BOL: Question: Why MeGAMerge terminated with minimus.fasta 1>/dev/null 2>/dev/null failed: error

Question: Question: Why MeGAMerge terminated with minimus.fasta 1>/dev/null 2>/dev/null failed: error

Neelam Jha
2674 days ago

Question: Why MeGAMerge terminated with minimus.fasta 1>/dev/null 2>/dev/null failed: error

I am trying to merge contigs, generated from different assemblies with MeGAMerge, but it failed after running few hour !! Following are the error I got on command prompt. Any suggestions??

perl MeGAMerge-1.1.pl -f MergedDIR allContigs_MIRA_assembled.fa
Running Newbler assembly with 308261 sequences
runAssembly -force -large -rip -mi 98 -ml 80 -pairt -cpu 4 -a 200 -o MergedDIR/newbler MergedDIR/newblerIn.fasta 1>/dev/null 2>/dev/null
Running Minimus2 with 331388 sequences
minimus2 -D CONSERR=0.06 -D MINID=98 -D OVERLAP=80 MergedDIR/minimus.fasta 1>/dev/null 2>/dev/null
minimus2 -D CONSERR=0.06 -D MINID=98 -D OVERLAP=80 MergedDIR/minimus.fasta 1>/dev/null 2>/dev/null failed:
Died at MeGAMerge-1.1.pl line 283.

Best Answer

Well, you might need to check the MeGAMerge log file for detail error message. Can you please reply with your error message from log file please?

Jit 2674 days ago

Thanks Jit, here is the tail section/error section of the log file

!!! 2016-12-23 19:47:50 Doing step 20: Getting overlaps
!!! 2016-12-23 19:47:50 Running: /usr/bin/nucmer -maxmatch -c 80 MergedDIR/minimus.fasta.ref.seq MergedDIR/minimus.fasta.qry.seq -p MergedDIR/minimus.fasta
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "MergedDIR/minimus.fasta.ntref" of length 1584056222
# construct suffix tree for sequence of length 1584056222
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 15840562 characters per dot
/usr/bin/mummer: suffix tree construction failed: textlen=1584056222 larger than maximal textlen=536870908
ERROR: mummer and/or mgaps returned non-zero
!!! 2016-12-23 19:48:43 Command: /usr/bin/nucmer -maxmatch -c 80 MergedDIR/minimus.fasta.ref.seq MergedDIR/minimus.fasta.qry.seq -p MergedDIR/minimus.fasta exited with status: 1
!!! END - Elapsed time: 0d 0h 4m 14s

— Neelam Jha 2674 days ago

Other Answers

Thanks for the update Neelam.

This is specific problem of Mummer,

/usr/bin/mummer: suffix tree construction failed: textlen=1584056222 larger than maximal textlen=536870908
ERROR: mummer and/or mgaps returned non-zero

so you might need to re-install mummer3 http://mummer.sourceforge.net/ with following command:

> make clean
> make CPPFLAGS="-O3 -DSIXTYFOURBITS"

And then set the path in MeGAMerge script and re-run it.

Cheers

Jit 2674 days ago

I got this new error, and just wondering why ???

1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "TESTDATA/minimus.fasta.ntref" of length 3144
# construct suffix tree for sequence of length 3144
# (maximum reference length is 2305843009213693948)
# (maximum query length is 18446744073709551615)
# CONSTRUCTIONTIME /home/urbe/Tools/MUMmer3.23/mummer TESTDATA/minimus.fasta.ntref 0.00
# reading input file "/home/urbe/Tools/MeGAMerge/TESTDATA/minimus.fasta.qry.seq" of length 3143
# matching query-file "/home/urbe/Tools/MeGAMerge/TESTDATA/minimus.fasta.qry.seq"
# against subject-file "TESTDATA/minimus.fasta.ntref"
# COMPLETETIME /home/urbe/Tools/MUMmer3.23/mummer TESTDATA/minimus.fasta.ntref 0.00
# SPACE /home/urbe/Tools/MUMmer3.23/mummer TESTDATA/minimus.fasta.ntref 0.01
4: FINISHING DATA
!!! 2017-01-23 10:50:08 Done! Elapsed time:0d 0h 0m 0s

!!! 2017-01-23 10:50:08 Doing step 21
!!! 2017-01-23 10:50:08 Running: /usr/local/bin/show-coords -H -c -l -o -r -I 98 TESTDATA/minimus.fasta.delta | /home/Tools/amos-3.1.0/bin/nucmerAnnotate | egrep 'BEGIN|END|CONTAIN|IDENTITY' > TESTDATA/minimus.fasta.coords
/bin/sh: 1: /usr/local/bin/show-coords: not found
!!! 2017-01-23 10:50:08 Command: /usr/local/bin/show-coords -H -c -l -o -r -I 98 TESTDATA/minimus.fasta.delta | /home/urbe/Tools/amos-3.1.0/bin/nucmerAnnotate | egrep 'BEGIN|END|CONTAIN|IDENTITY' > TESTDATA/minimus.fasta.coords exited with status: 1
!!! END - Elapsed time: 0d 0h 0m 0s

Neelam Jha 2644 days ago

You might need to update the path of following in minimus2 script

NUCMER=/home/Tools/MUMmer3.23/nucmer
DELTAFILTER=/home/Tools/MUMmer3.23/delta-filter
SHOWCOORDS=/home/Tools/MUMmer3.23/show-coords

with re-installed mummer3 path. By default, it look into bin directory.

Jit 2644 days ago

BOL

Neelam Jha

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Question: Question: Why MeGAMerge terminated with minimus.fasta 1>/dev/null 2>/dev/null failed: error