Changing read names

[stepa_t]

Hi all!

I'm trying to run MiSeq data through MIRA, but it gives me an error due to long read names.
Is there any tool to change read names in two splitted PE fastq files and conserve pairing information?
I've tried FASTX tool kit, but it discards pair identifier...

Thanks in adavance!
Cheers,
Stepan

[GenoMax]

Are you certain that the error is because of long read names or a space in the read names (e.g. with illumina files when you have multiplexed data)?

Can you post the exact error?

[stepa_t]

Yep:
Some read names were detected with more than 40 characters.
While MIRA and many other programs have no problem with that, some older
programs have restrictions concerning the length of the read name.

Example given: the pipeline
CAF -> caf2gap -> gap2caf
will stop working at the gap2caf stage if there are read names having > 40 characters
where the names differ only at >40 characters.

This is a warning only, but as a couple of people were bitten by this, the default
behaviour of MIRA is to stop when it sees that potential problem.

You might want to rename your reads to have <= 40 characters.

On the other hand, you also can ignore this potential problem and force MIRA to
continue by using the parameter: '-MI:somrnl=0'
"

->Thrown: void Assembly::checkForReadNameLength(uint32 stoplength)
->Caught: main

Aborting process, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.

Subscribing / unsubscribing to mira talk, see: http://www.freelists.org/list/mira_talk

CWD: /bacilla/ammonifex/mira.cor/indexed
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.

[mastal]

Changing read names

Hi Stepan,

Unless the amount of memory is going to be a problem, you
can do as the error message suggests and run mira with the parameter

'-MI:somrnl=0'


Best wishes,
Maria

[stepa_t]

Hi Maria, I had doubts about long read names and memory of my computer, but finally I ran that and it went smoothly (but for about 3 days). But at the end I saw nothing in results folder...
I'm not sure if it is software bug or my computer went out of memory, or it is something with my input data...

... end of log file also seems strange to me:

"Timing BFC setup AS_used_ids: 0
bfc 6/0
Timing BFC discard con: 1
bfc 7/0
Building new contig 533
Localtime: Sat Mar 2 17:07:01 2013
Unused reads: 631258
bfc 8/0
assemblymode_mapping: 0
use genomic pathfinder: 1
Timing n4_basicCSBSSetup cleararrays: 221
Timing n4_basicCSBSSetup init pf_banned: 0
Timing n4_basicCSBSSetup total: 227
+[1] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 381 4239 / 4703 / 0
[61] +++++++++++++++++++++++++++++++++++++++++++++++++s++++++++++ 500 6432 / 18145 / 14
[120] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 500 2493 / 10636 / 0
[180] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 604 1849 / 9562 / 0
[240] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 710 2383 / 5048 / 0
[300] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1012 3468 / 5720 / 0
[360] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1090 3500 / 5941 / 0
[420] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1159 503 / 6497 / 0
[480] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1159 1117 / 8065 / 0
[540] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1303 1409 / 6840 / 0
[600] +++++++++"