[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 10:55:02 -0400
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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