[mira_talk] Re: MIRA->Some good editor
- From: Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>
- To: Bastien Chevreux <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 15 Jul 2011 23:37:25 +0200
Dear Bastien,
Friday, July 15, 2011, 9:23:19 PM, you wrote:
> On Jul 15, 2011, at 18:03 , Nestor Zaburannyi wrote:
>> Why is .gap4da output not recommended nor created anymore? From the first
>> day of my MIRA usage, i can not convert my projects into Gap4, because of
>> !! FATAL ERROR: system error 12 Cannot allocate memory
>> !! Memory allocation failure when requesting -2147483648 bytes
> Uh oh ... you must have quite some large result projects.
> You have exactly 2.5 options left I think:
> 0.5: You write a bug report to the authors of caf2gap (you might want to do
> that anyway)
> 1.5: split the MIRA result into smaller parts to be worked on individually in
> gap4. You might for example want to try the "-s" option of convert_project to
> split by contigs:
Unfortunately, convert_project with "-s" option crashes. While it works fine
without this option. Attaching error message at the end of this letter.
> convert_project -f maf -t caf -s mira_output.maf mysplit
> 2.5: you scrap gap4 and use gap5. To input the project into gap5 use:
> tg_index -C mira_out.caf
> where tg_index is a tool supplied by the gap5 package.
>> Also, convert_project for "-t gap4da" is not available nowadays, too?
> In convert_project, it's called "-t exp".
> WARNING WARNING WARNING RED ALERT WARNING WARNING WARNING
> Do not do that with projects containing more than a couple of hundred
> thousand reads. That format implies that in a single directory, one file is
> created on disk for each and every read ... and your filesystem will not like
> that.
> You. Have. Been. Warned ;-)
> B.
Loading from maf, saving to: caf
First counting reads:
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%] ....|....
[50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|.... [90%] ....|....
[100%] tcmalloc: large alloc 1595297792 bytes == 0x28d2000 @
Now loading and processing data:
[0%] Localtime: Fri Jul 15 23:32:25 2011
Generated 42955 unique template ids for 65882 valid reads.
Localtime: Fri Jul 15 23:32:25 2011
Seeing strain 1: "J1405"
Generated 1 unique strain ids for 65882 reads.
Internal logic/programming/debugging error (*sigh* this should not have
happened).
Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/
"CAF open while it should not be?"
->Thrown: void ConvPro::saveContigList_helper(list<Contig> & clist, ReadPool &
rp)
->Caught: main
Aborting process, probably due to an internal error.
If you want to report the error, please do so on
http://sourceforge.net/apps/trac/mira-assembler/
and also give a short notice on the mira talk mailing list.
If reporting, please do not delete the log and checkpoint directories, there may
be files in them which could be needed to find the problem.
CWD: /home/neza001/data
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
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