[mira_talk] Re: Mira says "killed" as last word after being almost done
- From: Adrian Pelin <apelin20@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 12 May 2011 10:56:13 -0400
I have checked, no such log file was produced. MIRA was called with the
following command:
mira --fastq --project=gigaspora -proout=gigaspora_denovo
--job=denovo,genome,accurate,
454,solexa SOLEXA_SETTINGS -GE:tismin=50:tismax=350;tpbd=1 >& log_hybdn.txt
log_hybdn.txt is an empty file 0 bytes.
On Thu, May 12, 2011 at 10:55 AM, Adrian Pelin <apelin20@xxxxxxxxx> wrote:
> Intresting, there a setting in linux that has a max running time? I am
> using fedora.
>
> I did ask for a log redirection with >&file.log
>
> Unfortunatly the said file existed but was empty totaly.
>
>
>
>
> On Thu, May 12, 2011 at 10:44 AM, Lionel Guy <guy.lionel@xxxxxxxxx> wrote:
>
>> Hi Adrian,
>>
>> It's strange that your log file didn't show anything. Did you redirect the
>> output of mira to some file (e.g. mira -project=myproj --job=denovo,genome >
>> assembly_log.txt) ? It would be handy to see the command you typed to run
>> mira.
>>
>> If it says "killed", it is likely that something external to mira killed
>> it. Maybe an administrator? Or yourself, mistakenly? Or you exceed maximum
>> running time, or max disk quota or memory?
>>
>> Lionel
>>
>> On 12 May 2011, at 16:34 , Adrian Pelin wrote:
>>
>> > The results folder is empty and there is no log file that was created.
>> Here are a list of documents present after it got killed:
>> >
>> >
>> > [AdrianP@adrianpelin gigaspora]$ ls -al
>> > total 16
>> > drwxrwxr-x. 4 AdrianP AdrianP 4096 May 9 22:59 .
>> > drwxr-xr-x. 9 AdrianP AdrianP 4096 May 8 14:19 ..
>> > drwxrwxr-x. 6 AdrianP AdrianP 4096 May 9 22:59
>> gigaspora2_denovo_assembly
>> > drwxrwxr-x. 6 AdrianP AdrianP 4096 May 8 14:49
>> gigaspora_denovo_assembly
>> > lrwxrwxrwx. 1 AdrianP AdrianP 55 May 8 14:28 gigaspora_in.454.fastq
>> -> /home/AdrianP/assembly/data/G1P7DQF02.GIGASPO_DNA.fastq
>> > lrwxrwxrwx. 1 AdrianP AdrianP 42 May 8 14:20
>> gigaspora_in.solexa.fastq -> /home/AdrianP/assembly/data/all_GDR-10.txt
>> > lrwxrwxrwx. 1 AdrianP AdrianP 53 May 8 14:29
>> gigaspora_traceinfo_in.454.xml ->
>> /home/AdrianP/assembly/data/G1P7DQF02.GIGASPO_DNA.xml
>> > -rw-rw-r--. 1 AdrianP AdrianP 0 May 9 19:21 log_hybdn.txt
>> > [AdrianP@adrianpelin gigaspora_denovo_assembly]$ ls -al
>> gigaspora_denovo_d_log
>> > total 43325088
>> > drwxrwxr-x. 2 AdrianP AdrianP 4096 May 9 17:04 .
>> > drwxrwxr-x. 6 AdrianP AdrianP 4096 May 8 14:49 ..
