Pacbio Circularizing and trimming error
1
0
Entering edit mode
6.1 years ago
HG ★ 1.1k

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 • 1.8k views
ADD COMMENT
0
Entering edit mode
6.1 years ago
k.mamoud ▴ 10

Hello, Have you find any solution ?

 

Best,

ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2516 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6