Pacbio Circularizing and trimming error

Question

[HG]

Hi everyone,

Does anyone familiar with "Circularizing and trimming" of pacbio data. I am flowing as they mention here

Error: from log file like that:

!! 2015-03-24 09:42:42  Doing step 10:  Building AMOS bank & Dumping reads
!!! 2015-03-24 09:42:42  Running: rm -fr circularized.bnk
!!! 2015-03-24 09:42:42  Done! Elapsed time:0d 0h 0m 0s

!!! 2015-03-24 09:42:42  Doing step 11
!!! 2015-03-24 09:42:42  Running: /home/hiren/bio-tool/amos-3.1.0/bin/bank-transact -c -z -b circularized.bnk -m circularized.afg
START DATE: Tue Mar 24 09:42:42 2015
Bank is: circularized.bnk
    0%                                            100%
AFG ..................................................
Messages read: 6
Objects added: 6
Objects deleted: 0
Objects replaced: 0
END DATE:   Tue Mar 24 09:42:42 2015
!!! 2015-03-24 09:42:42  Done! Elapsed time:0d 0h 0m 0s

!!! 2015-03-24 09:42:42  Doing step 12
!!! 2015-03-24 09:42:42  Running: /home/hiren/bio-tool/amos-3.1.0/bin/dumpreads circularized.bnk -M 0 > circularized.ref.seq
Objects seen: 2
Objects written: 2
!!! 2015-03-24 09:42:45  Done! Elapsed time:0d 0h 0m 3s

!!! 2015-03-24 09:42:45  Doing step 13
!!! 2015-03-24 09:42:45  Running: /home/hiren/bio-tool/amos-3.1.0/bin/dumpreads circularized.bnk -m 0 > circularized.qry.seq
Objects seen: 2
Objects written: 2
!!! 2015-03-24 09:42:49  Done! Elapsed time:0d 0h 0m 4s

!!! 2015-03-24 09:42:49  Doing step 20:  Getting overlaps
!!! 2015-03-24 09:42:49  Running: /usr/bin/nucmer -maxmatch -c 40 circularized.ref.seq circularized.qry.seq -p circularized
1: PREPARING DATA

USAGE: /usr/lib/mummer/prenuc  [options]  <reference>

Try '/usr/lib/mummer/prenuc -h' for more information.
ERROR: prenuc returned non-zero
!!! 2015-03-24 09:42:49  Command: /usr/bin/nucmer -maxmatch -c 40 circularized.ref.seq circularized.qry.seq -p circularized exited with status: 1
!!! END - Elapsed time: 0d 0h 0m 7s

and finally it's not circularized the chromosome.

Thanks

[k.mamoud]

Hello, Have you find any solution?

Best,

[HG]

Till now no. But I hope HGAP output have lot of repeated element as I can see from my data. I think may be this is one problem. What do you think?

[k.mamoud]

Hello, I don't think that's the problem have you checked at the step 20, because I can see that you have an error

1: PREPARING DATA

USAGE: /usr/lib/mummer/prenuc  [options]  <reference>

Try '/usr/lib/mummer/prenuc -h' for more information.
ERROR: prenuc returned non-zero

[k.mamoud]

And check also if at the step 21 my *.ovl file is empty, have you the same problem?