[mira_talk] Re: Please consider
- From: monithamohan harilkumar <moniharil@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 15 May 2013 15:23:18 +0200
Hello ,
Thanks for your response, But MY doubt is , it kind of generated 2 terabyte
of tmp files, its expected to get full disk then..!!!!
I am trying to do mapping with paired end data where each file of paired
end is 13G and and my backbone file from oryza (reference) is 373M.The tmp
directory created in mira are
total 2303331840
drwxr-xr-x 2 monitha ctx 4096 May 15 14:16 .
drwxrwx--- 3 chris ctx 4096 Apr 30 13:36 ..
-rw-r--r-- 1 monitha ctx 16777216 May 15 14:16 hashstat.bin
-rw-r--r-- 1 monitha ctx 0 Apr 30 13:50 mira4_info_reads_invalid
-rw-r--r-- 1 monitha ctx 116189414 May 15 12:41
mira4_info_reads_tooshort
-rw-r--r-- 1 monitha ctx 3736931776 May 1 01:36
mira4_int_clippings.0.txt
-rw-r--r-- 1 monitha ctx 6882733 Apr 30 14:00
mira4_int_clippings_t0.0.txt
-rw-r--r-- 1 monitha ctx 6884499 Apr 30 14:00
mira4_int_clippings_t1.0.txt
-rw-r--r-- 1 monitha ctx 6969359 Apr 30 14:00
mira4_int_clippings_t10.0.txt
-rw-r--r-- 1 monitha ctx 6868049 Apr 30 14:00
mira4_int_clippings_t11.0.txt
-rw-r--r-- 1 monitha ctx 6817281 Apr 30 14:00
mira4_int_clippings_t12.0.txt
-rw-r--r-- 1 monitha ctx 6877402 Apr 30 14:00
mira4_int_clippings_t13.0.txt
-rw-r--r-- 1 monitha ctx 6996627 Apr 30 14:00
mira4_int_clippings_t14.0.txt
-rw-r--r-- 1 monitha ctx 6897405 Apr 30 14:00
mira4_int_clippings_t15.0.txt
-rw-r--r-- 1 monitha ctx 6918137 Apr 30 14:00
mira4_int_clippings_t16.0.txt
-rw-r--r-- 1 monitha ctx 6871877 Apr 30 14:00
mira4_int_clippings_t17.0.txt
-rw-r--r-- 1 monitha ctx 6866074 Apr 30 14:00
mira4_int_clippings_t18.0.txt
-rw-r--r-- 1 monitha ctx 6970417 Apr 30 14:00
mira4_int_clippings_t19.0.txt
-rw-r--r-- 1 monitha ctx 6964237 Apr 30 14:00
mira4_int_clippings_t2.0.txt
-rw-r--r-- 1 monitha ctx 6974073 Apr 30 14:00
mira4_int_clippings_t20.0.txt
-rw-r--r-- 1 monitha ctx 6810864 Apr 30 14:00
mira4_int_clippings_t21.0.txt
-rw-r--r-- 1 monitha ctx 6944239 Apr 30 14:00
mira4_int_clippings_t22.0.txt
-rw-r--r-- 1 monitha ctx 6884742 Apr 30 14:00
mira4_int_clippings_t23.0.txt
-rw-r--r-- 1 monitha ctx 6912521 Apr 30 14:00
mira4_int_clippings_t24.0.txt
-rw-r--r-- 1 monitha ctx 6873051 Apr 30 14:00
mira4_int_clippings_t25.0.txt
-rw-r--r-- 1 monitha ctx 6798298 Apr 30 14:00
mira4_int_clippings_t26.0.txt
-rw-r--r-- 1 monitha ctx 6929355 Apr 30 14:00
mira4_int_clippings_t27.0.txt
-rw-r--r-- 1 monitha ctx 6873334 Apr 30 14:00
mira4_int_clippings_t28.0.txt
-rw-r--r-- 1 monitha ctx 6780327 Apr 30 14:00
mira4_int_clippings_t29.0.txt
-rw-r--r-- 1 monitha ctx 6942660 Apr 30 14:00
mira4_int_clippings_t3.0.txt
-rw-r--r-- 1 monitha ctx 6804962 Apr 30 14:00
mira4_int_clippings_t30.0.txt
-rw-r--r-- 1 monitha ctx 6924239 Apr 30 14:00
mira4_int_clippings_t31.0.txt
-rw-r--r-- 1 monitha ctx 6890153 Apr 30 14:00
mira4_int_clippings_t4.0.txt
-rw-r--r-- 1 monitha ctx 6893426 Apr 30 14:00
mira4_int_clippings_t5.0.txt
-rw-r--r-- 1 monitha ctx 6919434 Apr 30 14:00
mira4_int_clippings_t6.0.txt
-rw-r--r-- 1 monitha ctx 6926114 Apr 30 14:00
mira4_int_clippings_t7.0.txt
-rw-r--r-- 1 monitha ctx 6917013 Apr 30 14:00
mira4_int_clippings_t8.0.txt
-rw-r--r-- 1 monitha ctx 6830587 Apr 30 14:00
mira4_int_clippings_t9.0.txt
-rw-r--r-- 1 monitha ctx 0 May 1 03:56
