pseudopipe pipeline (predict Pseudogenes)

shenzy@shenzy-pc:~/zhanglei/pgenes/ppipe_input/prodigal/input_file$ /usr/local/RepeatModeler/BuildDatabase -name tcs2 -engine ncbi /home/shenzy/zhanglei/pgenes/ppipe_input/prodigal/input_file/tcs2_prodigal.fa
Building database tcs2:
Adding /home/shenzy/zhanglei/pgenes/ppipe_input/prodigal/input_file/tcs2_prodigal.fa to database
Number of sequences (bp) added to database: 4407 ( 4099764 bp )
shenzy@shenzy-pc:~/zhanglei/pgenes/ppipe_input/prodigal/input_file$ /usr/local/RepeatModeler/BuildDatabase -name tcs3 -engine ncbi /home/shenzy/zhanglei/pgenes/ppipe_input/prodigal/input_file/tcs3_prodigal.fa
Building database tcs3:
Adding /home/shenzy/zhanglei/pgenes/ppipe_input/prodigal/input_file/tcs3_prodigal.fa to database
Number of sequences (bp) added to database: 4430 ( 4121190 bp )
shenzy@shenzy-pc:~/zhanglei/pgenes/ppipe_input/prodigal/input_file$ /usr/local/RepeatModeler/BuildDatabase -name tcs4 -engine ncbi /home/shenzy/zhanglei/pgenes/ppipe_input/prodigal/input_file/tcs4_prodigal.fa
Building database tcs4:
Adding /home/shenzy/zhanglei/pgenes/ppipe_input/prodigal/input_file/tcs4_prodigal.fa to database

nohup /usr/local/RepeatModeler/RepeatModeler -database tcs4 >& run4.out &
/home/shenzy/lib/RepeatMasker/RepeatMasker -lib consensi.fa.classified tcs4_genome.fasta &
./pseudopipe.sh /home/shenzy/lib/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/ /home/shenzy/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa /home/shenzy/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/Caenorhabditis_elegans.WS220.62.dna.chromosome.%s.fa /home/shenzy/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/pep/Caenorhabditis_elegans.WS220.62.pep.fa /home/shenzy/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/mysql/chr%s_exLocs 0

./pseudopipe.sh /home/shenzy/lib/pgenes/ppipe_output/caenorhabditis_elegans_62_220a /home/shenzy/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa /home/shenzy/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/Caenorhabditis_elegans.WS220.62.dna.chromosome.%s.fa /home/shenzy/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/pep/Caenorhabditis_elegans.WS220.62.pep.fa /home/shenzy/lib/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/mysql/chr%s_exLocs 0
./pseudopipe.sh /home/shenzy/lib/pgenes/ppipe_output/prodigal/tcs4/ /home/shenzy/lib/pgenes/ppipe_input/prodigal/tcs4/dna/tcs4_genome.fasta.masked /home/shenzy/lib/pgenes/ppipe_input/prodigal/tcs4/dna/tcs4_genome.%s.fasta /home/shenzy/lib/pgenes/ppipe_input/prodigal/tcs4/pep/tcs4_prodigal.pep /home/shenzy/lib/pgenes/ppipe_input/prodigal/tcs4/mysql/contig.%s_exlocs 0