OlyO_assembly report.pdfOlyO_detailed_assembly report.pdf
Fasta of contigs
local blast
robertsmac:bin sr320$ ./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/Ostrea_lur_transcriptome.fasta -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/pfu_aug1.0_Nall -outfmt 10 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/Ostrea_lur_pfu_aug_blastnout -task blastn -max_target_seqs 1 -num_threads 3
started 12:14 Thurs
pearl oyster
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./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/Ostrea_lur_transcriptome.fasta -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/cgigas_all_contigs_v8.fa -outfmt 10 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/Ostrea_lur_cgigas_sigv8_blastnout -task blastn -max_target_seqs 1 -num_threads 1
./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/Ostrea_lur_transcriptome.fasta -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/Haliotis_kam_transcriptome -outfmt 6 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/Ostrea_lur_Haliotis_kam_transcriptome_blastnout -task blastn -max_target_seqs 1 -num_threads 3
check if can evalue limit
./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/Ostrea_lur_transcriptome.fasta -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/Haliotis_kam_transcriptome -outfmt 6 -evalue 0.00001 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/Ostrea_lur_Haliotis_kam_transcriptome_blastnout_e -task blastn -max_target_seqs 1 -num_threads 2
----- also ruphibase
robertsmac:bin sr320$ ./makeblastdb -in /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/ruphibase_32606 -dbtype nucl -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/ruphibase_32606
Building a new DB, current time: 05/25/2012 06:41:59
New DB name: /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/ruphibase_32606
New DB title: /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/ruphibase_32606
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 32606 sequences in 1.67238 seconds.
./blastn -query /Volumes/Bay3/Software/ncbi-blast-2.2.26+/query/Ostrea_lur_transcriptome.fasta -db /Volumes/Bay3/Software/ncbi-blast-2.2.26+/db/ruphibase_32606 -outfmt 10 -out /Volumes/Bay3/Software/ncbi-blast-2.2.26+/out/Ostrea_lur_Ruphibase_blastnout -task blastn -max_target_seqs 1 -num_threads 1
runnning SP on Node2
./blastx -num_threads 14 -out /Users/admin/Dropbox/Cluster/BLAST/output/Ostrea_Lur_SP_node2_blastout -db /CLC_blastdatabases/swissprot -query /Users/admin/Dropbox/Cluster/BLAST/query/Ostrea_lur_transcriptome.fasta -outfmt 10
Took about 9 hours
Completed but forgot -max_target_seqs 1
redoing (going up to 16 cpus)
./blastx -num_threads 16 -out /Users/admin/Dropbox/Cluster/BLAST/output/Ostrea_Lur_SP_node2_blastout_v2 -db /CLC_blastdatabases/swissprot -query /Users/admin/Dropbox/Cluster/BLAST/query/Ostrea_lur_transcriptome.fasta -outfmt 10 -max_target_seqs 1
