Re: [wgs-assembler-users] Running Assembly only

[Brian W. <th...@gm...>]

The bad news is that it took me a week to reply.  Sorry.

The good news is that runCA and PBcR are quite tolerant of being killed.
Just rerun the same command and it'll pick up where it left off.  You might
need to remove the 'overlap.sh' file first (it will probably tell you to do
this).

I'd suggest decreasing the hash and ref parameters.  As set, you got one
ginormous overlap job.  Since it was PBS that killed the run, I assume
there are quite a few spare CPUs it could be using.  Remove the whole
0-overlaptrim-overlap directory before restarting with modified parameters.

I don't know if runCA/PBcR will submit to PBS directly.  Setting "useGrid=1
scriptOnGrid=0" will configure the overlap jobs (making the
0-overlaptrim-overlap directory and overlap.sh script) and print a command
for you to cut and paste to launch the jobs.  When those jobs finish, you
can restart PBcR to finish up.

b


On Thu, Apr 16, 2015 at 10:16 PM, Stefania Bertazzoni <
ste...@po...> wrote:

>  Good Morning Brian,
>
>
>  I was trying to assemble my set of Pacbio Reads with CA 8.3 and
> everything seemed to proceed beautifully, until I realised I allocated a
> walltime too short for the assembly to finish. I understand this is not a
> bug, just my fault in underestimating the required running time. I am very
> new to this field so I am sure asking for advice is much better than try
> myself to restart the assembly from where it ended.
>
>
>  In the online documentation is mentioned "you could run the assembly by
> hand" I'm not sure on how to do it. I am leaving unchanged the original
> folder structure.
>
>
>  Here is the exact moment in which my job was killed:
>
>
>  ----------------------------------------START Wed Apr 15 20:23:01 2015
> /home/ssb573/bin/wgs-8.3rc1/Linux-amd64/bin/meryl -Dt -n 238 -s
> /work1/ssb573/Pacbio/step1_IlluminaCorrect/PacbioSelfCorrection83/selfcorr14aprhipar/0-mercounts/asm-C-ms22-cm0
> >
> /work1/ssb573/Pacbio/step1_IlluminaCorrect/PacbioSelfCorrection83/selfcorr14aprhipar/0-mercounts/asm.nmers.ovl.fasta
> 2>
> /work1/ssb573/Pacbio/step1_IlluminaCorrect/PacbioSelfCorrection83/selfcorr14aprhipar/0-mercounts/asm.nmers.ovl.fasta.err
>
> ----------------------------------------END Wed Apr 15 20:23:06 2015 (5
> seconds)
> Reset OBT mer threshold from  to 238.
> Reset OVL mer threshold from  to 238.
> ----------------------------------------START Wed Apr 15 20:23:06 2015
> /home/ssb573/bin/wgs-8.3rc1/Linux-amd64/bin/overlap_partition \
>  -g
> /work1/ssb573/Pacbio/step1_IlluminaCorrect/PacbioSelfCorrection83/selfcorr14aprhipar/asm.gkpStore
> \
>  -bl 1000000000 \
>  -bs 0 \
>  -rs 0 \
>  -rl 100000000000 \
>  -o
> /work1/ssb573/Pacbio/step1_IlluminaCorrect/PacbioSelfCorrection83/selfcorr14aprhipar/0-overlaptrim-overlap
> \
> >
> /work1/ssb573/Pacbio/step1_IlluminaCorrect/PacbioSelfCorrection83/selfcorr14aprhipar/0-overlaptrim-overlap/overlap_partition.err
> 2>&1
> ----------------------------------------END Wed Apr 15 20:23:06 2015 (0
> seconds)
> Created 1 overlap jobs.  Last batch '001', last job '000001'.
> ----------------------------------------START CONCURRENT Wed Apr 15
> 20:23:06 2015
> /work1/ssb573/Pacbio/step1_IlluminaCorrect/PacbioSelfCorrection83/selfcorr14aprhipar/0-overlaptrim-overlap/overlap.sh
> 1 >
> /work1/ssb573/Pacbio/step1_IlluminaCorrect/PacbioSelfCorrection83/selfcorr14aprhipar/0-overlaptrim-overlap/000001.out
> 2>&1
> =>> PBS: job killed: walltime 180082 exceeded limit 180000
>
>
>  can you please point me in the right direction?
>
>
>  Kind Regards
>
>
>  Stefania
>
>
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