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sivarajankumar / fluxcapacitor

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Problem with GTF sorter #64

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
[desktop:~/bin/FluxSimulator-1.0-RC4/bin] suninsky% ./flux -t simulator -p 
mm9.par
[INFO] I am the Flux Toolbox (v1.0-RC4 build 298), nice to meet you!

[INFO] No mode selected, executing the full pipeline (-x -l -s)
[INFO] I am collecting information on the run.

[INFO] Checking GTF file
checking * Unsorted in line 6 transcript id ENSMUST00000162897 used twice, on: 
1,1
[GTF FILE] The GTF reference file given is not sorted, sorting it right now…
sorting GTF file java.util.concurrent.ExecutionException: java.io.IOException: 
No such file or directory
at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)

Original issue reported on code.google.com by thasso.g...@gmail.com on 21 Sep 2011 at 2:49

GoogleCodeExporter commented 8 years ago 
thasso, 

thanks a lot for your reply. I bypassed this problem by running fllux simulator 
on my laptop. I was having troubles on my desktop. So I am not sure whether 
this is something wrong with my system. 

The GTF file I used is downloaded from 

http://useast.ensembl.org/info/data/ftp/index.html

here are more of the error message:

[INFO] Checking GTF file
    checking * Unsorted in line 220 - cannot perform gene clustering: 18 - ENSMUST00000122958 @ 3299448 after ENSMUST00000154135 @ 3337378
[GTF FILE] The GTF reference file given is not sorted, sorting it right now...
    sorting GTF file java.util.concurrent.ExecutionException: java.io.IOException: No such file or directory
    at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
    at java.util.concurrent.FutureTask.get(FutureTask.java:83)
    at fbi.commons.tools.UnixStreamSorter.divide(UnixStreamSorter.java:295)
    at fbi.commons.tools.UnixStreamSorter.sort(UnixStreamSorter.java:123)
    at fbi.commons.tools.Sorter$1.call(Sorter.java:193)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:680)
Caused by: java.io.IOException: No such file or directory
    at java.io.UnixFileSystem.createFileExclusively(Native Method)
    at java.io.File.checkAndCreate(File.java:1704)
    at java.io.File.createTempFile(File.java:1792)
    at fbi.commons.file.FileHelper.createTempFile(FileHelper.java:993)
    at fbi.commons.tools.UnixStreamSorter.sortAndWriteTempFile(UnixStreamSorter.java:363)
    at fbi.commons.tools.UnixStreamSorter.access$200(UnixStreamSorter.java:33)
    at fbi.commons.tools.UnixStreamSorter$2.call(UnixStreamSorter.java:275)
    at fbi.commons.tools.UnixStreamSorter$2.call(UnixStreamSorter.java:272)
    ... 5 more
java.util.concurrent.ExecutionException: java.io.IOException: No such file or 
directory
    at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
    at java.util.concurrent.FutureTask.get(FutureTask.java:83)
    at fbi.commons.tools.UnixStreamSorter.divide(UnixStreamSorter.java:295)
    at fbi.commons.tools.UnixStreamSorter.sort(UnixStreamSorter.java:123)
    at fbi.commons.tools.Sorter$1.call(Sorter.java:193)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:680)
Caused by: java.io.IOException: No such file or directory
    at java.io.UnixFileSystem.createFileExclusively(Native Method)
    at java.io.File.checkAndCreate(File.java:1704)
    at java.io.File.createTempFile(File.java:1792)
    at fbi.commons.file.FileHelper.createTempFile(FileHelper.java:993)
    at fbi.commons.tools.UnixStreamSorter.sortAndWriteTempFile(UnixStreamSorter.java:363)
    at fbi.commons.tools.UnixStreamSorter.access$200(UnixStreamSorter.java:33)
    at fbi.commons.tools.UnixStreamSorter$2.call(UnixStreamSorter.java:275)
    at fbi.commons.tools.UnixStreamSorter$2.call(UnixStreamSorter.java:272)
    ... 5 more
java.util.concurrent.ExecutionException: java.io.IOException: No such file or 
directory
    at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:222)
    at java.util.concurrent.FutureTask.get(FutureTask.java:83)
    at fbi.commons.tools.UnixStreamSorter.divide(UnixStreamSorter.java:295)
    at fbi.commons.tools.UnixStreamSorter.sort(UnixStreamSorter.java:123)
    at fbi.commons.tools.Sorter$1.call(Sorter.java:193)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
    at java.util.concurrent.FutureTask.run(FutureTask.java:138)
    at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
    at java.lang.Thread.run(Thread.java:680)
Caused by: java.io.IOException: No such file or directory
    at java.io.UnixFileSystem.createFileExclusively(Native Method)
    at java.io.File.checkAndCreate(File.java:1704)
    at java.io.File.createTempFile(File.java:1792)
    at fbi.commons.file.FileHelper.createTempFile(FileHelper.java:993)
    at fbi.commons.tools.UnixStreamSorter.sortAndWriteTempFile(UnixStreamSorter.java:363)
    at fbi.commons.tools.UnixStreamSorter.access$200(UnixStreamSorter.java:33)
    at fbi.commons.tools.UnixStreamSorter$2.call(UnixStreamSorter.java:275)
    at fbi.commons.tools.UnixStreamSorter$2.call(UnixStreamSorter.java:272)
    ... 5 more

Original comment by sunway1...@hotmail.com on 25 Sep 2011 at 3:56

GoogleCodeExporter commented 8 years ago 
Hi,

from the stacktrace it looks like a problem with the systems tmp directory 
where it either does not exist or is not writable. Did you specify a custom 
TMP_DIR in your parameters file ? What operating system are you using ?

The RC-4 misses a check for the tmp directory and does currently not ensure 
that it exists and is writable. To verify that this is in fact the problem, 
could you add the TMP_DIR parameter to your settings file, i.e.

TMP_DIR <file>

where <file> is a full path to a directory that exists and where you have write 
permissions.

Original comment by thasso.g...@gmail.com on 29 Sep 2011 at 12:56

GoogleCodeExporter commented 8 years ago 
Fix added to RC5

Original comment by thasso.g...@gmail.com on 18 Oct 2011 at 4:54