on an assembly (mapping) of small genome ~1M bacteria with x10 to x20 coverage
on Mira 4.0.2. Process got to 'ATG PREDICTIONS' before timing out on my cluster
job. I attempted to utilise the fabulous resume function. The log file got to
'File / directory output names: ..... Wiggle:
P4710_101_mapd2_AAA028-C07_out.wig' when Mira issued the following error:
Deleting old directory
P4710_101_mapd2_AAA028-C07_assembly/P4710_101_mapd2_AAA028-C07_d_results ...
done.
Creating directory
P4710_101_mapd2_AAA028-C07_assembly/P4710_101_mapd2_AAA028-C07_d_results ...
done.
A 'standard' exception occured (that's NOT normal):
boost::filesystem::create_symlink: File exists:
"/scratch//P4710_101_mapd2_AAA028-C07_d_tmp_Nu6X7Z",
"P4710_101_mapd2_AAA028-C07_assembly/P4710_101_mapd2_AAA028-C07_d_tmp"
In future assemblies I'll b eincreasing requested runtime to prevent, but I'd
prefer to continue this particular one rather than re-run from scracth. There
was also a warning about exceeded step memory so I'll allocate CPUs in a
threads(n.o.t.)+1 basis which i hope should prevent future memory issues.?
any and all help appreciated, thanking you in advance
Rhiannon
Rhiannon Mondav | 9-18 må, ti, tors, fre | Evolutionary Biology Centre, Uppsala
University, Sweden
