ted above, but the same error is produced.
wo different commands, one is for the first part of the pipeline that can b=
e run in parallel (I stop it at phase 1, before AdjList is run with a modif=
ied version of abyss-pe makefile:
p; touch delete_me
p; AdjList $v -k$k -m$m $< >$@
ouch delete_me tells me if I got to the right point. The command I use with=
the modified makefile (abyss-pe_FIRST_PHASE) on 6 nodes of our cluster, ea=
ch with 8 CPUs, is:
rbose=3D-v aligner=3Dbowtie2 b=3D1000000 p=3D0.95 s=3D500 np=3D48 n=3D10 na=
me=3D’assembly_lovell_k71_b1000000_p0.95_s500′ lib=3D’lib134′ se=3D’/projec=
Note that this trick of splitting abyss-pe has always worked previously=
and saved me from booking n-1 nodes for the remaining phases that do not r=
un in parallel.