Minimus2 error at step 41

[k2bhide]

Hello everyone,
I used Minimus2 to combine 454 sequence data's newbler assembly and Illumina data's velvet assembly. I was not able to use Minimus2 to combine some set of velvet assembly files with newbler assembly files. Minimus stopped at step41 and job got killed.

Error in the log file is as follows
Command:/usr/local/bin/make-consensus -B -e 0.06 -b combined.bnk -w 15 failed:likely through abort() or coredump

It would be really helpful if someone could suggest a fix for the problem.

Regards
Ketaki

[sagarutturkar]

I got the similar error at step 41. Log is as below:
--------------------------------------------------------------------------------------------------
!!! 2011-10-11 15:55:22 Doing step 41
!!! 2011-10-11 15:55:22 Running: /usr/local/amos-3.0.1/bin/make-consensus -B -e 0.06 -b combine.bnk -w 15
Starting on Tue Oct 11 15:55:22 2011

Read bank is combine.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
Failed on 8'th layout/contig
** Standard Exception **
WHAT: std::bad_alloc

!!! 2011-10-11 16:52:35 Command: /usr/local/amos-3.0.1/bin/make-consensus -B -e 0.06 -b combine.bnk -w 15 exited with status: 1
!!! END - Elapsed time: 0d 0h 57m 37s
---------------------------------------------------------------------------------------------------------------------

Suggest some fix

[danbrami]

I too am getting the same sort of error;
I have feeling its related to the length of your input contigs. I wonder if tweaking the overlap parameters will push it through...

[chienchi]

I have same issue.

I try to lower the alignment error rate to 0.05 and it is running....

-e <x> Set alignment error rate to <x>

[zhoufan]

I have same issue too.With "-D CONSERR=0.07" it's ok now.

[zhoufan]

I've encountered another issue:
!!! 2014-04-18 16:48:48 Doing step 41
!!! 2014-04-18 16:48:48 Running: /home/liangdq/bin/assemble/AMOS/amos-3.1.0/bin/make-consensus -B -e 0.06 -b asm.bnk -w 15
Starting on Fri Apr 18 16:48:48 2014

Read bank is asm.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
Killed
AMOS/amos-3.1.0/bin/make-consensus -B -e 0.06 -b asm.bnk -w 15 exited with status: 137

Any suggestion would be helpful.