[mira_talk] Re: Mira says "killed" as last word after being almost done

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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