[wgs-assembler-users] Running Assembly only

[Stefania B. <ste...@po...>]

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