mira4_int_posmatch_megahubs_pass.1.lst
-rw-r--r-- 1 monitha ctx 1163968322784 May 12 14:43
mira4_int_posmatchc_pass.1.bin
-rw-r--r-- 1 monitha ctx 1184842895360 May 12 15:22
mira4_int_posmatchf_pass.1.bin
-rw-r--r-- 1 monitha ctx 5704632584 Apr 30 14:32
mira4_log_readpoolinfo.lst
-rw-r--r-- 1 monitha ctx 0 May 15 12:41 miralog.noqualities
So as you see its a lot!!!! I really want to use mira for my project , now
i have resumed mira again by using mira -r .....command, and as you see
above some files have been created/modified on todays date, i hope it
works out. I have created a little more space but There are several others
who are doing their project here and i am afraid that it should not affect
the other projects .Just incase if you could help me out or if i have to
change any parameters , please let me know.I also saw in te skim option
that there is a parameter called [memcap_hitreduction(mchr)=*integer ≥ 10*]
Default is 1024, 2048 when Solexa sequences are used. Maximum memory used
(in MiB) during the reduction of skim hits.
-Should i change this to 2048 and run???
Thanks ,
Monitha
On Wed, May 15, 2013 at 2:41 PM, Sebastian Juenemann <
jueneman@xxxxxxxxxxxxxxxxxxxxxxxx> wrote:
> Monithamohan - it seems that you run into disk quota problems. It's
> somewhat hard to digest your email but all errors reported by MIRA point to
> problems related either to insufficient disk space or permissions (i doubt
> you change permissions).
>
> So redirecting the MIRA tmp folder to a place with more free space can
> help, i.e. -DI:trt=/lots/of/space.
>
> How many reads are you trying to map against your backbone anyway and how
> is your backbone made up exactly?
>
> Also, "nohup mira mira4_manifest.conf >$log4_assembly.txt" does not
> redirect STDOUT to "log4_assembly.txt" but to anything dependent on what
> the $log4_assembly environmental variable is currently set. If this
> variable is empty (i guess that's your case: 'echo $log4_assembly'), then
> all output is written to ".txt". Just omit the "$" character.
>
> And on a side note, as i see you use nohup? If you're running from a bash,
> you can check the built-in option ('shopt') and look to what huponexit is
> set. If it's false (this is default; or you can set it to false via 'shopt
> -u huponexit'), there is no need to wrap MIRA with nohup as BASH prevents
> to propagate the SIGHUP signal to child processes on exit from the active
> session (though you need to redirect both STDERR and STDOUT, otherwise the
> job may fail if trying to write to a non-existent terminal).
>
> - Sebastian
>
>
>
> On 05/15/13 13:28, monithamohan harilkumar wrote:
>
>> Hello bastien,
>>
>> Afetr resolving all the errors before in the config file , I had finally
>> left mira to run on April 30 which finished finally on May 12th but with
>> error ..:(
>> I really wish you could help me with this,
>>
>> ERROR, in the output txt file
>> Thank you for noticing that this is *NOT* a crash, but a
>> controlled program stop.
>> CWD: /tmp1/monithesis/mira/mira3/**mira4
>> Thank you for noticing that this is *NOT* a crash, but a
>> controlled program stop.
>>
>> Fatal error (may be due to problems of the input data or parameters):
>>
>> "Could not write anymore to skimhit save5. Disk full? Changed
>> permissions?"
