[mira_talk] Could not rename checkpoint directory in preparation of saving new checkpoint?
- From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 10 Feb 2014 16:46:14 +0000
Hi all,
Using MIRA 4.0 from mira_4.0_linux-gnu_x86_64_static.tar.bz2 to
run a de novo bacterial assembly on our cluster I just got this
during pass 4 or 5:
Fatal error (may be due to problems of the input data or parameters):
********************************************************************************
* Could not rename checkpoint directory in preparation of saving new *
* checkpoint? *
* Error message is boost::filesystem::rename: Directory not empty: *
* "XXX_assembly/XXX_d_chkpt", "XXX_assembly/XXX_d_chkpt_tmp" *
********************************************************************************
->Thrown: void Assembly::performSnapshot(uint32 actpass)
->Caught: main
$ ls XXX_assembly/
XXX_d_chkpt XXX_d_info XXX_d_results XXX_d_tmp
$ ls XXX_assembly/XXX_d_chkpt
bannedOverlaps.txt maxCovReached.txt passInfo.txt readpool.maf
(i.e. not empty)
Note that the working directory is on a network file system, but
/tmp is a local drive and I've got that set in my manifest:
project = LCN4
job = denovo,genome,accurate
#OUT:rtd = Output: remove_tmp_directory
#NW:cmrnl = Nag and Warn: check_maxreadnamelength
#DI:trt = Directory: tmp_redirected_to
parameters = -OUT:rtd=y -NW:cmrnl=no -DI:trt=/tmp
...
Deleting the entire output folder and re-running worked.
Might this have been a left over folder from my trying MIRA 3.9
or something like that?
Regards,
Peter
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