Error message in Tracer - Problem with trace file: State 24708...

[Dave]

I loaded a log file into Tracer while the Beast run was going. The
Beast run is finished, and now the log file will not load in Tracer.
I get the error message: Problem with trace file: State 24708000 is
not consistent with previous spacing. (line 4118) This is at the
point where I loaded the log file into tracer while Beast was running.

I tried removing the offending line, but the error just gets shifted
to the next line.

Anyone know how to edit this file to fix it? Or, do I have to redo
the Beast run (which took 3 days)?

I am using Beast on Windows and notepad to edit the file.

thanks,
Dave

[jcs]

Try running the broken log file through LogCombiner - try some
different resamplings - this might salvage most of the file. That's
what I've done in the past with broken log files.

[Alfred]

I just had the same problem. I processed it with LogCombiner by loading it and saving it under a new name.  It then opened in Tracer.  There was no need to resample or burnin or make any other changes to the file. 

[Cuong trinh dinh]

Hi all,

I run the same file on MAC and on LINUX the I check them on Tracer v 1.6, the I combined those files by Logcombiner then i got a file, then i checked it on Tracer and i received a notation ¨problem with trace file: State 12200. Expected correct number type (Double, Integer or String) in column 6 (line 200). I tried with Logcombiner some times and i still got the same problem. I did not understand why? if anybody know please tell me know!!

Thanks a lot!

Dinh

Vào 22:52:15 UTC+1 Thứ sáu, ngày 12 tháng mười một năm 2010, Dave đã viết:

[Pankaj Koparde]

I had a similar problem. I exported the file through LogCombiner without burnin, just renaming the file. It was processed in Tracer.

[Simey]

I am getting a similar error, but running it through logcombiner also throws an error:

java.lang.IllegalArgumentException: ERROR: The number of columns in file C:\BEAST.v2.4.1.Windows\BEAST\snap1.log does not match that of the first file

                at beast.app.tools.LogCombiner.readLogFile(Unknown Source)

                at beast.app.tools.LogCombiner.combineLogs(Unknown Source)

                at beast.app.tools.LogCombiner.main(Unknown Source)

                at beast.app.tools.LogCombinerLauncher.main(Unknown Source)

When I look at the log file, I notice that the offending line is much longer than all the other lines (sample 6000). I am running six parallel SNAPP analyses (8 threads each) on an Ubuntu box (beast 2.4.1) and all but 1 of the log files has the same problem. If I delete all of the lines prior to sample 8000 then it will load into Tracer normally.

 

Sample posterior             likelihood            prior      u             v              theta0   theta1   theta2   theta3   theta4   theta5                theta6   theta7   theta8   theta9   theta10 theta11 theta12 theta13 theta14 theta15 theta16 theta17 theta18                theta19 theta20 theta21 theta22 TreeHeightLogger           

0              -21619.79769497771        -20393.45291368419        -1226.3447812935235     7.074607933579335                0.5380250811190038       0.2          0.2          0.2          0.2          0.2          0.2          0.2          0.2          0.2          0.2          0.2                0.2          0.2          0.2          0.2          0.2          0.2          0.2          0.2          0.2          0.2          0.1746886051982879       0.2                0.22546846657491432    

1000       -20194.541956726513     -19000.802654224353     -1193.7393025021606     3.4816909236279923                0.5838450417576516       0.04241663694706088     0.14096550403194216     0.11459697181058272                0.08163585224294688     0.1584977156257583       0.2555116265952683       0.29576785606161954                0.10237725644099571     0.11868955660004421     0.12055738414289857     0.006793690175032509                0.013064611482752616  0.1851310341191909       0.14835666634435346     0.10022391739959646                0.11890354237455897     0.1125174093395538       0.06160407537327494     0.07734544121924414                0.11584694239698862     0.04459308476880699     0.07935576820391764     0.2112286328856265                0.2982508082908788      

2000       -20101.052343972366     -18903.621108885058     -1197.4312350873076     3.234372391117356                0.5914286586611716       0.048369358480780396  0.14756994551981678     0.11825781843855698                0.07937215949573323     0.16889183642810351     0.23297784823309406     0.22643791367741423                0.10665981950534478     0.16472196053904178     0.12785680554727336     0.005328254806452743                0.011841357940250059  0.2005734786616486       0.06788355667121052     0.1218967577905309                0.16801202163831644     0.08113793749474775     0.06018583760476948     0.09154492049039024                0.15322727591928548     0.04361660292371663     0.09358539638458994     0.2916841033107897                0.2697787357961922      

