I started the PBcR to selfcorrect PB-reads from 62 SMRTcells.
As its quite time-consuming, i run it with -pbCNS and started the overlap jobs myself by executing:
qsub -A assembly -pe smp 31 -l mem=2GB -cwd -N "pBcR_ovl_asm" -t 1-9579 -j y -o /dev/null /data/users/mmoser/PBcR//temppbcns/1-overlapper/overlap.sh
It all finished and i now try reentering the pipeline by starting the inital command:
pacBioToCA -length 100 -s /data/users/mmoser/PBcR/peaxiPBcR.spec1 -t 20 -partitions 300 -pbCNS -l pbcns -fastq /data/users/mmoser/Petunia_correct/allReads/data/filtered_subreads.fastq maxCoverage=30
This terminated becasue of a wrongly set qsub paramter after removing all ovls-files:
Unable to run job: job rejected: the requested parallel environment "threads" does not exist.
When i corrected the qsub parameter it continous terminating because all the .ovls-files are already removed. So i am stuck.
rm 000001.ovls rm: cannot remove `000001.ovls': No such file or directory END Mon Feb 10 11:36:50 2014 (0 seconds) Failed to execute rm 000001.ovls
Can i somehow prevent this from happening by skipping this command and reenter the PBcR pipeline afterwards (i couldnt find the script)?
Or would it be quicker to just gather all the correct_reads_part-files (assuming these are already error-corrected, which i dont know) in the temp/1-overlapper/-directory, merge them and use them for the assembly?
Any help would be appreciated!