nofillmetrics

[Takeo Katsuki]

I've installed PBSuite_14.1.15 and run it on my data. It went through without producing any errors I think, but gaps didn't seem to be filled at all. All the lines in gap_fill_status.txt are "nofillmetrics", and output.err contains the following lines.

2014-01-23 10:05:32,425 [INFO] Number of Gaps Addressed 37856
2014-01-23 10:05:32,425 [INFO] No Filling Metrics 37856
2014-01-23 10:05:32,425 [INFO] Filled 0
2014-01-23 10:05:32,426 [INFO] NFilled 0
2014-01-23 10:05:32,426 [INFO] Single-End Reduced 0
2014-01-23 10:05:32,426 [INFO] Double-End Reduced 0

What does "nofillmetrics" mean? And why gaps were not filled? There is a 4MB of .gml file in the support directory, and a 17MB of .m4 file in the mapping directory, the first five lines of which look like below.

ctg7180000203828 scaffold_3132|ref0011432 -1718 87.7682 0 868 1329 1332 1 18862 19318 35032 0
ctg7180000203825 scaffold_163|ref0009488 -4129 99.2849 0 603 1442 1442 1 76985 77824 121345 254
ctg7180000203837 scaffold_32139|ref0009825 -1462 98.9967 0 0 299 1419 1 870 1169 1169 254
ctg7180000203847 scaffold_19661|ref0020512 -5795 100 0 0 1159 1744 1 1588 2747 2747 254
ctg7180000203826 scaffold_693|ref0008259 -2508 82.2722 0 1302 2048 2398 0 45715 46506 72760 0

My settings were similar to the default (meaning without options or flags) except that I added -x "--nproc=16 --tempDir=/tkatsuki/data/assemblies/gapcorrection5/tmp/" to Jelly.py assembly and -x "--nproc=16" to Jelly.py output.

My blasr setting in Protocol.xml was <blasr>-minMatch 8 -minPctIdentity 70 -bestn 1 -nCandidates 20 -maxScore -500 -nproc 16 -noSplitSubreads</blasr>.

Are there any parameters I should modify to get better results?

Thanks for your help.

Takeo

[Takeo Katsuki]

OK, it seems that it was simply because the tmp directory didn't exist. I manually created a tmp directory before running the assembly step, then it worked. I somehow assumed that the program would automatically create a directory.

Takeo