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]$ >> > >> > >> >> >> -- >> You have received this mail because you are subscribed to the mira_talk >> mailing list. For information on how to subscribe or unsubscribe, please >> visit http://www.chevreux.org/mira_mailinglists.html >> > >