Run SSPACE in loop
Save the script and config file in SSPACE-LongRead_v1-1 folder, and run as follow
jitendra@jitendra-UNLOCK-INSTALL[SSPACE-LongRead_v1-1] perl loopOverSSPACE.pl -i contigs.fasta -o OUT -c loopOverSSPACE.conf -l 5 -t 6 -p pacbio.fastq
Working on 5 round for scaffoldings
Working on loop number 0 scaffoldings
Fri May 5 20:10:42 2017: Formatting contig sequences...
Fri May 5 20:10:42 2017: Aligning PacBio reads to contigs...
Fri May 5 20:17:48 2017: Processing alignment output...
Fri May 5 20:18:24 2017: Filtering contig links...
Fri May 5 20:18:24 2017: Scaffolding...
Fri May 5 20:18:27 2017: Finishing
Scaffolded 1904 contigs into 1748 scaffolds
DONE ... round 0!
Working on loop number 1 scaffoldings
Fri May 5 20:18:58 2017: Formatting contig sequences...
Fri May 5 20:18:58 2017: Aligning PacBio reads to contigs...
Fri May 5 20:26:00 2017: Processing alignment output...
Fri May 5 20:26:36 2017: Filtering contig links...
Fri May 5 20:26:36 2017: Scaffolding...
Fri May 5 20:26:39 2017: Finishing
Scaffolded 1748 contigs into 1718 scaffolds
DONE ... round 1!
Working on loop number 2 scaffoldings
Fri May 5 20:27:07 2017: Formatting contig sequences...
Fri May 5 20:27:07 2017: Aligning PacBio reads to contigs...
Fri May 5 20:34:05 2017: Processing alignment output...
Fri May 5 20:34:43 2017: Filtering contig links...
Fri May 5 20:34:43 2017: Scaffolding...
Fri May 5 20:34:47 2017: Finishing
Scaffolded 1718 contigs into 1712 scaffolds
DONE ... round 2!
Working on loop number 3 scaffoldings
Fri May 5 20:35:16 2017: Formatting contig sequences...
Fri May 5 20:35:16 2017: Aligning PacBio reads to contigs...
Fri May 5 20:42:14 2017: Processing alignment output...
Fri May 5 20:42:50 2017: Filtering contig links...
Fri May 5 20:42:50 2017: Scaffolding...
Fri May 5 20:42:53 2017: Finishing
Scaffolded 1712 contigs into 1710 scaffolds
DONE ... round 3!
Working on loop number 4 scaffoldings
Fri May 5 20:43:23 2017: Formatting contig sequences...
Fri May 5 20:43:23 2017: Aligning PacBio reads to contigs...
Fri May 5 20:50:24 2017: Processing alignment output...
Fri May 5 20:51:01 2017: Filtering contig links...
Fri May 5 20:51:01 2017: Scaffolding...
Fri May 5 20:51:04 2017: Finishing
Scaffolded 1710 contigs into 1706 scaffolds
DONE ... round 4!
Working on loop number 5 scaffoldings
Fri May 5 20:51:35 2017: Formatting contig sequences...
Fri May 5 20:51:35 2017: Aligning PacBio reads to contigs...
Fri May 5 20:58:40 2017: Processing alignment output...
Fri May 5 20:59:16 2017: Filtering contig links...
Fri May 5 20:59:16 2017: Scaffolding...
Fri May 5 20:59:20 2017: Finishing
Scaffolded 1706 contigs into 1705 scaffolds
DONE ... round 5!
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