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Re: [wgs-assembler-users] Long time for PacBiocorrection
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From: Francois S. <fra...@ir...> - 2013-09-30 08:48:25
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Hi
Still have a weird bug, it cannot find (again) bank-transact, even if
AMOS is in the path (I checked)
Here is the end of my asm.layout error for this step
Using partition 10 to re-estimate insert sizes, total partitions so far
1/200
Using partition 58 to re-estimate insert sizes, total partitions so far
2/200
Using partition 66 to re-estimate insert sizes, total partitions so far
3/200
Using partition 83 to re-estimate insert sizes, total partitions so far
4/200
Using partition 118 to re-estimate insert sizes, total partitions so far
5/200
Using partition 122 to re-estimate insert sizes, total partitions so far
6/200
Using partition 136 to re-estimate insert sizes, total partitions so far
7/200
Using partition 163 to re-estimate insert sizes, total partitions so far
8/200
Using partition 175 to re-estimate insert sizes, total partitions so far
9/200
Using partition 200 to re-estimate insert sizes, total partitions so far
10/200
openLayFile()-- Failed to open 'asm.200.olaps' for reading: No such file
or directory
Couldn't open 'asm.200.olaps' for read: No such file or directory from 0-0
IlluminaTog5681
400.00 +- 100.00 -> 315.38 +- 76.35 I 37774891/37919939
samples external happy 34167579 sad 112016534
N/A +- N/A -> 845.33 +- 1030.84 O 198321/218601 samples
N/A +- N/A -> 2521.31 +- 1937.73 N 65640/69560 samples
N/A +- N/A -> 2592.02 +- 2017.69 A 55226/58297 samples
Tog5681_corrected
Filtering mates
openLayFile()-- Failed to open 'asm.200.olaps' for reading: No such file
or directory
Couldn't open 'asm.200.olaps' for write: No such file or directory from 0-0
CorrectPacBio.cc:445: int main(int, char**): Assertion `system(command)
== 0' failed.
Failed with 'Aborted'
Backtrace (mangled):
/home/sabotf/sources/wgs/Linux-amd64/bin//(_Z17AS_UTL_catchCrashiP7siginfoPv+0x27)[0x412797]
/lib64/libpthread.so.0[0x3bdd20f500]
/lib64/libc.so.6(gsignal+0x35)[0x3bdce328a5]
/lib64/libc.so.6(abort+0x175)[0x3bdce34085]
/lib64/libc.so.6[0x3bdce2ba1e]
/lib64/libc.so.6(__assert_perror_fail+0x0)[0x3bdce2bae0]
/home/sabotf/sources/wgs/Linux-amd64/bin//(main+0x2cf2)[0x40e742]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3bdce1ecdd]
/home/sabotf/sources/wgs/Linux-amd64/bin//[0x40b989]
Backtrace (demangled):
[0] /home/sabotf/sources/wgs/Linux-amd64/bin//::AS_UTL_catchCrash(int,
siginfo*, void*) + 0x27 [0x412797]
[1] /lib64/libpthread.so.0() [0x3bdd20f500]
[2] /lib64/libc.so.6::(null) + 0x35 [0x3bdce328a5]
[3] /lib64/libc.so.6::(null) + 0x175 [0x3bdce34085]
[4] /lib64/libc.so.6() [0x3bdce2ba1e]
[5] /lib64/libc.so.6::(null) + 0 [0x3bdce2bae0]
[6] /home/sabotf/sources/wgs/Linux-amd64/bin//::(null) + 0x2cf2 [0x40e742]
[7] /lib64/libc.so.6::(null) + 0xfd [0x3bdce1ecdd]
[8] /home/sabotf/sources/wgs/Linux-amd64/bin//() [0x40b989]
GDB:
Any idea ??
Francois
On 27/09/2013 13:12, Francois Sabot wrote:
> The script still continues to generate correction steps...
>
> Here are the asm.layout.err for run 25 and the output of run24
>
> Francois
>
> PS: I changed the -t value
>
> On 25/09/2013 18:17, Serge Koren wrote:
>> Hi,
>>
>> There is only one step in runCorrection.sh. If you are using CA 7.0,
>> there is a known bug in the code that causes it to fail. The wiki
>> documents a workaround:
>> http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=PacBioToCA#Error_in_runCorrection.sh_Step
>>
>> Re-launching the script will restart the step from the beginning. The
>> output of the step is in asm.layout.err. If you can share this, it might
>> give more information on how far the step is and why it may be failing.
>>
>> Sergey
>>
>> On Sep 23, 2013, at 5:22 AM, Francois Sabot <fra...@ir...
>> <mailto:fra...@ir...>> wrote:
>>
>>> Hi folks
>>>
>>> I am running the PacBioToCa on my entire set of data (coverage 12x
>>> PacBio, 55x Illumina, genome size ~ 400-450 Mb).
>>>
>>> I have few weird errors of missed linked, and i re-launch regularly the
>>> script to ensure its completion.
>>>
>>> My question s how can you calculate the numbers of steps in the
>>> runCorrection.sh part ? It is already on the 19th one, and it ran for
>>> days....
>>>
>>> Can someone help me ?
>>>
>>> Francois
>>>
>>> --
>>> --------------------------------------------------------
>>> Francois Sabot, PhD
>>>
>>> Be realistic. Demand the Impossible.
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>>> http://www.mpl.ird.fr/rice
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>>
>
--
--------------------------------------------------------
Francois Sabot, PhD
Be realistic. Demand the Impossible.
http://bioinfo.mpl.ird.fr/
http://www.mpl.ird.fr/rice
-----------------------------------------
UMR DIversity, Adaptation & DEvelopment
Centre IRD
911, Av Agropolis BP 64501
34394 Montpellier Cedex 5
France
Phone: +33 4 67 41 64 18
-----------------------------------------
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