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Old 06-01-2009, 10:31 AM   #1
greigite
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Exclamation celera assembler to ace file problem

Has anyone been able to work with ace files generated from Celera assemblies using the ca2ace utility in AMOS? We are finding that these files cannot actually be opened in consed. The problem seems to be a glitch in how the conversion utility writes the BS lines, which indicate which read is the source of the consensus base for each position in the contig sequence. Seems like something we can fix with some scripting, but it would be great if the conversion utility was modified to fix this issue. Any alternative suggestions for a workaround?
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Old 06-01-2009, 10:32 PM   #2
sklages
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You could work with 'ca2ace' from the ca package at sourceforge. In both cases you will need to fix the TIME: tags in the DS line so they will match the TIME: tags
in the phd file. This is necessary if you want to use consed without the '-nophd' switch.

There are still some BS issues sometimes with 454 data, these can be fixed manually in the ace file itself.

hth,
Sven
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Old 06-02-2009, 08:04 AM   #3
greigite
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Thanks- We had noticed the time tag issue. I was hoping there was an automated way of fixing the BS line problem, but sounds like manual editing is needed. Do you happen to know what causes it?

Quote:
Originally Posted by sklages View Post
You could work with 'ca2ace' from the ca package at sourceforge. In both cases you will need to fix the TIME: tags in the DS line so they will match the TIME: tags
in the phd file. This is necessary if you want to use consed without the '-nophd' switch.

There are still some BS issues sometimes with 454 data, these can be fixed manually in the ace file itself.

hth,
Sven
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Old 06-02-2009, 08:13 AM   #4
sklages
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Quote:
Originally Posted by greigite View Post
Thanks- We had noticed the time tag issue. I was hoping there was an automated way of fixing the BS line problem, but sounds like manual editing is needed. Do you happen to know what causes it?
Not really, .. we have never really examined what went wrong, as this only happens ooccasionally.

I still have my own ca2ace on my todo list .. ;-)

cheers,
Sven
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Old 05-27-2010, 08:37 AM   #5
amanzano
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Default problems with celera assembler ace

I ran an assembly using 454 reads paired ends and paired ends titanium and when im loading my ace file to consed i get this:

no ~/.consedrc file so no user resources will be used--that's ok
no ./.consedrc file so no project-specific resources--that's ok
couldn't open readOrder.txt--that's ok
0% done. 1 reads read so far...
0% done. 2 reads read so far...
0% done. 3 reads read so far...
0% done. 4 reads read so far...
0% done. 5 reads read so far...
0% done. 6 reads read so far...
0% done. 7 reads read so far...
0% done. 8 reads read so far...
0% done. 9 reads read so far...
0% done. 10 reads read so far...
0% done. 11 reads read so far...
0% done. 12 reads read so far...
0% done. 13 reads read so far...
0% done. 14 reads read so far...
0% done. 15 reads read so far...
0% done. 16 reads read so far...
0% done. 17 reads read so far...
0% done. 18 reads read so far...
0% done. 19 reads read so far...
0% done. 1000 reads read so far...
0% done. 2000 reads read so far...
0% done. 3000 reads read so far...
0% done. 4000 reads read so far...
0% done. 5000 reads read so far...
0% done. 6000 reads read so far...
0% done. 7000 reads read so far...
0% done. 8000 reads read so far...
0% done. 9000 reads read so far...
0% done. 10,000 reads read so far...
1% done. 20,000 reads read so far...
1% done. 30,000 reads read so far...
2% done. 40,000 reads read so far...
2% done. 50,000 reads read so far...
3% done. 60,000 reads read so far...
3% done. 70,000 reads read so far...
4% done. 80,000 reads read so far...
4% done. 90,000 reads read so far...
5% done. 100,000 reads read so far...
10% done. 200,000 reads read so far...
15% done. 300,000 reads read so far...
20% done. 400,000 reads read so far...
25% done. 500,000 reads read so far...
30% done. 600,000 reads read so far...
35% done. 700,000 reads read so far...
40% done. 800,000 reads read so far...
46% done. 900,000 reads read so far...
Base segment in contig 7180000185764 from padded cons pos 233 to 591 is not within read GDQTYB102FLAX8 which lies within padded cons pos 233 to 589 in contig 7180000185764
Consed is repairing base segments.
Base segment in contig 7180000185835 from padded cons pos 470 to 576 is not within read GDQTYB102HPTRP which lies within padded cons pos 470 to 575 in contig 7180000185835
Consed is repairing base segments.
Base segment in contig 7180000186047 from padded cons pos 1 to 451 is not within read GDQTYB102GBED1b which lies within padded cons pos -72 to 142 in contig 7180000186047
Consed is repairing base segments.
severe warning--cannot fix corrupted base segment at padded consensus base143
Last base segment 0 in contig 7180000186047 is from 1 to 142 but contig ends at 451 so attempting to fix this
severe warning--cannot fix corrupted base segment at padded consensus base143
In contig 7180000186047 last base segment (0) should end on the last padded consensus base (451) but instead ends on 142
exception thrown: assembly3.cpp:183 Failed assertion 'pContig->baseSegArray_.bGetDataStructureOk( true )'

