ALLPATHS-lg aborts during assembly step
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Entering edit mode
4.6 years ago
bio_d ▴ 20

Hi,

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:

  1. CRD::exit(int), in Exit.cc:30
  2. MakeMgr::RunMake(int), in Assert.h:51
  3. MakeMgr::RunMake(int), in MiscUtil.cc:989
  4. main, in RunAllPathsLG.cc:3135

Could anyone please suggest how do I complete the assembly.

ALLPATHS-lg Assembly software error • 882 views
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