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Old 11-11-2014, 01:48 PM   #1
milo0615
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Location: Walnut, California

Join Date: Dec 2012
Posts: 39
Default Amos/MuMMer/Minimus2 postnuc running multikmer assembly

Hello,

I am using the following protocol to Merge a multikmer assembly using CDHit && Amos.
protocol: http://ged.msu.edu/angus/metag-assem...et-multik.html

However, after running minimus2, it just hangs on step 20. It has been 6 days now. I was wondering if the software usually takes long on step 20. I dont see any erros on the log file. Have anyone experience anything like this?

Command used:
> minimus2 all-gjcombs &
[1] 44931
[root@b30-fac-staff-134-71-20-58 gerjamdata]# The log file is: all-gjcombs.runAmos.log
Doing step 10: Building AMOS bank & Dumping reads
Doing step 11
Doing step 12
Doing step 13
Doing step 20: Getting overlaps

The following is the log file output for minimus2:

!!! 2014-11-04 13:18:13 Running: /root/Downloads/MUMmer3.23/nucmer -maxmatch -c 40 all-gjcombs.ref.seq all-gjcombs.qry.seq -p all-gjcombs
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "all-gjcombs.ntref" of length 1065681070
# construct suffix tree for sequence of length 1065681070
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# process 10656810 characters per dot
#....................................................................................................
# CONSTRUCTIONTIME /root/Downloads/MUMmer3.23/mummer all-gjcombs.ntref 1055.62
# reading input file "/raid/MultiK_Assembly/gerjamdata/all-gjcombs.qry.seq" of length 1065681069
# matching query-file "/raid/MultiK_Assembly/gerjamdata/all-gjcombs.qry.seq"
# against subject-file "all-gjcombs.ntref"
# COMPLETETIME /root/Downloads/MUMmer3.23/mummer all-gjcombs.ntref 11556.20
# SPACE /root/Downloads/MUMmer3.23/mummer all-gjcombs.ntref 2086.07
4: FINISHING DATA


I would really appreciate your help/suggestions.

thank you,

-Milo
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