>>
>> ->Thrown: void Skim::**selectPotentialHitsForSave2(**const int8
>> direction,
>> const uint3
>> 2 actreadid, cfh_threaddata_t & cfhd)
>> ->Caught: void Skim::threadloop(const uint32 threadnr)
>>
>> 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:
>> //www.freelists.org/list/**mira_<//www.freelists.org/list/mira_>
>> talk
>>
>>
>> Fatal error (may be due to problems of the input data or parameters):
>>
>> "Could not write anymore to skimhit save5. Disk full? Changed
>> permissions?"CWD:
>>
>> ->Thrown: /tmp1/monithesis/mira/mira3/**mira4void
>> Skim::**selectPotentialHitsForSave2(
>> const int8 direction, const uint32 actreadid, cfh_threaddata_t & cfhd)
>>
>> ->Caught: void Skim::threadloop(const uint32 threadnr)
>>
>> 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:
>> //www.freelists.org/list/**mira_<//www.freelists.org/list/mira_>
>> talk
>>
>> Thank you for noticing that this is *NOT* a crash, but a
>> controlled program stop.
>> CWD: /tmp1/monithesis/mira/mira3/**mira4
>> Thank you for noticing that this is *NOT* a crash, but a
>> controlled program stop.
>>
>> Fatal error (may be due to problems of the input data or parameters):
>>
>> "Could not write anymore to skimhit save5. Disk full? Changed
>> permissions?"
>>
>> ->Thrown: void Skim::**selectPotentialHitsForSave2(**const int8
>> direction,
>> const uint3
>> 2 actreadid, cfh_threaddata_t & cfhd)
>> ->Caught: void Skim::threadloop(const uint32 threadnr)
>>
>> 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:
>> //www.freelists.org/list/**mira_<//www.freelists.org/list/mira_>
>> talk
>>
>> CWD: /tmp1/monithesis/mira/mira3/**mira4
>> Thank you for noticing that this is *NOT* a crash, but a
>> controlled program stop.
>>
>> Fatal error (may be due to problems of the input data or parameters):
>>
>> ****Also I found out tht it created files terabytes in the tmp
>> folder.....I really don't understand what to do next***
>> *#manifest file for mira4*
>>
>> project=mira4
>> job=mapping,genome,accurate
>> parameters = -GE:not=32\
>> COMMON_SETTINGS -AS:nop=1\
>> -MI:somrnl=0\
>> -SK:mnr=no:mmhr=1\
>> SOLEXA_SETTINGS -CO:msr=no
>>
>> readgroup=illuminaassembly
>> data = mira4_backbone_in.fna
>> as_reference
>> strain = mira4_bft
>> parameters = COMMON_SETTINGS -DI:trt = /tmp2/tmp
>> default_qual = 30
>>
>>
>> readgroup = solexareads
>> data = /ctx/tmp1/monithesis/mira/**mira3/mira4/mira41_in.solexa.**fastq
>> /ctx/tmp1/mon
>> ithesis/mira/mira3/mira4/**mira42_in.solexa.fastq
>> technology = solexa
>> templatesize= 250 750 infoonly
>> segment_placement= ---> <--- infoonly
>> strain = mira4_sol
>>
>>
>> "Could not write anymore to skimhit save5. Disk full? Changed
>> permissions?"
>>
>> ->Thrown: void Skim::**selectPotentialHitsForSave2(**const int8
>> direction,
>> const uint3
>> 2 actreadid, cfh_threaddata_t & cfhd)
>> ->Caught: void Skim::threadloop(const uint32 threadnr)
>>
>> 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:
>> //www.freelists.org/list/**mira_<//www.freelists.org/list/mira_>
>> talk
>>
>> CWD: /tmp1/monithesis/mira/mira3/**mira4
>> Thank you for noticing that this is *NOT* a crash, but a
>> controlled program stop.
>>
>> **Also I there was no output file was produced, instead there was a
>> hidden output txt file , I had run mira using command "nohup mira
>> mira4_manifest.conf >$log4_assembly.txt"..however i did not get this
>> log4_assembly.txt file , instead i got a hidden .txt file.
>>
>> Please guide me,
>> Monitha
>> "
>>
>
>
> --
> Sebastian Jünemann
> CeBiTec - Center for Biotechnology
> Bielefeld University, D-33594 Bielefeld, Germany
> Office: V6-147 -- Phone: +49-(0)521-106-4827
> eMail: jueneman@xxxxxxxxxxx-**Bielefeld.de<jueneman@xxxxxxxxxxxxxxxxxxxxxxxx>
>
> --
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