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Old 09-27-2013, 03:44 PM   #1
ewilbanks
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Location: Davis, CA

Join Date: Mar 2009
Posts: 82
Default 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 ewilbanks@gpu-0-0.merlot.genomecenter.ucdavis.edu 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
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Old 09-29-2013, 08:35 PM   #2
Kennels
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Location: Sydney

Join Date: Feb 2011
Posts: 149
Default

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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