Re: DistanceEst: error: ABySS 1.3.3

Hi Tony,

I apologize for the delay but I am back only no=
w.
We got the proper installation ready, as sugges=
ted above, but the same error is produced.
I use t=
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:
“%-1.adj: %-1.fa
&nbs=
p;       touch delete_me
#     &nbs=
p; AdjList $v -k$k -m$m $< >$@
t=
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:
abyss-pe_FIRST_PHASE k=3D71 ve=
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=
ts/drupomics/lanes/sequences/dna/Lovell/trimmed/exp134_lovell_GCCAAT_L003_u=
npaired.fastq /projects/drupomics/lanes/sequences/dna/Lovell/trimmed/exp134=
_lovell_GCCAAT_L005_unpaired.fastq’ lib134=3D’/projects/drupomics/lanes/seq=
uences/dna/Lovell/trimmed/exp134_lovell_GCCAAT_L003_1.fastq /projects/drupo=
mics/lanes/sequences/dna/Lovell/trimmed/exp134_lovell_GCCAAT_L003_2.fastq /=
projects/drupomics/lanes/sequences/dna/Lovell/trimmed/exp134_lovell_GCCAAT_=
L005_1.fastq /projects/drupomics/lanes/sequences/dna/Lovell/trimmed/exp134_=
lovell_GCCAAT_L005_2.fastq’ >assembly_lovell_k71_b1000000_p0.95_s500.std=
2>assembly_lovell_k71_b1000000_p0.95_s500.err

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.

For the second phase I run the=
standard makefile, restarting from the point where it got interrupted (on =
a single 8 core node):
abyss-pe k=3D71 verbose=3D-=
v aligner=3Dbowtie2 b=3D1000000 p=3D0.95 s=3D500 np=3D8 n=3D10 name=3D’asse=
mbly_lovell_k71_b1000000_p0.95_s500′ lib=3D’lib134′ se=3D’/projects/drupomi=
cs/lanes/sequences/dna/Lovell/trimmed/exp134_lovell_GCCAAT_L003_unpaired.fa=
stq /projects/drupomics/lanes/sequences/dna/Lovell/trimmed/exp134_lovell_GC=
CAAT_L005_unpaired.fastq’ lib134=3D’/projects/drupomics/lanes/sequences/dna=
/Lovell/trimmed/exp134_lovell_GCCAAT_L003_1.fastq /projects/drupomics/lanes=
/sequences/dna/Lovell/trimmed/exp134_lovell_GCCAAT_L003_2.fastq /projects/d=
rupomics/lanes/sequences/dna/Lovell/trimmed/exp134_lovell_GCCAAT_L005_1.fas=
tq /projects/drupomics/lanes/sequences/dna/Lovell/trimmed/exp134_lovell_GCC=
AAT_L005_2.fastq’ >>assembly_lovell_k71_b1000000_p0.95_s500.std 2>=
>assembly_lovell_k71_b1000000_p0.95_s500.err
Th=
e directory I use is clean (I previously experienced this error when it was=
not clean).
I am currently running abyss-map on t=
he same partial results (starting from phase 3, unitigs created).