ace file: SCt_PE_RAW.ace
Version 19.0 (090206)
assembly3.cpp:183 Failed assertion 'pContig->baseSegArray_.bGetDataStructureOk( true )'
ace file = SCt_PE_RAW.ace
Version 19.0 (090206)


I dont know what went wrong can anyone helop me or give em directivesd on what to do?
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Old 05-27-2010, 12:01 PM   #6
sklages
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Hi,

just two questions ...

- which version of celera assembler?
- how did you convert from ASM to ACE?

You may want to try http://asm2ace.sourceforge.net/ for asm-to-ace conversion.

This issue is known and can AFAIK only be fixed manually. The consensus and the base segments disagree. You need to manually cure this by shortening the contig mentioned to fit into the base segments boundaries. CA in some cases creates (ends of) contigs without (physical) read coverage.

hth,
Sven
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Old 08-17-2010, 02:17 PM   #7
aprasad
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Quote:
Originally Posted by sklages View Post
Hi,

just two questions ...

- which version of celera assembler?
- how did you convert from ASM to ACE?

You may want to try http://asm2ace.sourceforge.net/ for asm-to-ace conversion.

This issue is known and can AFAIK only be fixed manually. The consensus and the base segments disagree. You need to manually cure this by shortening the contig mentioned to fit into the base segments boundaries. CA in some cases creates (ends of) contigs without (physical) read coverage.
I'm having similar error messages with trying to convert to ace format. I've tried asm2ace, but it chokes on my fragment files with multiple {LIB} sections. (At least I'm assuming that's why it chokes, because if I remove the 2nd {LIB} the asm2whatever.pl doesn't crash)

I'm using Celera Assembler 6.1, and AMOS (toAmos and amos2ace) to convert from ASM to ACE format.

I'm not sure I understand exactly what the issue is and how to shorten the contig. I'm pretty new at this, so apologies if this seems obvious. The actual warning/error messages I'm seeing form consed are below.