>> > -rw-rw-r--. 1 AdrianP AdrianP 0 May 8 14:51
>> gigaspora_denovo_error_reads_invalid
>> > -rw-rw-r--. 1 AdrianP AdrianP 54510239 May 9 17:04
>> gigaspora_denovo_info_consensustaglist.1.txt
>> > -rw-rw-r--. 1 AdrianP AdrianP 150430571 May 9 17:04
>> gigaspora_denovo_info_contigreadlist_pass.1.txt
>> > -rw-rw-r--. 1 AdrianP AdrianP 5463568 May 9 17:04
>> gigaspora_denovo_info_contigstats_pass.1.txt
>> > -rw-rw-r--. 1 AdrianP AdrianP 105015720 May 9 17:04
>> gigaspora_denovo_info_debrislist_pass.1.txt
>> > -rw-rw-r--. 1 AdrianP AdrianP 12764694 May 8 15:10
>> gigaspora_denovo_info_reads_tooshort
>> > -rw-rw-r--. 1 AdrianP AdrianP 1459307936 May 9 17:04
>> gigaspora_denovo_info_readtaglist.1.txt
>> > -rw-rw-r--. 1 AdrianP AdrianP 328044202 May 8 15:49
>> gigaspora_denovo_int_clippings.0.txt
>> > -rw-rw-r--. 1 AdrianP AdrianP 13055712128 May 8 15:54
>> gigaspora_denovo_int_normalisedskims_preassembly.0.bin
>> > -rw-rw-r--. 1 AdrianP AdrianP 2234065416 May 8 15:49
>> gigaspora_denovo_int_posmatchc_preassembly.0.lst
>> > -rw-rw-r--. 1 AdrianP AdrianP 715096296 May 8 16:00
>> gigaspora_denovo_int_posmatchc_preassembly.0.lst.reduced
>> > -rw-rw-r--. 1 AdrianP AdrianP 2661826632 May 8 15:49
>> gigaspora_denovo_int_posmatchf_preassembly.0.lst
>> > -rw-rw-r--. 1 AdrianP AdrianP 864158976 May 8 16:00
>> gigaspora_denovo_int_posmatchf_preassembly.0.lst.reduced
>> > -rw-rw-r--. 1 AdrianP AdrianP 0 May 8 15:17
>> gigaspora_denovo_int_posmatch_megahubs_preassembly.0.lst
>> > -rw-rw-r--. 1 AdrianP AdrianP 0 May 8 15:49
>> gigaspora_denovo_int_posmatch_multicopystat_preassembly.0.txt
>> > -rw-rw-r--. 1 AdrianP AdrianP 2523216918 May 9 17:04
>> gigaspora_denovo_out_pass.1.caf
>> > -rw-rw-r--. 1 AdrianP AdrianP 232766668 May 8 14:51
>> gigaspora_denovo_readpoolinfo.lst
>> > -rw-rw-r--. 1 AdrianP AdrianP 1014834464 May 8 15:13 hashstat.bin
>> > -rw-rw-r--. 1 AdrianP AdrianP 3000650484 May 8 16:40
>> miralog.ads_pass.1.adsfacts
>> > -rw-rw-r--. 1 AdrianP AdrianP 214925035 May 8 16:45
>> miralog.ads_pass.1.adsfacts.pclusters
>> > -rw-rw-r--. 1 AdrianP AdrianP 1778880160 May 8 16:40
>> miralog.ads_pass.1.complement
>> > -rw-rw-r--. 1 AdrianP AdrianP 2252002749 May 8 16:40
>> miralog.ads_pass.1.forward
>> > -rw-rw-r--. 1 AdrianP AdrianP 1017515760 May 8 16:40
>> miralog.ads_pass.1.reject
>> > -rw-rw-r--. 1 AdrianP AdrianP 0 May 8 15:10
>> miralog.noqualities
>> > -rw-rw-r--. 1 AdrianP AdrianP 187902039 May 8 15:10 miralog.usedids
>> > -rw-rw-r--. 1 AdrianP AdrianP 1641613900 May 9 19:21
>> repeat_resolve.1.adsfacts
>> > -rw-rw-r--. 1 AdrianP AdrianP 2241239073 May 9 19:21
>> repeat_resolve.1.complement
>> > -rw-rw-r--. 1 AdrianP AdrianP 2973604403 May 9 18:19
>> repeat_resolve.1.forward
>> > -rw-rw-r--. 1 AdrianP AdrianP 3639107589 May 9 19:21
>> repeat_resolve.1.reject
>> > AdrianP@adrianpelin gigaspora_denovo_assembly]$ ls -al
>> gigaspora_denovo_d_info
>> > total 149324
>> > drwxrwxr-x. 2 AdrianP AdrianP 4096 May 9 17:04 .
>> > drwxrwxr-x. 6 AdrianP AdrianP 4096 May 8 14:49 ..
>> > -rw-rw-r--. 1 AdrianP AdrianP 2368 May 9 17:04
>> gigaspora_denovo_info_assembly.txt
>> > -rw-rw-r--. 1 AdrianP AdrianP 139 May 8 14:49
>> gigaspora_denovo_info_callparameters.txt
>> > -rw-rw-r--. 1 AdrianP AdrianP 152890262 May 8 15:17
>> gigaspora_denovo_info_readrepeats.lst
>> > [AdrianP@adrianpelin gigaspora_denovo_assembly]$ ls -al
>> gigaspora_denovo_d_chkpt
>> > total 2117620
>> > drwxrwxr-x. 2 AdrianP AdrianP 4096 May 8 16:01 .
>> > drwxrwxr-x. 6 AdrianP AdrianP 4096 May 8 14:49 ..
>> > -rw-rw-r--. 1 AdrianP AdrianP 2 May 8 16:01 passInfo.txt
>> > -rw-rw-r--. 1 AdrianP AdrianP 2168424930 May 8 16:01 readpool.maf
>> > [AdrianP@adrianpelin gigaspora_denovo_assembly]$
>> >
>> >
>>
>>
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>
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