3000       -20064.21757755161        -18874.523818488233     -1189.69375906338          3.3370746658643777                0.5881189356797673       0.049911568469045715  0.15566541743326123     0.13048934089678357                0.07195655275154426     0.15148488555725204     0.25657598887574773     0.23861364793301446                0.09590129523271264     0.1368600516081232       0.12056078958031008     0.0037915624809569917                0.014227868251265085  0.15980937206773588     0.10050625157364945     0.11936371790784192                0.12083073840181062     0.13728795455769724     0.15730422541444802     0.08048191967583673                0.15910362433283332     0.052511019985885844  0.09319819171485089     0.1606105079878873                0.33621643408629404    

4000       -20011.284510261637     -18807.38749166661        -1203.897018595029        3.337482485822675                0.5881062706991537       0.0534026123942513       0.1554440342857984       0.14321355847206022                0.06838022152279927     0.1586333027410585       0.24818539008029364     0.3059217109128541                0.10570779079524475     0.15617312065825986     0.13872919753776544     0.003333359245969278                0.014328422468047136  0.17241494747434463     0.1266329660827069       0.06251954641449088                0.0710268195742064       0.09147904766537972     0.04289069929838025     0.08098980469497002                0.1190886851522731       0.07297015016948268     0.12624730162056355     0.11620941975473263                0.7790496280460664      

5000       -19983.74898135331        -18794.591587760086     -1189.1573935932245     2.947256352367947                0.6021552154755271       0.05356478000754795     0.12657828879768065     0.12853104698490952                0.06655463980940968     0.1556583985428105       0.21984226550220634     0.20968441266068144                0.1522555148004346       0.1486733469569345       0.1223512172710878       0.005857953427954812                0.012132750468464834  0.16724890280017837     0.11056703316293166     0.06675201511473691                0.08954979606814768     0.2266480192389119       0.11305415312995312     0.07252898191418779                0.12395630246116549     0.06744312954463162     0.15105784243478604     0.14634251984999225                0.6987355785484817      

6000       -19973.507891884034     -18784.88489623599        -1188.622995648041        3.2856166105328315                0.5897467365231499       0.05321807801078776     0.11716464192972946     0.09235340804723927                0.07209005123952461     0.14095934659441778     0.207815244052988         0.22905047528738048                0.10915221376463057     0.17537833106607995     0.11106382253469453     0.007843225386536553                0.009258866616626364  0.17135460083167148     0.14056772722153926     0.168210442147602                0.10435612609242632     0.24609218116839132     0.09333760662290842     0.10266619928247744                0.12096762250013886     0.06084946587067328     0.087000              -19974.86474633295        -18778.767167546957                -1196.097578785994        3.1327782426602777       0.5949567251617017       0.05294265974419102                0.08988702642096533     0.0884786180579358       0.06883165359840418     0.1490162233473812                0.2505700661274986       0.2940487276821102       0.1200980379240749       0.14807637624807854                0.10997091138141793     0.006319822130299096  0.017592316307077263  0.1142300691870118                0.17301408287886544     0.14197790998143578     0.08667238475983782     0.2950700989050676                0.05483735954081548     0.11519817320230913     0.06847203747975615     0.05989660212150921                0.1568005613103559       0.07993203128479053     0.5869353952702241      

8000       -19975.74827545863        -18780.241125712186     -1195.5071497464444     2.950684072307572                0.6020123331379059       0.05076908797887532     0.10580435828256661     0.09284846231021546                0.0676617238913026       0.1589748048326592       0.2161584584750038       0.3657503103335417                0.12123903650697199     0.17456327512463002     0.11375767458286681     0.006813585977761885                0.021225191968880532  0.06149980098552765     0.1407310994369414       0.10403001092622989                0.11829289809538854     0.26840399018498057     0.09902765582157066     0.09502448506773516                0.08141230092397818     0.046353643075328875  0.15013885057180185     0.16713708164172247                0.6738535247443563

[catherine ludden]

Hi,

I had the same problem as you and when I opened the file in LogCombiner and resaved the file under a new name. The file now opens in tracer, but there is a different number of states-  instead of 100000000 which was in the initial log file there is now 99976000. Did this happen to you also? Do you have any reason why this is happening?

Catherine

[Rebecca Stubbs]

Hello all,

I am also having this problem. Loading and re-exporting in Log Combiner fixed the log file and I was then able to open it in Tracer. But, has anyone thought about why this is happening? If you look at the original problem Log file in a text editor you'll see that whatever state is listed as the culprit in the error message is missing data. Why does Log Combiner fix this? Is there a problem with the original Beauti file? Anyone else thought about this as more than just a glitch?

Any input is appreciated!

Thanks,

Rebecca