Question: Pacbio Circularizing and trimming error
0
gravatar for HG
5.6 years ago by
HG1.1k
Germany
HG1.1k wrote:

Hi everyone,

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

https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Circularizing-and-trimming

 

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 its not circularized the chromosome. 

Thanks

 

 

pacbio • 1.7k views
ADD COMMENTlink modified 5.6 years ago by k.mamoud10 • written 5.6 years ago by HG1.1k
0
gravatar for k.mamoud
5.6 years ago by
k.mamoud10
Switzerland
k.mamoud10 wrote:

Hello, Have you find any solution ?

 

Best,

ADD COMMENTlink written 5.6 years ago by k.mamoud10

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 ?? 

ADD REPLYlink written 5.6 years ago by HG1.1k

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

ADD REPLYlink written 5.6 years ago by k.mamoud10

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

ADD REPLYlink written 5.6 years ago by k.mamoud10
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