastA file
    !!! 2013-09-27 10:26:11 Running: /home/ewilbanks/software/amos-3.1.0/bin/bank2fasta -b asmMeta.hyb1-contig-250-500.bnk > asmMeta.hyb1-contig-250-500.fasta
    !!! 2013-09-27 10:26:23 Done! Elapsed time:0d 0h 0m 12s

    !!! 2013-09-27 10:26:23 Doing step 70: Getting singletons
    !!! 2013-09-27 10:26:23 Running: /home/ewilbanks/software/amos-3.1.0/bin/listReadPlacedStatus -S -E asmMeta.hyb1-contig-250-500.bnk > asmMeta.hyb1-contig-250-500.singletons
    !!! 2013-09-27 10:26:23 Done! Elapsed time:0d 0h 0m 0s

    !!! 2013-09-27 10:26:23 Doing step 71
    !!! 2013-09-27 10:26:23 Running: /home/ewilbanks/software/amos-3.1.0/bin/dumpreads -e -E asmMeta.hyb1-contig-250-500.singletons asmMeta.hyb1-contig-250-500.bnk > asmMeta.hyb1-contig-250-500.singletons.seq
    Objects seen: 58438
    Objects written: 58438
    !!! 2013-09-27 10:26:41 Done! Elapsed time:0d 0h 0m 18s

    !!! END - Elapsed time: 0d 0h 7m 27s
    Tags: amos, assembly, merge, minimus2
    • Kennels
      Senior Member
      • Feb 2011
      • 149
      #2
      I've run minimus2 before without setting any -D parameters. The default for overlap is supposed to be 40, but in my log file it says the same as you: minimum overlap is 5.

      So maybe this is just a log file reporting issue? I tried to find this in the code but couldn't pinpoint it. Perhaps you will have better luck?

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