prediction output format selected: geneid (-) geneid prediction run on: D.melanogaster genome geneid prediction using: ensembl_4_3 version of D.melanogaster genome geneidv1.1 output format selected: geneid the masked contig sequence file "Drosophila_melanogaster.latestgp.masked.fa" is to be broken into 24 files to be analyzed by geneid on aleph ################ proceeding to ftp Drosophila_melanogaster.latestgp.masked.fa.gz, Time it took: real 0m19.930s user 0m0.110s sys 0m1.180s Download of Drosophila_melanogaster.latestgp.masked.fa.gz terminated, proceed to gunzip ######################### Time it took to gunzip Drosophila_melanogaster.latestgp.masked.fa.gz: real 0m24.016s user 0m5.670s sys 0m2.300s Drosophila_melanogaster.latestgp.masked.fa.gz decompressed, proceed to count for total number of contigs in sequence and to test for blank lines in fasta file: ######################### There are 422 contigs on Drosophila_melanogaster.latestgp.masked.fa There are 6 empty lines on Drosophila_melanogaster.latestgp.masked.fa; process aborted; check for errors (i.e. look at "geneid.geneid_run_report_blank_lines" to identify empty lines and run script "empty_contigs.sh\) ######################### NO empty contigs on Drosophila_melanogaster.latestgp.masked.fa; proceed to split sequence file into 24 files to be analyzed on aleph ########################### Splitting of Drosophila_melanogaster.latestgp.masked.fa started The PERL script -mfasta2split2.pl- finds: 422 contig sequences in the FASTA file and it took 3 wallclock secs ( 2.89 usr + 0.33 sys = 3.22 CPU) to complete the process end of splitting of contig-containing file into 24 files to be analyzed on aleph Now running "get_ensembl_contigs.sh" on aleph LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS End of geneid prediction, check that every contig has been analyzed for predictions by running "check_geneid_pred.sh": There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_1 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_10 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_11 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_12 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_13 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_14 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_15 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_16 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_17 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_18 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_19 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_2 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_20 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_21 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_22 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_23 There are 31 contigs in Drosophila_melanogaster.latestgp.masked.fa_24 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_3 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_4 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_5 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_6 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_7 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_8 There are 17 contigs in Drosophila_melanogaster.latestgp.masked.fa_9 ######################### 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_1.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_10.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_11.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_12.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_13.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_14.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_15.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_16.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_17.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_18.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_19.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_2.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_20.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_21.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_22.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_23.geneid.reports 31/31 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_24.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_3.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_4.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_5.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_6.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_7.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_8.geneid.reports 17/17 predictions were obtained for contigs in Drosophila_melanogaster.latestgp.masked.fa_9.geneid.reports ###################### DONE Now running "get_ensembl_contigs.sh" on aleph Now running "get_ensembl_contigs.sh" on aleph LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS LAUNCHING PBS End of contig-prediction checking; Start formatting data for mysql database population (DAS) "format4mysql_das.sh": ######################### Formatting for Mysql DON