[mira_talk] Re: Mira says "killed" as last word after being almost done
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 12 May 2011 16:44:38 +0200
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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