I have been trying to assemble a reptile genome (approx ~ 2.5Gbp) for a couple of months now. I have three paired-end and two mate-pair illumina libraries (adapter and quality trimmed) and a six pacbio libraries (5-6X coverage and corrected by lordec). The "PrepareAllPathsInputs.pl" step completes successfully each time but the "RunAllPathsLG" step fails.
I am using 2016GB RAM and 42 CPUs.
I used the following command:
RunAllPathsLG PRE=$PWD DATA_SUBDIR=data REFERENCE_NAME=reptile RUN=run OVERWRITE=True CLOSE_UNIPATH_GAPS=False
I passed the last optional argument because I read it speeds up the process without effecting the assembly [Allpaths-LG is stuck on CloseUnipathGraphs?].
The following is my stdout snippet:
Tue Feb 16 20:01:27 2018: Starting ALLPATHS-LG Pipeline.
Tue Feb 16 20:01:27 2018 : Preparing makefile.
forceTargets = 0
Creating $(DATA)/makeinfo Creating $(RUN)/makeinfo Creating $(SUB)/makeinfo Creating $(RUN)/unipath_patch/makeinfo
targets with no rule: 2 $(RUN)/filled_reads.jumpomatic.CLR_modified.unipath_adjgraph.k96 ( needed by LittleHelpsBig to make $(RUN)/extended40.unibases.k96 when Extend unipaths with K=40 unipaths ) $(RUN)/filled_reads.jumpomatic.CLR_modified.unipaths.k96 ( needed by LittleHelpsBig to make $(RUN)/extended40.unibases.k96 when Extend unipaths with K=40 unipaths )
ForceAssert(targetsWithNoRule.empty()) at system/MiscUtil.cc:989 failed in function int MakeMgr::RunMake(int)
Tue Feb 16 20:01:27 2018. Abort. Stopping.
Generating a backtrace...
Dump of stack:
- CRD::exit(int), in Exit.cc:30
- MakeMgr::RunMake(int), in Assert.h:51
- MakeMgr::RunMake(int), in MiscUtil.cc:989
- main, in RunAllPathsLG.cc:3135
Could anyone please suggest how do I complete the assembly.