[mira_talk] Setting input file format & return code from MIRA 4.0RC2 failure
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Tue, 24 Sep 2013 17:47:16 +0100
Hi Bastien,
I have two queries: Can I specify the file format in the manifest
(since Galaxy stores all user data in files with the extension .dat,
it would be useful if I could tell MIRA that these particular files
are FASTQ).
Second, shouldn't there be a non-zero return code in the
following failed example? I seem to be getting zero indicating
success :(
Thanks,
Peter
--
$ more example.manifest
project = MIRA
job = denovo,genome,accurate
parameters = -GE:not=1 -DI:trt=/tmp
readgroup
technology = solexa
data = /mnt/galaxy/galaxy-central/database/files/000/dataset_193.dat
$ ~/downloads/mira_4.0rc2_linux-gnu_x86_64_static/bin/mira example.manifest
This is MIRA 4.0rc2 .
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
To (un-)subscribe the MIRA mailing lists, see:
http://www.chevreux.org/mira_mailinglists.html
After subscribing, mail general questions to the MIRA talk mailing list:
mira_talk@xxxxxxxxxxxxx
To report bugs or ask for features, please use the SourceForge ticketing
system at:
http://sourceforge.net/p/mira-assembler/tickets/
This ensures that requests do not get lost.
Compiled by: bach
Sun Sep 22 16:20:04 CEST 2013
On: Linux vk10464 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34
UTC 2012 x86_64 GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compiled with ENABLE64 activated.
Runtime settings (sorry, for debug):
Size of size_t : 8
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux ppserver 2.6.32-358.11.1.el6.x86_64 #1 SMP Wed
Jun 12 03:34:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Looking for files named in data ...Pushing back filename:
"/mnt/galaxy/galaxy-central/database/files/000/dataset_193.dat"
Could not determine filetype from data
'/mnt/galaxy/galaxy-central/database/files/000/dataset_193.dat'
("/mnt/galaxy/galaxy-central/database/files/000/dataset_193.dat")
Fatal error (may be due to problems of the input data or parameters):
*******************************************************************************
* Some 'data' entries named in the manifest file could not be verified, see *
* the log above. *
* Maybe some files are missing, not readable or there is a typo in the *
* manifest file? *
*******************************************************************************
->Thrown: void Manifest::loadManifestFile(string & mfilename)
->Caught: main
Aborting process, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD: /mnt/galaxy/pico_galaxy/tools/mira_4_0
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Failure, process aborted.
--
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
Other related posts:
