newbler ace to amos bnk

[coldturkey]

does anyone know how to convert a newbler derived ace file to amos bnk so i can use amosvalidate. I know the standard command to do this using toAmos, however, we i do this lose mate pair information.
I tried using toAmos with a traceinfo file derived from sff_extract which seemed to work but when i ran amosvalidate i encountered the following error

Command: /usr/local/bioinf/Amos/bin/asmQC -b 454Contigs.bnk -scaff -recompute -update -numsd 2 exited with status:1

can anyone help?

regards

Brian

[coldturkey]

in case anyone is interested



Unfortunately, we don't support 454 mates at this time, so I recommend you skip
the mate analysis of amosvalidate. Copy the amosvalidate script to a new
location:

$ cp /path/to/amos/bin/amosvalidate amosvalidate-nomates

Edit the script to remove the mate analysis by commenting out steps 300-340

## Analyzing mate-pairs
## 300: $(BINDIR)/asmQC -b $(PREF).bnk -scaff -recompute -update -numsd 2
## 310: $(BINDIR)/asmQC -b $(PREF).bnk -scaff -recompute -update -numsd 2
## 320: $(BINDIR)/asmQC -b $(PREF).bnk -scaff -feat -numsd 3 -shortcvg -1 -longcvg
-1
## 330: $(BINDIR)/cestat-cov -i -f 4 $(PREF).bnk > $(PREF).ce.feat
## 340: $(BINDIR)/loadFeatures -i $(PREF).bnk $(PREF).ce.feat

Then try the new script
$ amosvalidate-nomates 454Contigs

Good luck!

Michael Schatz


Which leads me to ask if there is any program which can be used to validate 454 mate pair assemblies

[AppleInformatics]

Hi All,
I am attempting to use amosalidate to perform assembly forensics. I am stuck, however, as everytime I follow the instructions on the amos wiki to convert my newbler .ace file to a .bnk, I get the following error:

$ toAmos -ace 454Contigs.ace.1 -o - | bank-transact -m - -o 454Contigs.bnk -c
bank-transact: invalid option -- o
ERROR: The -b option is mandatory
ERROR: Bank directory is not accessible, No such file or directory


.USAGE.
bank-transact [options] -b <bank path> -m <message path>
Try 'bank-transact -h' for more information.



Any suggestions? Thanks a bunch!

[shahid.manzoor]

hi me shahid plz can any body help me i m using velvet for denovo and producing afg file and from that afg file creating amos bank file but when i run amos validate command on that bnk folder it give error like this:
Doing step 100: Creating FastA
Command: /usr/local/amos/bin/bank2fasta -b /home/shahid/denovo_run2/bank/assembly.bnk/.bnk > /home/shahid/denovo_run2/bank/assembly.bnk/.fasta exited with status: 1

so any body can help me what this error come and any suggestion for solution.thanks

[ZhigangLi]

hi me shahid plz can any body help me i m using velvet for denovo and producing afg file and from that afg file creating amos bank file but when i run amos validate command on that bnk folder it give error like this:
Doing step 100: Creating FastA
Command: /usr/local/amos/bin/bank2fasta -b /home/shahid/denovo_run2/bank/assembly.bnk/.bnk > /home/shahid/denovo_run2/bank/assembly.bnk/.fasta exited with status: 1

so any body can help me what this error come and any suggestion for solution.thanks

A similar error is returned when i use amosvalidate!

[Irsan_Kooi]

I have the same problem exactly the same problem as shahid.manzoor. I do velvet assembly with create .afg file option, put it in the AMOS bank, no problem. When I do amosvalidate I get the same response unfortunately...

Does anyone know how to do it the right way?

[nathanhaigh]

I am attempting to use amosalidate to perform assembly forensics. I am stuck, however, as everytime I follow the instructions on the amos wiki to convert my newbler .ace file to a .bnk, I get the following error:

[I]$ toAmos -ace 454Contigs.ace.1 -o - | bank-transact -m - -o 454Contigs.bnk -c
bank-transact: invalid option -- o
ERROR: The -b option is mandatory
ERROR: Bank directory is not accessible, No such file or directory

I know this is an old thread, but thought I would add what I've done recently to convert Newbler ACE files to AMOS bank:

toAmos -ace newbler_assembly.ace -o - | bank-transact -m - -b newbler_assembly.bnk -c

[nangillala]

I have the same problem exactly the same problem as shahid.manzoor. I do velvet assembly with create .afg file option, put it in the AMOS bank, no problem. When I do amosvalidate I get the same response unfortunately...

Does anyone know how to do it the right way?

Hi,
I know it's an old thread but I ran into the same problem. It seems as if the solution is the following:
I guess you used tab-complete to write the bank name?
So you would have something like this as an input:

amosvalidate assembly.bnk/

just cut off the "/". So:

amosvalidate assembly.bnk

seems to work for me.

Maybe this helps someone running into similar problems.