Thanks,
Arjun

Code:
Base segment in contig 150 from padded cons pos 98334 to 98732 is not within read F5ZRF5K02D5OURa which lies within padded cons pos 98334 to 98600 in contig 150
Consed is repairing base segments.
severe warning--cannot fix corrupted base segment at padded consensus base98601
Base segment in contig 150 from padded cons pos 96886 to 97106 is not within read F5ZRF5K02D6XZHb which lies within padded cons pos 96886 to 97006 in contig 150
Consed is repairing base segments.
severe warning--cannot fix corrupted base segment at padded consensus base97007
Base segment in contig 150 from padded cons pos 96619 to 96875 is not within read F5ZRF5K02EWTCTa which lies within padded cons pos 96619 to 96839 in contig 150
Consed is repairing base segments.
severe warning--cannot fix corrupted base segment at padded consensus base96840
Base segment in contig 150 from padded cons pos 96234 to 96562 is not within read F5ZRF5K02E1MZRa which lies within padded cons pos 96234 to 96478 in contig 150
Consed is repairing base segments.
severe warning--cannot fix corrupted base segment at padded consensus base96479
Base segment in contig 150 from padded cons pos 2860 to 3107 is not within read F5ZRF5K02C38X8b which lies within padded cons pos 2860 to 3057 in contig 150
Consed is repairing base segments.
severe warning--cannot fix corrupted base segment at padded consensus base3058
Base segment in contig 150 from padded cons pos 1673 to 2116 is not within read F5ZRF5K02ENMKSb which lies within padded cons pos 1673 to 1858 in contig 150
Consed is repairing base segments.
severe warning--cannot fix corrupted base segment at padded consensus base1859
Base segment in contig 150 from padded cons pos 1338 to 1672 is not within read F5ZRF5K02EDUAFb which lies within padded cons pos 1338 to 1669 in contig 150
Consed is repairing base segments.
severe warning--cannot fix corrupted base segment at padded consensus base1670
Base segment in contig 150 from padded cons pos 519 to 1223 is not within read F5ZRF5K02DF2SBb which lies within padded cons pos 519 to 671 in contig 150
Consed is repairing base segments.
severe warning--cannot fix corrupted base segment at padded consensus base672
Base segment in contig 150 from padded cons pos 210 to 518 is not within read F5ZRF5K02DXMSTb which lies within padded cons pos 210 to 463 in contig 150
Consed is repairing base segments.
severe warning--cannot fix corrupted base segment at padded consensus base464
Base segment 0 of contig 150 is from 210 to 463 but should start at 1 so attempting to fix this
severe warning--cannot fix corrupted base segment at padded consensus base1
Last base segment 2128 in contig 150 is from 98334 to 98600 but contig ends at 98732 so attempting to fix this
severe warning--cannot fix corrupted base segment at padded consensus base98601
could not make base segments contiguous at padded pos 464 after read F5ZRF5K02DXMSTb
could not make base segments contiguous at padded pos 672 after read F5ZRF5K02DF2SBb
could not make base segments contiguous at padded pos 1670 after read F5ZRF5K02EDUAFb
could not make base segments contiguous at padded pos 1859 after read F5ZRF5K02ENMKSb
could not make base segments contiguous at padded pos 3058 after read F5ZRF5K02C38X8b
could not make base segments contiguous at padded pos 96479 after read F5ZRF5K02E1MZRa
could not make base segments contiguous at padded pos 96840 after read F5ZRF5K02EWTCTa
could not make base segments contiguous at padded pos 97007 after read F5ZRF5K02D6XZHb
Base segment 0 of contig 150 is not at position 1--it should be
exception thrown: assembly3.cpp:183 Failed assertion 'pContig->baseSegArray_.bGetDataStructureOk( true )' 

ace file: sepi.ace
Version 19.0 (090206)
assembly3.cpp:183 Failed assertion 'pContig->baseSegArray_.bGetDataStructureOk( true )' 
ace file = sepi.ace
Version 19.0 (090206)
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Old 04-29-2014, 05:19 PM   #8
Boonie
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I am having trouble accessing asm2ace on Sourceforge. Can you provide an active link?
Do you know of any other scripts that would convert a CA assembly to ace (or even bam)?
Thanks.
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Old 04-29-2014, 11:04 PM   #9
sklages
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Quote:
Originally Posted by Boonie View Post
I am having trouble accessing asm2ace on Sourceforge. Can you provide an active link?
Do you know of any other scripts that would convert a CA assembly to ace (or even bam)?
Thanks.
What kind of trouble did you have?
It can be downloaded here http://sourceforge.net/projects/asm2ace/files/

I haven't used CA for quite a while now, I have no idea about other converters.

best,
Sven
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