prediction output format selected: geneid (-) geneid prediction run on: M.musculus genome geneid prediction using: ensembl_4_1 version of M.musculus genome geneidv1.1 output format selected: geneid the masked contig sequence file "Mus_musculus.latestgp.masked.fa" is to be broken into 24 files to be analyzed by geneid on aleph ################ proceeding to ftp Mus_musculus.latestgp.masked.fa.gz, Time it took: real 9m12.795s user 0m5.020s sys 0m25.930s Download of Mus_musculus.latestgp.masked.fa.gz terminated, proceed to gunzip ######################### Time it took to gunzip Mus_musculus.latestgp.masked.fa.gz: real 20m42.493s user 3m19.650s sys 1m32.480s Mus_musculus.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 677 contigs on Mus_musculus.latestgp.masked.fa There are NO blank lines on Mus_musculus.latestgp.masked.fa; proceed to check for contigs with NO sequence: ######################### NO empty contigs on Mus_musculus.latestgp.masked.fa; proceed to split sequence file into 24 files to be analyzed on aleph ########################### Splitting of Mus_musculus.latestgp.masked.fa started The PERL script -mfasta2split2.pl- finds: 677 contig sequences in the FASTA file and it took 307 wallclock secs (141.46 usr + 44.74 sys = 186.20 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 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 28 contigs in Mus_musculus.latestgp.masked.fa_1 There are 28 contigs in Mus_musculus.latestgp.masked.fa_10 There are 28 contigs in Mus_musculus.latestgp.masked.fa_11 There are 28 contigs in Mus_musculus.latestgp.masked.fa_12 There are 28 contigs in Mus_musculus.latestgp.masked.fa_13 There are 28 contigs in Mus_musculus.latestgp.masked.fa_14 There are 28 contigs in Mus_musculus.latestgp.masked.fa_15 There are 28 contigs in Mus_musculus.latestgp.masked.fa_16 There are 28 contigs in Mus_musculus.latestgp.masked.fa_17 There are 28 contigs in Mus_musculus.latestgp.masked.fa_18 There are 28 contigs in Mus_musculus.latestgp.masked.fa_19 There are 28 contigs in Mus_musculus.latestgp.masked.fa_2 There are 28 contigs in Mus_musculus.latestgp.masked.fa_20 There are 28 contigs in Mus_musculus.latestgp.masked.fa_21 There are 28 contigs in Mus_musculus.latestgp.masked.fa_22 There are 28 contigs in Mus_musculus.latestgp.masked.fa_23 There are 33 contigs in Mus_musculus.latestgp.masked.fa_24 There are 28 contigs in Mus_musculus.latestgp.masked.fa_3 There are 28 contigs in Mus_musculus.latestgp.masked.fa_4 There are 28 contigs in Mus_musculus.latestgp.masked.fa_5 There are 28 contigs in Mus_musculus.latestgp.masked.fa_6 There are 28 contigs in Mus_musculus.latestgp.masked.fa_7 There are 28 contigs in Mus_musculus.latestgp.masked.fa_8 There are 28 contigs in Mus_musculus.latestgp.masked.fa_9 ######################### 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_1.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_10.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_11.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_12.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_13.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_14.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_15.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_16.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_17.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_18.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_19.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_2.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_20.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_21.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_22.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_23.geneid.reports 33/33 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_24.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_3.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_4.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_5.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_6.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_7.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_8.geneid.reports 28/28 predictions were obtained for contigs in Mus_musculus.latestgp.masked.fa_9.geneid.reports ###################### DONE