prediction output format selected: geneid (-) geneid prediction run on: H.sapiens genome geneid prediction using: ensembl_4_28 version of H.sapiens genome geneidv1.1 output format selected: geneid the masked contig sequence file "Homo_sapiens.latestgp.masked.fa" is to be broken into 24 files to be analyzed by geneid on aleph ################ proceeding to ftp Homo_sapiens.latestgp.masked.fa.gz, Time it took: real 9m45.811s user 0m5.280s sys 0m30.290s Download of Homo_sapiens.latestgp.masked.fa.gz terminated, proceed to gunzip ######################### Time it took to gunzip Homo_sapiens.latestgp.masked.fa.gz: real 21m41.832s user 3m27.570s sys 1m36.970s Homo_sapiens.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 81501 contigs on Homo_sapiens.latestgp.masked.fa There are 1448 empty lines on Homo_sapiens.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 Homo_sapiens.latestgp.masked.fa; proceed to split sequence file into 24 files to be analyzed on aleph ########################### Splitting of Homo_sapiens.latestgp.masked.fa started The PERL script -mfasta2split2.pl- finds: 81501 contig sequences in the FASTA file and it took 374 wallclock secs (132.16 usr + 48.15 sys = 180.31 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 3395 contigs in Homo_sapiens.latestgp.masked.fa_1 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_10 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_11 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_12 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_13 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_14 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_15 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_16 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_17 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_18 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_19 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_2 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_20 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_21 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_22 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_23 There are 3416 contigs in Homo_sapiens.latestgp.masked.fa_24 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_3 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_4 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_5 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_6 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_7 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_8 There are 3395 contigs in Homo_sapiens.latestgp.masked.fa_9 ######################### 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_1.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_10.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_11.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_12.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_13.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_14.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_15.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_16.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_17.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_18.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_19.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_2.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_20.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_21.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_22.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_23.geneid.reports 3416/3416 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_24.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_3.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_4.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_5.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_6.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_7.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_8.geneid.reports 3395/3395 predictions were obtained for contigs in Homo_sapiens.latestgp.masked.fa_9.geneid.reports ###################### DONE End of contig-prediction checking; Start formatting data for mysql database population (DAS) "format4mysql_das.sh": ######################### Formatting for Mysql DONE